Method for identifying oil palm plants with improved resistance to heart rot

Abstract

The invention relates to the field of plant breeding and more specifically to marker-based selection methods. In particular, the invention relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting improved resistance to heart rot, said method comprising the detection in all or part of said plant of a QTL (Quantitative Trait Locus) associated with resistance to heart rot, preferably via the identification of at least one specific SNP (Single Nucleotide Polymorphism) on chromosome 2.

Description

Title of the invention: Method for identifying oil palm plants exhibiting improved resistance to heart rot technical field

[0001] The invention relates to the field of plant breeding and more specifically to marker-based selection methods.

[0002] In particular, the invention relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting improved resistance to heart rot, said method comprising the detection in all or part of the plant of a specific QTL (Quantitative Trait Locus) associated with resistance to heart rot located on chromosome 2. The present invention further relates to an isolated nucleic acid and its use for marker-assisted selection of a plant belonging to the genus Elaeis. Finally, the present invention also relates to a composition comprising at least one primer pair (sense and antisense) selected from a particular group intended for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot. State of the art

[0003] The oil palm, also known as Elaeis guineensis, is the most widely cultivated oilseed plant in the world.

[0004] The first supplier of vegetable fat, surpassing soybean, sunflower and rapeseed crops, the oil palm produces two types of oil: *crude palm oil; and *crude palm kernel oil.

[0005] Crude palm oil is the world's main source of edible oil, representing more than a third of global vegetable oil production. Extracted from the mesocarp of the fruit, palm oil is highly valued for its versatility and yield per hectare, making it an attractive crop, particularly for developing countries.

[0006] However, the cultivation of oil palm presents certain constraints, notably the appearance of palm heart rot.

[0007] Heart rot of oil palm is a disease of concern that represents a significant threat to palm oil production. This disease can cause substantial losses by reducing plantation productivity and severely affecting the health of the palm trees.

[0008] In addition to affecting oil palms belonging to the species Elaeis guineensis, heart rot also threatens plantations using interspecific hybrid material, particularly Elaeis oleifera x Elaeis guineensis hybrids. These hybrids are widely studied and developed to improve various agronomic traits, including disease resistance, but they are not immune to heart rot, making them an important target for breeding efforts.

[0009] This pathology is characterized by the progressive decomposition of the palm's internal tissues, particularly in the heart, the central and vital part of the tree. Symptoms generally include a progressive weakening of the tree, manifested by leaf wilting and a decrease in fruit production, eventually followed by the death of the tree.

[0010] To date, the causative agent of heart rot has not yet been clearly identified, which greatly complicates the fight against this disease. Hypotheses suggest a possible involvement of various microorganisms, but no direct link has yet been demonstrated.

[0011] This uncertainty underlines the crucial importance of developing effective means to combat and / or prevent this pathology.

[0012] Among the different populations of oil palm, individuals have been found exhibiting varying levels of resistance to heart rot (from highly resistant to highly susceptible), highlighting the need to develop effective methods for detecting resistance or susceptibility to this disease at an early stage, before the appearance of visible symptoms. This would help to curb its spread within plantations and minimize economic losses.

[0013] Selecting disease-resistant palm trees using currently available phenotypic methods is both lengthy and expensive. These methods involve planting palm trees and waiting for the appearance of disease symptoms, a process that can take several years due to the random and unpredictable nature of field epidemics.

[0014] Furthermore, these approaches lack precision and effectiveness, as environmental factors can strongly influence the manifestation of the disease. For example, a palm tree may remain unaffected not because of its intrinsic resistance, but because it is planted in an area where exposure to the pathogen is limited. Conversely, a truly resistant palm tree may become infected if it is exposed to conditions more favorable to infection.

[0015] Moreover, the pathogen responsible for heart rot has not yet been identified, making it impossible to use inoculation tests under controlled conditions. This limits the possibilities of accelerating the selection process and reducing its costs through more rigorous and faster methods.

[0016] Given these limitations, there is a major interest in developing a reliable and economically accessible early detection method to identify palm trees exhibiting resistance factors. Such a method would accelerate selection and facilitate the development of commercial varieties with improved resistance, thereby reducing the time and costs associated with traditional breeding. Summary of the invention

[0017] To meet this need, the invention proposes a new marker-assisted selection (MAS) method for identifying oil palm plants with increased resistance to heart rot.

[0018] Based on genotype observation, this method uses genetic markers identified near a QTL of interest associated with the phenotype of interest. Thus, this technique makes it possible to make selections at an early stage of development, often well before the phenotype of interest is observable, such as resistance to heart rot in oil palms.

[0019] More particularly, the invention relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting increased resistance to heart rot, said method comprising the detection in all or part of said plant of a QTL associated with resistance to heart rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0020] Advantageously, the method according to the invention makes it possible to identify oil palms belonging to the genus Elaeis exhibiting increased resistance to heart rot. Surprisingly, the inventors identified a QTL associated with oil palm heart rot located on chromosome 2 between positions 71954369 and 77339690 of the Egu.V3 reference genome.

[0021] The identification of this QTL thus makes it possible to develop a marker selection method that identifies early oil palm plants exhibiting the phenotype of interest.

[0022] According to a preferred embodiment, the invention relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting increased resistance to heart rot, said method comprising the detection in all or part of said plant of a QTL associated with resistance to rot located on chromosome 2 between positions 71954369 and 77339690 of the Egu.V3 reference genome, wherein said QTL can be identified by at least one SNP (Single Nucleotide Polymorphism) marker selected from the group consisting of: - SNP_1 comprising a Cytosine at position 91 of SEQ ID NO: 1 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 1; - SNP_2 comprising a Thymine at position 91 of SEQ ID NO: 2 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 2; - SNP_3 comprising a Guanine at position 91 of SEQ ID NO: 3 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 3; - SNP_4 comprising a Cytosine at position 91 of SEQ ID NO: 4 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 4; - SNP_5 comprising an Adenine at position 91 of SEQ ID NO: 5 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 5; - SNP_6 comprising a Thymine at position 91 of SEQ ID NO: 6 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 6; - SNP_7 comprising a Thymine at position 91 of SEQ ID NO: 7 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 7; - SNP_8 comprising a Thymine at position 91 of SEQ ID NO: 8 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 8; - SNP_9 comprising a Thymine at position 91 of SEQ ID NO: 9 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 9; and - their combinations.

[0023] By identifying these specific markers, the inventors have found a suitable means for identifying oil palms belonging to the genus Elaeis exhibiting increased resistance to heart rot, in particular by overcoming inter-species and inter-population variability.

[0024] Thus, the method according to the invention is suitable for the identification of oil palms chosen from Elaeis guineensis, Elaeis oleifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera exhibiting resistance to heart rot.

[0025] According to a particularly suitable embodiment, the method according to the invention also includes the detection of at least one other QTL associated with resistance to core rot selected from the group consisting of: *a QTL located on chromosome 5 between position 115766007 and 116766006 of the Egu.V3 reference genome; *a QTL located on chromosome 7 between position 119773060 and 120773059 of the Egu.V3 reference genome; *a QTL located on chromosome 9 between position 1567660 and 2567659 of the Egu.V3 reference genome; *a QTL located on chromosome 10 between position 11569544 and 12569543 of the Egu.V3 reference genome; and * their combinations.

[0026] Advantageously, the inventors have identified 4 other QTLs of interest which, in association with the QTL identified on chromosome 2, allow the prediction of the phenotype of interest.

[0027] The inventors have thus developed a method based on the detection of several QTLs in order to obtain a predictive method with optimal accuracy for predicting the phenotype of interest.

[0028] The invention also relates to an isolated nucleic acid comprising a nucleotide sequence; or the complementary sequence of said nucleotide sequence; or a fragment of said nucleotide sequence, said fragment comprising at least 15 nucleotides and the nucleotide in position 91; or the complementary sequence of said fragment.

[0029] In particular, the invention relates to an isolated nucleic acid comprising a nucleotide sequence or its complementary sequence, said nucleotide sequence being selected from the group consisting of: *SEQ ID NO: 1 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 1; *SEQ ID NO: 2 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 2; *SEQ ID NO: 3 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 3; *SEQ ID NO: 4 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 4; *SEQ ID NO: 5 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 5; *SEQ ID NO: 6 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 6; *SEQ ID NO: 7 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 7; *SEQ ID NO: 8 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 8; *SEQ ID NO: 9 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 9; *SEQ ID NO: 10 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 10; *SEQ ID NO: 11 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 11; *SEQ ID NO: 12 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 12; and *SEQ ID NO: 13 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 13.

[0030] The invention also relates to the use of one or more of these isolated nucleic acids, for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot.In particular, the invention relates to the use of one or more nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO: 13 or a fragment of one of these sequences, for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting increased resistance to heart rot in which said fragment consists of at least 15 nucleotides including nucleotide 91 of said nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO: 13 or a complementary sequence to said nucleotide sequence(s).

[0031] Finally, the invention relates to a composition comprising at least one set of primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, said composition comprising at least one set of primers (forward and reverse) selected from the group consisting of: * a forward primer comprising a SEQ ID NO: 14 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 14 and / or a forward primer comprising a SEQ ID NO: 15 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 15 and a reverse primer, comprising a SEQ sequence ID NO: 16, or a sequence showing at least 80% identity with SEQ ID NO: 16; * a sense primer comprising a SEQ ID NO: 17 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 17 and / or a sense primer comprising a SEQ ID NO: 18 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 18 and an antisense primer, comprising a SEQ ID NO: 19 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 19; *a sense primer comprising a SEQ ID NO: 20 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 20 and / or a sense primer comprising a SEQ ID NO: 21 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 21 and an antisense primer, comprising a SEQ ID NO: 22 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 22; *a sense primer comprising a SEQ ID NO: 23 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 23 and / or a sense primer comprising a SEQ ID NO: 24 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 24 and an antisense primer, comprising a SEQ ID NO: 25 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 25; *a sense primer comprising a SEQ ID NO: 26 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 26 and / or a sense primer comprising a SEQ ID NO: 27 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 27 and an antisense primer, comprising a SEQ ID NO: 28 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 28; *a sense primer comprising a SEQ ID NO: 29 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 29 and / or a sense primer comprising a SEQ ID NO: 30 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 30 and an antisense primer, comprising a SEQ ID NO: 31 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 31; *a sense primer comprising a SEQ ID NO: 32 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 32 and / or a sense primer comprising a SEQ ID NO: 33 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 33 and an antisense primer, comprising a SEQ ID NO: 34 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 34; *a sense primer comprising a SEQ ID NO: 35 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 35 and / or a sense primer comprising a SEQ ID NO: 36 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 36 and an antisense primer, comprising a SEQ ID NO: 37 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 37; *a sense primer comprising a SEQ ID NO: 38 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 38 and / or a sense primer comprising a SEQ ID NO: 39 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 39 and an antisense primer, comprising a SEQ ID NO: 40 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 40; *a sense primer comprising a SEQ ID NO: 41 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 41 and / or a sense primer comprising a SEQ ID NO: 42 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 42 and an antisense primer, comprising a SEQ ID NO: 43 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 43; *a sense primer comprising a SEQ ID NO: 44 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 44 and / or a sense primer comprising a SEQ ID NO: 45 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 45 and an antisense primer, comprising a SEQ ID NO: 46 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 46; *a sense primer comprising a SEQ ID NO: 47 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 47 and / or a sense primer comprising a SEQ ID NO: 48 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 48 and an antisense primer, comprising a SEQ ID NO: 49 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 49; *a sense primer comprising a SEQ ID NO: 50 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 50 and / or a sense primer comprising a SEQ ID NO: 51 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 51 and an antisense primer, comprising a SEQ ID NO: 52 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 52.

[0032] Other features and advantages will become apparent from the detailed description of the invention and the examples that will follow. Brief description of the figures

[0033] [Fig.1]: The [Fig.1] is a graphical representation of the survival curves in the overall trial and for the offspring constituting the mapping population with the highest and lowest risks.

[0034] [Fig.2]: The [Fig.2] is a graphical representation of the effect of the presence of a resistant or sensitive haplotype on the survival of individuals in the mapping population, on the 3 identified QTLs.

[0035] [Fig.3] : The [Fig.3] is a graphical representation of the effect of the presence of a resistant or sensitive haplotype on the survival of individuals in the validation population, on the major QTL identified, according to the information from the markers SNP_1 to SNP_4.

[0036] [Fig. 4] Figure 4 is a graphical representation of the incidence of heart rot in the 6 Deli x FR4 crosses of the validation population, as a function of the haplotype inherited from the male parent on the major QTL of chromosome 2. The incidence shown on the y-axis is expressed as a proportion of the total number of individuals in each group. The number of individuals per group is indicated at the base of each bar.

[0037] [Fig.5] The [Fig.5] is a graphical representation of the pedigree of the pseudo-backcross 1 used in example 2.

[0038] [Fig.6] Fig.6 is a graphical representation of the results of QTL detection in test_1 using the SIM and CIM methods. The 5% significance thresholds are indicated by dashed lines.

[0039] [Fig.7] Fig.7 is a graphical representation of the results of QTL detection in trial_2 using the SIM and CIM methods. The 5% significance thresholds are indicated by dashed lines.

[0040] [Fig.8] The [Fig.8] is a graphical representation showing the position of the markers and intervals of the heart rot resistance QTL located on chromosome 2 (reference Egu.v3). Detailed description of the invention

[0041] Definitions:

[0042] For the purposes of this invention, "allele" means one or more alternative forms of a gene, all alleles being linked to a trait at a specific locus.

[0043] For the purposes of this invention, a "direction primer" is defined as a DNA or RNA sequence designed to be complementary to the template strand (or non-coding strand) of a DNA segment. This primer hybridizes to the template strand and is oriented in the 5' to 3' direction during a polymerization reaction.

[0044] For the purposes of this invention, an "antisense primer" is defined as a DNA or RNA sequence complementary to the coding strand. This primer hybridizes to the coding strand and is oriented in the 3' to 5' direction, allowing DNA amplification in the opposite direction during the polymerization reaction.

[0045] For the purposes of this invention, "cross involving Elaeis guineensis and / or Elaeis oleifera" means: a) Any direct cross between Elaeis guineensis and Elaeis oleifera', b) Any cross between an oil palm resulting from a previous cross involving the species Elaeis guineensis and / or Elaeis oleifera, and an oil palm of the species Elaeis guineensis, of the species Elaeis oleifera, or resulting from another cross involving Elaeis guineensis and / or Elaeis oleifera; And c) Any backcross involving an oil palm resulting from a previous cross and a plant of the species Elaeis guineensis or Elaeis oleifera.

[0046] For the purposes of this invention, "Egu.V3" refers to the reference sequence of an Elaeis guineensis plant, which allows the QTLs and SNPs of interest to be located. This reference sequence is accessible via the Chinese national Genebank database under accession number CNA0047477 or via the genome repository at the National Genomic Data Center under accession number GWHBKAS00000000.

[0047] For the purposes of this invention, "linking group" means a set of genes located on the same chromosome and which tend to be inherited together.

[0048] For the purposes of this invention, "genome" means the genetic material of an organism. Composed of DNA, the genome includes both genes and non-coding sequences of DNA.

[0049] By "sequence identity" in the sense of the invention, we mean the percentage of identical positions between these sequences when they are aligned optimally, that is to say by maximizing the number of exact matches while minimizing insertions, deletions and substitutions.

[0050] To calculate sequence identity, the following procedure is generally used. Sequence alignment: The two nucleotide sequences are aligned using an alignment algorithm, such as BLAST, Needleman-Wunsch or Smith-Waterman, to obtain the best possible alignment.

[0051] To calculate the percentage of identity, it is necessary to determine the number of positions where the nucleotides of the two sequences are identical. This number is then divided by the length of the shorter sequence in the alignment (or by the length of the overall alignment, depending on the method used), and the result is multiplied by 100 to obtain a percentage.

[0052] For example, if the optimal alignment of two sequences of 100 nucleotides each reveals that 90 positions are identical, the sequence identity would be 90%.

[0053] For the purposes of this invention, "haplotype" refers to a set of genetic variations (or alleles) located close to one another on the same chromosome and often inherited together. In other words, it is a specific combination of genetic markers (such as SNPs) on a chromosome segment that is transmitted as a whole from one generation to the next without being recombined.

[0054] For the purposes of this invention, a "primer set" is defined as a specific mixture of primers composed of at least two oligonucleotide sequences, preferably a sense primer and an antisense primer, designed to hybridize complementaryly to specific regions of the target DNA. This primer set enables the amplification of a particular DNA sequence during a polymerization reaction, such as PCR (polymerase chain reaction) or other genotyping methods. A primer set may include additional primers, such as reporter primers, depending on the requirements of the method used.

[0055] For the purposes of this invention, "locus" or "loci" means one or more specific locations on a chromosome where, for example, a gene or a genetic marker is located.

[0056] For the purposes of this invention, a "marker" is defined as an indicator that allows for the comparison of nucleotide sequences. In the context of this invention, markers are preferably SNPs ("Single Nucleotide Polymorphism").

[0057] By "phenotype of interest" in the meaning of the invention, we mean an oil palm exhibiting resistance to heart rot.

[0058] By "population" in the sense of the invention, also called "genetic background" or "genetic origin", we mean a group of individuals of the same species or resulting from various types of crosses involving Elaeis guineensis and / or Elaeis oleifera sharing a common genetic reservoir, that is to say a common set of alleles that can be transmitted from one generation to the next.

[0059] By "having increased resistance" or "having improved resistance" in the meaning of the invention, means oil palm plants having increased / improved resistance compared to the commercial oil palm variety Elaeis guineensi s DA115D x LM2T.

[0060] For the purposes of this invention, "QTL" or "Quantitative Trait Locus" means a hereditary unit that occupies a specific location on a chromosome and contains the genetic information associated with a phenotypic trait. The QTL codes for at least one gene whose expression, alone or in combination with other genes, results in the expression of the phenotypic trait, or codes for at least one regulatory region that controls the expression of at least one gene whose expression, alone or in combination with other genes, results in the expression of the phenotypic trait. QTL can be defined by indicating its genetic location in the introgression donor genome that contains the QTL using one or more molecular genomic markers.

[0061] By "SNP" also called "Single Nucleotide Polymorphism" or "Nucleotide Polymorphism" in the sense of the invention, we mean a genetic mutation corresponding to the replacement of a single nucleotide by another nucleotide.

[0062] For the purposes of this invention, "trait" means a phenotype of the plant.

[0063] For the purposes of this invention, "all or part of said plant" means the entire of the plant or any of its parts, including but not limited to: roots, leaves, stems, flowers, fruits, seeds, or internal tissues, such as cells or DNA extracts from these parts. This definition also encompasses samples of plant tissue or genetic material derived from the plant, for the purpose of genotyping to detect a phenotype of interest.

[0064] In vitro method for identifying a plant belonging to the genus Elaeis exhibiting resistance to heart rot

[0065] The invention therefore relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting resistance to heart rot, said method comprising the detection in all or part of said plant of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0066] Advantageously, the inventors have discovered a QTL that allows them to predict the resistance to heart rot of oil palms. Therefore, the method according to the invention allows, in particular: * to improve productivity: By selecting resistant palm trees from the early stages of development, it is possible to avoid yield losses caused by heart rot, thus increasing the overall productivity of plantations; * to achieve rapid and precise selection: Thanks to the identification of a QTL associated with resistance to rot, marker-assisted selection allows for rapid detection of the phenotype of interest, without having to wait for the appearance of disease symptoms. This accelerates the varietal improvement process, compared to classical selection based on the observation of visible traits; * to reduce the use of plant protection products: By cultivating naturally resistant populations, it is possible to reduce or eliminate the use of chemical treatments to control heart rot, which lowers input costs and promotes more sustainable agricultural practices.

[0067] Preferably, the QTL associated with resistance to rot is located on chromosome 2 between position 73013312 and 74228450 of the Egu.V3 reference genome.

[0068] According to one embodiment, the method according to the invention the QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690, preferably between position 73013312 and 74228450, of the Egu.V3 reference genome can be identified by at least one marker chosen from an SNP (Single Nucleotide Polymorphism) marker, an RFLP (Restriction Fragment Length Polymorphism) marker, a CPAS (cleaved amplified polymorphism sequence) marker, a RAPD (Random Amplified Polymorphism DNA) marker, an AFLP (Amplified Fragment Length Polymorphism) marker, an S SR (simple sequence repeats) marker and their combinations.

[0069] Advantageously, any type of DNA marker genetically linked to the QTL of interest is usable in the context of the invention.

[0070] Preferably, the rot-resistant QTL located on chromosome 2 between position 71954369 and 77339690, preferably between position 73013312 and 74228450, of the Egu.V3 reference genome can be identified by at least one SNP marker.

[0071] According to one embodiment, the method according to the invention comprises the detection of a rot-resistance QTL located on chromosome 2 between positions 71954369 and 77339690, preferably between positions 73013312 and 74228450, of the Egu.V3 reference genome by at least one SNP marker selected from the group consisting of: - SNP_1 comprising a Cytosine at position 91 of SEQ ID NO: 1 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 1, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 1; - SNP_2 comprising a Thymine at position 91 of SEQ ID NO: 2 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 2, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 2; - SNP_3 comprising a Guanine at position 91 of SEQ ID NO: 3 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 3, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 3; - SNP_4 comprising a Cytosine at position 91 of SEQ ID NO: 4 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:4, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO:4; - SNP_5 comprising an Adenine at position 91 of SEQ ID NO: 5 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 5, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 5; - SNP_6 comprising a Thymine at position 91 of SEQ ID NO: 6 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 6, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 6; - SNP_7 comprising a Thymine at position 91 of SEQ ID NO: 7 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 7, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 7; - SNP_8 comprising a Thymine at position 91 of SEQ ID NO: 8 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 8, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 8; - SNP_9 comprising a Thymine at position 91 of SEQ ID NO: 9 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 9, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 9; and - their combinations.

[0072] Advantageously, the SNP markers as a whole exhibit a detection accuracy greater than 80%, in particular greater than 85%. Thus, in the context of the invention, each SNP marker is capable of detecting the correct phenotype in at least 80% of the oil palms tested.

[0073] More specifically, SNPs_1 to 9 taken individually or in combination allow the detection of a QTL on chromosome 2 of the Egu.V3 reference genome associated with the alleles producing the phenotype linked to resistance to heart rot in a plant belonging to the genus Elaeis, preferably chosen from Elaeis guineensis, Elaeis oleifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera

[0074] The inventors have thus developed a method for identifying oil palms belonging to the genus Elaeis exhibiting the phenotype of interest by detecting the different alleles responsible for the phenotype of interest. Indeed, one of the challenges of the method according to the invention is to provide markers capable of detecting the set of alleles responsible for the phenotype of interest in order to overcome inter-species and inter-population genotypic variability.

[0075] Although the SNP_5 and SNP_6 markers are located outside the defined interval for the QTL of interest on chromosome 2 (interval [71954369; 77339690] of the Egu.V3 reference genome), they remain relevant and informative as neighboring markers due to the genetic linkage that connects them to the targeted QTL. This genetic proximity, although external to the QTL definition interval, confers upon SNP_5 and SNP_6 a predictive capacity regarding the presence of this QTL of interest.

[0076] Preferably, the method according to the invention comprises the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome, wherein said QTL can be identified by at least 2 SNP markers, more preferably by at least 3, 4, 5, 6, 7, 8, 9 SNP markers selected from the group consisting of SNP_1, SNP_2, SNP_3, SNP_4, SNP_5, SNP_6, SNP_7, SNP_8, SNP_9 and any combinations thereof.

[0077] According to a particular embodiment, the method according to the invention comprises the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome, in which said QTL can be identified by the combination of all the markers SNP_1, SNP_2, SNP_3, SNP_4, SNP_5, SNP_6, SNP_7, SNP_8 and SNP_9.

[0078] Advantageously, when the method according to the invention combines all the SNP_1 to SNP_9 markers, the accuracy of detection of the phenotype of interest is greater than 90%, in particular greater than 95%.

[0079] Advantageously, the method according to the invention is thus able to identify oil palms belonging to the genus Elaeis exhibiting resistance to heart rot by overcoming the variabilities between species and populations of oil palms.

[0080] Preferably, the method according to the invention comprises the detection in all or part of said plant of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690, preferably between position 73013312 and 74228450, of the Egu.V3 reference genome by SNP markers selected from the group consisting of: - SNP_1 comprising a Cytosine at position 91 of SEQ ID NO: 1 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 1, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 1; - SNP_2 containing a Thymine at position 91 of SEQ ID NO: 2 or at position 91 of a sequence having at least 90% identity with SEQ ID NO:2, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO:2; and - SNP_3 comprising a Guanine at position 91 of SEQ ID NO:3 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:3, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO:3.

[0081] According to one embodiment, the method according to the invention comprises the detection in all or part of said plant of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690, preferably between position 73013312 and 74228450, of the Egu.V3 reference genome by SNP markers selected from the group consisting of: - SNP_1 comprising a Cytosine at position 91 of SEQ ID NO: 1 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 1, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 1; - SNP_2 comprising a Thymine at position 91 of SEQ ID NO: 2 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 2, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 2; - SNP_3 comprising a Guanine at position 91 of SEQ ID NO: 3 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 3, preferably at least 95%, in particular at least 98%, and even more preferably at least 99% identity with SEQ ID NO: 3; and - SNP_4 comprising a Cytosine at position 91 of SEQ ID NO: 4 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 4, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 4.

[0082] According to another embodiment, the method according to the invention comprises the detection in all or part of said plant of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690, preferably between position 73013312 and 74228450, of the Egu.V3 reference genome by SNP markers selected from the group consisting of: - SNP_5 comprising an Adenine at position 91 of SEQ ID NO: 5 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 5, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 5; - SNP_6 containing a Thymine at position 91 of SEQ ID NO: 6 or at position 91 of a sequence containing at least 90% identity with SEQ ID NO:6, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO:6; - SNP_7 comprising a Thymine at position 91 of SEQ ID NO: 7 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 7, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 7; - SNP_8 comprising a Thymine at position 91 of SEQ ID NO: 8 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 8, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 8; - SNP_9 comprising a Thymine at position 91 of SEQ ID NO: 9 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 9, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 9; and - their combinations.

[0083] The method according to the invention thus makes it possible to identify oil palms belonging to the genus Elaeis exhibiting the phenotype of interest, in particular oil palms chosen from Elaeis guineensis, Elaeis oleifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera.

[0084] Thus, according to a preferred embodiment, the plant belonging to the genus Elaeis is chosen from Elaeis guineensis, Elaeis oleifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera.

[0085] According to another embodiment, the method according to the invention comprises the detection of a QTL associated with resistance to rot located on chromosome 2 between positions 71954369 and 77339690 of the Egu.V3 reference genome, wherein said QTL can be identified by: 1) at least one SNP marker chosen from the group consisting of SNP_1, SNP_2, SNP_3 or SNP_4 and their combinations; and / or 2) at least one SNP marker chosen from the group consisting of SNP_5, SNP_6, SNP_7, SNP_8, SNP_9 and their combinations.

[0086] Advantageously, the combination of markers belonging to groups 1) and 2) allows the identification of oil palms belonging to the genus Elaeis exhibiting the phenotype of interest, preferably oil palms chosen from Elaeis guineensis, Elaeis oleifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera, regardless of the population to which they belong.

[0087] Oil palms belonging to different populations such as La Mé, Deli, Yangambi, Nifor, Yocoboué, Pobè, Cameroon, Avros, Ekona, Dumpy, Angola, Nigeria, Ghana, Marihat, Binga, Yaligimba, Sibiti, Calabar, Brabanta, Bingerville, Widikoum, Lobé, Pamol, Brazil, Colombia, Ecuador, Peru, Panama, Costa Rica, Nicaragua, Honduras, Guyana, Suriname exhibit genotypic variability making it difficult to select oil palms with the phenotype of interest.

[0088] Advantageously, the method according to the invention proposes a set of markers allowing us to overcome the variability dependent on the population to which the oil palms belong.

[0089] According to one embodiment, the plant belonging to the genus Elaeis belongs to a population of oil palms selected from La Mé, Deli, Yangambi, Nifor, Yocoboué, Pobè, Cameroon, Avros, Ekona, Dumpy, Angola, Nigeria, Ghana, Marihat, Binga, Yaligimba, Sibiti, Calabar, Brabanta, Bingerville, Widikoum, Lobé, Pamol, Brazil, Colombia, Ecuador, Peru, Panama, Costa Rica, Nicaragua, Honduras, Guyana, Suriname.

[0090] According to one embodiment, the plant belonging to the genus Elaeis belongs to a population of oil palms selected from La Mé or Deli.

[0091] According to one embodiment, the method according to the invention also includes the detection of at least one other QTL associated with resistance to core rot selected from the group consisting of: *a QTL located on chromosome 5 between position 115766007 and 116766006 of the Egu.V3 reference genome; *a QTL located on chromosome 7 between position 119773060 and 120773059 of the Egu.V3 reference genome; *a QTL located on chromosome 9 between position 1567660 and 2567659 of the Egu.V3 reference genome; *a QTL located on chromosome 10 between position 11569544 and 12569543 of the Egu.V3 reference genome; and their combinations.

[0092] According to a particular embodiment, the invention relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting resistance to heart rot, said method comprising detection in all or part of said plant: *of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome; *of a QTL located on chromosome 5 between position 115766007 and 116766006 of the Egu.V3 reference genome; *of a QTL located on chromosome 7 between position 119773060 and 120773059 of the Egu.V3 reference genome; *of a QTL located on chromosome 9 between positions 1567660 and 2567659 of the Egu.V3 reference genome; and *of a QTL located on chromosome 10 between positions 11569544 and 12569543 of the Egu.V3 reference genome

[0093] Preferably, the method according to the invention also includes the detection of a rot-resistant QTL located on chromosome 5 between positions 115766007 and 116766006 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_10 comprising an Adenine at position 91 of SEQ ID NO: 10 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 10, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 10.

[0094] Preferably, the method according to the invention also includes the detection of a QTL associated with resistance to located on chromosome 7 between position 119773060 and 120773059 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_11 comprising an Adenine at position 91 of SEQ ID NO: 11 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 11, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 11.

[0095] Preferably, the method according to the invention also includes the detection of a rot-resistant QTL located on chromosome 9 between positions 1567660 and 2567659 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_12 comprising a Thymine at position 91 of SEQ ID NO: 12 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 12, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 12.

[0096] Preferably, the method according to the invention also includes the detection of a rot-resistant QTL located on chromosome 10 between positions 11569544 and 12569543 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_13 comprising a Cytosine at position 91 of SEQ ID NO: 13 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 13, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 13.

[0097] Thus, according to a particular embodiment, the method according to the invention comprises detection in or part of said plant: *of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome, in which said QTL can be identified by at least one SNP (nucleotide polymorphism) marker chosen from the group consisting of SNP_1, SNP_2, SNP_3, SNP_4, SNP_5, SNP_6, SNP_7, SNP_8, or SNP_9 and any combination thereof; and * a rot-resistance QTL located on chromosome 5 between positions 115766007 and 116766006 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_10 comprising an Adenine at position 91 of SEQ ID NO: 10 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 10, preferably at least 95%, in particular at least 98%, and even more preferably at least 99% identity with SEQ ID NO: 10; and / or *of a QTL associated with resistance to rot located on chromosome 7 between positions 119773060 and 120773059 of the Egu.V3 reference genome, in which said QTL can be identified by SNP_11 comprising an Adenine at position 91 of SEQ ID NO: 11 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 11, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 11; and / or * of a QTL associated with resistance to rot located on chromosome 9 between positions 1567660 and 2567659 of the Egu reference genome.V3, wherein said QTL can be identified by SNP_12 comprising a Thymine at position 91 of SEQ ID NO: 12 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 12, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 12; and / or * of a rot-resistant QTL located on chromosome 10 between positions 11569544 and 12569543 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_13 comprising a Cytosine at position 91 of SEQ ID NO: 13 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 13, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 13. .

[0098] Isolated nucleic acid

[0099] According to another aspect, the present invention also relates to an isolated nucleic acid comprising a nucleotide sequence, or its complementary sequence, or a fragment of said nucleotide sequence.

[0100] Advantageously, the fragment of said nucleotide sequence comprises at least 15 nucleotides and the nucleotide at position 91 of one of the sequences SEQ ID NO:1 to SEQ ID NO:13. Very advantageously, the fragment of said nucleotide sequence consists of 15 nucleotides, including the nucleotide at position 91 of one of the sequences SEQ ID NO:1 to SEQ ID NO:13.

[0101] According to another preferred object, said nucleotide sequence is selected from the group consisting of: SEQ ID NO: 1 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 1; *SEQ ID NO: 2 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 2; *SEQ ID NO: 3 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 3; *SEQ ID NO: 4 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 4; *SEQ ID NO: 5 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 5; *SEQ ID NO: 6 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 6; *SEQ ID NO: 7 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 7; *SEQ ID NO: 8 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 8; *SEQ ID NO: 9 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 9; *SEQ ID NO: 10 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 10; *SEQ ID NO: 11 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 11; *SEQ ID NO: 12 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 12; and *SEQ ID NO: 13 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 13.

[0102] Thus, according to one object, the nucleic acid isolated according to the invention comprises at least 15 nucleotides including nucleotide 91 of any of the nucleotide sequences selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13.

[0103] Furthermore, according to another object, the isolated nucleic acid according to the invention comprises the complementary sequence of the isolated nucleic acid comprising at least 15 nucleotides including nucleotide 91 of any of the nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13.

[0104] According to another embodiment, the nucleic acid isolated according to the invention comprises a fragment of any one of the nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 of at least 15 nucleotides, said fragment further comprising nucleotide 91 of said nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or complementary nucleotide sequences of these.

[0105] Preferably, the isolated nucleic acid comprises more than 15 nucleotides, in particular at least 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nucleotides and comprises nucleotide 91 of one of the nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or a nucleotide sequence complementary thereto.

[0106] Use of at least one nucleic acid according to the invention

[0107] The present invention also relates to the use of at least one nucleic acid according to the invention for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot.

[0108] Preferably, said plant belonging to the genus Elaeis is chosen from Elaeis guineensis, Elaeis o leifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis o leifera.

[0109] Advantageously, the invention also relates to the use of one or more nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or a fragment thereof for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting reduced endogenous lipase activity, wherein said fragment consists of at least 15 nucleotides comprising nucleotide 91 of said nucleotide sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13 or a complementary sequence to said nucleotide sequence(s).

[0110] Primer mixture

[0111] The present invention also relates to a composition comprising at least one set of primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, said composition comprising at least one set of primers selected from the group consisting of: * a sense primer comprising a SEQ ID NO: 14 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 14 and / or a sense primer comprising a SEQ ID NO: 15 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 15 and an antisense primer, comprising a SEQ ID NO: 16 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 16; * a sense primer comprising a SEQ ID NO: 17 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 17 and / or a sense primer comprising a SEQ ID NO: 18 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 18 and an antisense primer, comprising a SEQ ID NO: 19 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 19; *a sense primer comprising a SEQ ID NO: 20 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 20 and / or a sense primer comprising a SEQ ID NO: 21 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 21 and an antisense primer, comprising a SEQ ID NO: 22 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 22; *a sense primer comprising a SEQ ID NO: 23 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 23 and / or a sense primer comprising a SEQ ID NO: 24 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 24 and an antisense primer, comprising a SEQ ID NO: 25 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 25; *a sense primer comprising a SEQ ID NO: 26 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 26 and / or a sense primer comprising a SEQ ID NO: 27 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 27 and an antisense primer, comprising a SEQ ID NO: 28 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 28; *a sense primer comprising a SEQ ID NO: 29 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 29 and / or a sense primer comprising a SEQ ID NO: 30 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 30 and an antisense primer, comprising a SEQ ID NO: 31 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 31; *a sense primer comprising a SEQ ID NO: 32 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 32 and / or a sense primer comprising a SEQ ID NO: 33 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 33 and an antisense primer, comprising a SEQ ID NO: 34 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 34; *a sense primer comprising a SEQ ID NO: 35 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 35 and / or a sense primer comprising a SEQ ID NO: 36 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 36 and an antisense primer, comprising a SEQ ID NO: 37 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 37; *a forward primer comprising a sequence SEQ ID NO: 38, or a sequence with at least 80% identity with SEQ ID NO: 38 and / or a forward primer comprising a sequence SEQ ID NO: 39, or a sequence with at least 80% identity with SEQ ID NO: 39 and a reverse primer comprising a sequence SEQ ID NO: 40, or a sequence with at least 80% identity with SEQ ID NO: 40; and * their combinations.

[0112] Advantageously, the composition according to the invention allows the detection in all or part of a plant belonging to the genus Elaeis of a QTL associated with resistance to heart rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0113] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 14, or a sequence having at least 80% identity with SEQ ID NO: 14 and / or a sense primer comprising a sequence SEQ ID NO: 15, or a sequence having at least 80% identity with SEQ ID NO: 15 and an antisense primer, comprising a sequence SEQ ID NO: 16, or a sequence having at least 80% identity with SEQ ID NO: 16, this advantageously allows the detection of the presence of SNP_1 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0114] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 17, or a sequence having at least 80% identity with SEQ ID NO: 17 and / or a sense primer comprising a sequence SEQ ID NO: 18, or a sequence having at least 80% identity with SEQ ID NO: 18 and an antisense primer, comprising a sequence SEQ ID NO: 19, or a sequence having at least 80% identity with SEQ ID NO: 19, this advantageously allows the detection of the presence of SNP_2 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0115] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 20, or a sequence having at least 80% identity with SEQ ID NO: 20 and / or a sense primer comprising a sequence SEQ ID NO: 21, or a sequence having at least 80% identity with SEQ ID NO: 21 and an antisense primer, comprising a sequence SEQ ID NO: 22, or a sequence having at least 80% identity with SEQ ID NO: 22, this advantageously allows the detection of the presence of SNP_3 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0116] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 23, or a sequence having at least 80% identity with SEQ ID NO: 23 and / or a sense primer comprising a sequence SEQ ID NO: 24, or a sequence having at least 80% identity with SEQ ID NO: 24 and an antisense primer, comprising a sequence SEQ ID NO: 25, or a sequence having at least 80% identity with SEQ ID NO: 25, this advantageously allows the detection of the presence of SNP_4 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0117] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 29, or a sequence having at least 80% identity with SEQ ID NO: 29 and / or a sense primer comprising a sequence SEQ ID NO: 30, or a sequence having at least 80% identity with SEQ ID NO: 30 and an antisense primer, comprising a sequence SEQ ID NO: 31, or a sequence having at least 80% identity with SEQ ID NO: 31, this advantageously allows the detection of the presence of SNP_6 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0118] When the composition according to the invention comprises a primer set including a direction primer comprising a sequence SEQ ID NO: 32, or a sequence showing at least 80% identity with SEQ ID NO: 32 and / or a sense primer comprising a sequence SEQ ID NO: 33, or a sequence showing at least 80% identity with SEQ ID NO: 33 and an antisense primer, comprising a sequence SEQ ID NO: 34, or a sequence showing at least 80% identity with SEQ ID NO: 34, this advantageously allows the detection of the presence of SNP_7 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0119] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 35, or a sequence having at least 80% identity with SEQ ID NO: 35 and / or a sense primer comprising a sequence SEQ ID NO: 36, or a sequence having at least 80% identity with SEQ ID NO: 36 and an antisense primer, comprising a sequence SEQ ID NO: 37, or a sequence having at least 80% identity with SEQ ID NO: 37, it advantageously allows the detection of the presence of SNP_8 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0120] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 38, or a sequence having at least 80% identity with SEQ ID NO: 38 and / or a sense primer including a sequence SEQ ID NO: 39, or a sequence having at least 80% identity with SEQ ID NO: 39 and an antisense primer, including a sequence SEQ ID NO: 40, or a sequence having at least 80% identity with SEQ ID NO: 40, this advantageously allows the detection of the presence of SNP_9 and therefore the detection of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

[0121] According to one embodiment, the composition according to the invention comprises at least one set of primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, comprising a sense primer comprising a sequence SEQ ID NO: 44, or a sequence exhibiting at least 80% identity with SEQ ID NO: 44 and / or a sense primer comprising a sequence SEQ ID NO: 45, or a sequence exhibiting at least 80% identity with SEQ ID NO: 45 and an antisense primer, comprising a sequence SEQ ID NO: 46, or a sequence exhibiting at least 80% identity with SEQ ID NO: 46.

[0122] Where the composition according to the invention comprises a primer set including a forward primer comprising a sequence SEQ ID NO: 44, or a sequence having at least 80% identity with SEQ ID NO: 44 and / or a forward primer comprising a sequence SEQ ID NO: 45, or a sequence having at least 80% identity with SEQ ID NO: 45 and an antisense primer, comprising a sequence SEQ ID NO: 46, or a sequence exhibiting at least 80% identity with SEQ ID NO: 46, advantageously allows the detection of the presence of SNP_10 and therefore the detection of a QTL associated with resistance to rot located on chromosome 5 between positions 115766007 and 116766006 of the Egu.V3 reference genome.

[0123] According to one embodiment, the composition according to the invention comprises at least one set of primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, comprising a sense primer comprising a sequence SEQ ID NO: 41, or a sequence exhibiting at least 80% identity with SEQ ID NO: 41 and / or a sense primer comprising a sequence SEQ ID NO: 42, or a sequence exhibiting at least 80% identity with SEQ ID NO: 42 and an antisense primer, comprising a sequence SEQ ID NO: 43, or a sequence exhibiting at least 80% identity with SEQ ID NO: 43.

[0124] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 41, or a sequence having at least 80% identity with SEQ ID NO: 41 and / or a sense primer comprising a sequence SEQ ID NO: 42, or a sequence having at least 80% identity with SEQ ID NO: 42 and an antisense primer, comprising a sequence SEQ ID NO: 43, or a sequence having at least 80% identity with SEQ ID NO: 43, this advantageously allows the detection of the presence of SNP_11 and therefore the detection of a QTL associated with resistance to located on chromosome 7 between position 119773060 and 120773059 of the Egu.V3 reference genome.

[0125] According to one embodiment, the composition according to the invention comprises at least one set of primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, comprising a sense primer including a sequence SEQ ID NO: 47, or a sequence exhibiting at least 80% identity with SEQ ID NO: 47 and / or a sense primer including a sequence SEQ ID NO: 48, or a sequence exhibiting at least 80% identity with SEQ ID NO: 48 and an antisense primer, including a sequence SEQ ID NO: 49, or a sequence exhibiting at least 80% identity with SEQ ID NO: 49.

[0126] When the composition according to the invention comprises a primer set including a forward primer comprising a sequence SEQ ID NO: 47, or a sequence having at least 80% identity with SEQ ID NO: 47 and / or a forward primer comprising a sequence SEQ ID NO: 48, or a sequence having at least 80% identity with SEQ ID NO: 48 and an antisense primer, comprising a sequence SEQ ID NO: 49, or a sequence having at least 80% identity with SEQ ID NO: 49, this advantageously allows the detection of the presence of SNP_12 and therefore the detection of a QTL associated with resistance to rot located on chromosome 9 between positions 1567660 and 2567659 of the Egu.V3 reference genome.

[0127] According to one embodiment, the composition according to the invention comprises at least one set of primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, comprising a sense primer comprising a sequence SEQ ID NO: 50, or a sequence exhibiting at least 80% identity with SEQ ID NO: 50 and / or a sense primer comprising a sequence SEQ ID NO: 51, or a sequence exhibiting at least 80% identity with SEQ ID NO: 51 and an antisense primer, comprising a sequence SEQ ID NO: 52, or a sequence exhibiting at least 80% identity with SEQ ID NO: 52.

[0128] When the composition according to the invention comprises a primer set including a sense primer comprising a sequence SEQ ID NO: 50, or a sequence having at least 80% identity with SEQ ID NO: 50 and / or a sense primer comprising a sequence SEQ ID NO: 51, or a sequence having at least 80% identity with SEQ ID NO: 51 and an antisense primer, comprising a sequence SEQ ID NO: 52, or a sequence having at least 80% identity with SEQ ID NO: 52, it advantageously allows the detection of the presence of SNP_13 and therefore the detection of a QTL associated with resistance to rot located on chromosome 10 between position 11569544 and 12569543 of the Egu.V3 reference genome.

[0129] According to one embodiment, the composition according to the invention consists of primer sets selected from the group consisting of: * a sense primer comprising a SEQ ID NO: 14 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 14 and / or a sense primer comprising a SEQ ID NO: 15 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 15 and an antisense primer, comprising a SEQ ID NO: 16 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 16; * a sense primer comprising a SEQ ID NO: 17 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 17 and / or a sense primer comprising a SEQ ID NO: 18 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 18 and an antisense primer, comprising a SEQ ID NO: 19 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 19; *a sense primer comprising a SEQ ID NO: 20 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 20 and / or a sense primer comprising a SEQ ID NO: 21 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 21 and an antisense primer, comprising a SEQ ID NO: 22 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 22; *a sense primer comprising a SEQ ID NO: 23 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 23 and / or a sense primer comprising a SEQ ID NO: 24 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 24 and an antisense primer, comprising a SEQ ID NO: 25 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 25; *a sense primer comprising a SEQ ID NO: 26 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 26 and / or a sense primer comprising a SEQ ID NO: 27 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 27 and an antisense primer, comprising a SEQ ID NO: 28 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 28; *a sense primer comprising a SEQ ID NO: 29 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 29 and / or a sense primer comprising a SEQ ID NO: 30 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 30 and an antisense primer, comprising a SEQ ID NO: 31 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 31; *a sense primer comprising a SEQ ID NO: 32 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 32 and / or a sense primer comprising a SEQ ID NO: 33 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 33 and an antisense primer, comprising a SEQ ID NO: 34 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 34; *a sense primer comprising a SEQ ID NO: 35 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 35 and / or a sense primer comprising a SEQ ID NO: 36 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 36 and an antisense primer, comprising a SEQ ID NO: 37 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 37; *a sense primer comprising a SEQ ID NO: 38 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 38 and / or a sense primer comprising a SEQ ID NO: 39 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 39 and an antisense primer, comprising a SEQ ID NO: 40 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 40; *a direction primer comprising a SEQ ID NO: 41 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 41 and / or a direction primer including a SEQ ID NO: 42 sequence, or a sequence showing at least 80% identity with SEQ ID NO: 42 and an antisense primer, including a SEQ ID NO: 43 sequence, or a sequence showing at least 80% identity with SEQ ID NO: 43; *a sense primer comprising a SEQ ID NO: 44 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 44 and / or a sense primer comprising a SEQ ID NO: 45 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 45 and an antisense primer, comprising a SEQ ID NO: 46 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 46; * a forward primer comprising a sequence SEQ ID NO: 47, or a sequence with at least 80% identity with SEQ ID NO: 47 and / or a forward primer comprising a sequence SEQ ID NO: 48, or a sequence with at least 80% identity with SEQ ID NO: 48 and a reverse primer comprising a sequence SEQ ID NO: 49, or a sequence with at least 80% identity with SEQ ID NO: 49; and

[0130] * a direction primer comprising a SEQ ID NO: 50 sequence, or a sequence showing at least 80% identity with SEQ ID NO: 50 and / or a sense primer comprising a SEQ ID NO: 51 sequence, or a sequence showing at least 80% identity with SEQ ID NO: 51 and an antisense primer, comprising a SEQ ID NO: 52 sequence, or a sequence showing at least 80% identity with SEQ ID NO: 52. Examples

[0131] Example 1:

[0132] Experimental design:

[0133] A field trial planted in 2012 in Ecuador at Shushufindi tested the resistance of various E. guineensis crosses to heart rot according to a randomized incomplete block design, with elementary plots of 9 palms and 15 replicates.

[0134] 25 crosses were selected within this trial to perform a detection of QTL.

[0135] These 25 crosses are from 17 mothers belonging to the Deli population and 7 fathers belonging to the La Mé population according to an incomplete factorial crossover design.

[0136] An incomplete factorial crossover design is a type of experimental design in which the effect of several factors (independent variables) on one or more dependent variables is examined, but with certain combinations of factor levels deliberately omitted. This type of design is used when a crossover design comprehensive (in which each level of each factor is tested with each level of the other factors) is impossible or inefficient due to time, cost, or resource constraints.

[0137] In March 2022, the incidence rate of the disease varied between 4% and 81% for these crosses, thus demonstrating a wide variation of genetic origin.

[0138] The incidence rate of a disease is an epidemiological measure that represents the number of new cases of that disease in a specific population over a given period of time. An incidence rate of 4% means that, in a given population, 4% of individuals have developed the disease.

[0139] For comparison, the incidence of the disease was 68% in a cross present in the same trial, of the variety DA115D x LM2T, which is a reference variety susceptible to the disease.

[0140] In 2018, leaf samples for DNA extraction were taken from 1178 palm trees in these 25 crosses, i.e. almost 50 palm trees from each cross, at a time when the incidence of the disease was still low.

[0141] Subsequently, a subset of 362 individuals was chosen for QTL detection, fixing the number of individuals per cross proportionally to the number of palm trees still alive at the time of sampling, which represents between 5 and 18 palm trees per cross.

[0142] Genotypic data

[0143] These 362 individuals and their ancestors were genotyped on a 67K SNP chip.

[0144] Phenotypic data

[0145] A monthly health census was conducted across the entire trial for 10 years, recording for each palm the time until the onset of symptoms of heart rot or other diseases. Palms affected by other diseases were censored for analysis.

[0146] QTL Detection

[0147] A survival analysis was performed using a Cox model incorporating plot and crossover effects as fixed effects ([Fig. 1]). The calculations were performed in R (R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https: / / www.R-project.org / ) using the coxph() function from the survival package (Bittencourt et al. 2021). This model was used to obtain, using the coefficients() function, a vector of correction coefficients to account for the effects of the plots in the subsequent QTL detection model.

[0148] For QTL detection, a multilocus GWAS approach was used. Several Bayesian models (Bayes A and Bayesian Lasso) were tested using the The R package BGLR (Pérez and de los Campos, 2014) and the function of the same name were used. This package allows for the analysis of censored data. The parameters for the Bayes A model are dfO: 4, S0: half the phenotypic variance var(y), 50,000 iterations, burn-in 2000, lambda: 25, rate: le-4, and shape: 0.55. The parameters for the Bayesian Lasso model are dfO: 5, S0: var(y) / 2*df0, 40,000 iterations, burn-in 2000, lambda: 25, rate: le-4, and shape: 0.55. The models included corrections for the parcel effect calculated with the Cox model and integrated as a fixed effects vector. A marker was considered to be associated with a QTL if the 60% confidence interval of its estimated effect as posterior to the model does not contain 0.

[0149] 7 SNP markers were identified in common by both models, 5 on the chromosome 2 (QTL_mkl at 5, positions 73213312, 73415467, 73436547, 73915201 and 74028450 on chromosome 2), one on chromosome 5 (SNP_10, position 116266006) and one on chromosome 7 (SNP_11, position 120273059) (reference Egu.v3).

[0150] The study of the effect of these QTLs on the survival probability of individuals in the mapping population ([Fig. 2]) indicates that the chr2 QTL corresponds to a QTL with a strong effect (major QTL), unlike the other two with weaker effects (minor QTLs). The haplotype resistant to the major QTL thus reduces the risk of contracting the disease by 60% in the study population.

[0151] The segregation study of the 7 identified markers indicates that the major QTL (chr2) and one of the two minor QTLs (that of chr7) are segregated on the maternal side only, thus indicating the presence of segregating resistance alleles in the Deli population. The minor QTL of chr5, on the other hand, is segregated on the paternal origin, and therefore highlights the presence of segregating resistance alleles in the La Mé population.

[0152] The five markers identified on chromosome 2 (major QTL) are distributed within a window of -815 kb, around position 73620881 (reference Egu.v3). The origin of the resistance allele identified on the major QTL was traced back to an ancestral palm belonging to the Deli population using pedigree information.

[0153] This ancestral individual is heterozygous on a genomic segment containing the 5 markers. Markers were sought to more specifically mark the resistant haplotype covering this window, by selecting SNPs located in this interval, heterozygous in the ancestral individual and highly specific to this individual (MAF < 14%).

[0154] In the context of the invention, MAF stands for "Minor Allele Frequency." It indicates the frequency of the less frequent of the two alleles of a SNP (Single Nucleotide Polymorphism) in a given population.

[0155] This work was carried out on the basis of information from -5000 individuals from various E. guineensis populations genotyped on a 67K SNP chip.

[0156] The populations represented were as follows: Deli, Deli x Avros, Angola, Ivory Coast, Cameroon, La Mé, La Mé x Sibiti, Yangambi, Nifor, Nigeria, Benin, Congo, Sibiti, Sierra Leone, Yocoboué, Sao Tomé.

[0157] This yielded three markers that allow for the identification of the resistant haplotype of the major QTL on chromosome 2 present in the resistant Deli ancestor (SNP_1 to SNP_3). To better cover the QTL range, SNP_4 was also included despite its lower specificity (MAF > 14%). For the two secondary QTLs identified, the markers used are those identified during QTL detection (SNP_10 and SNP_11).

[0158] Validation

[0159] To validate the identified major QTL, an additional population of 370 individuals was analyzed. This population consisted of palm trees from the same trial, taken from 17 different crosses from those used in the initial detection. The mothers were of Deli origin, and the fathers of Nifor or FR4 (La Mé x unknown) origin. These individuals were genotyped for SNP_1 to SNP_4 markers using PACE® (PCR Allele Competitive Extension) genotyping. A survival analysis showed that the effect of the major QTL in this population was very similar to that observed in the initial detection. In this analysis, the maternal genotype at the major QTL was determined using the genotype of SNP_1 to SNP_4 markers, thus confirming the identified major QTL and the effectiveness of the selected markers ([Fig. 3]).

[0160] On the other hand, the results from the validation population showed segregation of SNP_1 to 4 markers and varying levels of paternal resistance in the FR4 population. Information from SNP_1 to 4 allowed us to determine that there are at least 3 different haplotypes among the analyzed FR4 fathers. To better differentiate the haplotypes present, we analyzed the genotype of the FR4 fathers using additional SNP markers located in the QTL region of chromosome 2, which allow us to discriminate between the different haplotypes present in the FR4 population. These data were obtained by genotyping on a 67K SNP array.

[0161] The combined information from the pedigree, the genotype of the individuals in the validation population on the SNP_1 to 4 markers, and the genotype of the parents on the additional markers in the major QTL area, made it possible to identify 4 different haplotypes among the fathers of the FR4 population (FR4_hapl, FR4_hap2a, FR4_hap2b and FR4_hap3) and to trace these in the validation population.

[0162] The FR4_hap2b haplotype, present in two crosses (Cross #2 and Cross #4) is associated with a low incidence of the disease ([Fig.4]).

[0163] This result suggests the presence in the FR4 population of a resistance QTL at the same location or near the major QTL identified in the Deli population.

[0164] Example 2:

[0165] Since the American oil palm Elaeis oleifera is free from heart rot, genetic resistance appears to be present in this species. In order to identify the genetic basis and markers of this resistance in this species, an analysis was carried out on a population of individuals from an interspecific pseudo-backcross 1 derived from an E. oleifera ancestor of Panamanian origin (cross (E. oleifera Panama x E. guineensis 1) x E. guineensis 2, [Fig.5]).

[0166] This backcross population was planted as embryo clones at different sites. 184 clones were genotyped on a 67K SNP chip.

[0167] These data made it possible to establish a genetic map comprising 829 non-redundant markers, using the R / qtl package in R (Broman KW, Wu H, Sen S, Churchill GA (2003) R / qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890).

[0168] In a first trial (trial_1) conducted in Colombia, 177 clones were genotyped and evaluated for their resistance to heart rot on 5 plots. 138 clones were represented by at least 3 palms and 39 clones by only one or two palms.

[0169] Monthly records were taken to record the presence of symptoms of heart rot. Follow-up was carried out for at least 8 years.

[0170] At the end of the follow-up in January 2019, the number of cases had reached a plateau on all plots, the overall rate of heart rot reached 39% on the trial (between 29% and 48% depending on the plots) and about 30% of the clones had shown cases.

[0171] A logit model was used to estimate a percentage of diseased palm trees per clone, taking into account the effect of the plots. This adjusted percentage per clone was used to perform QTL detection using the R / qtl package, by the SIM and CIM methods ([Fig.6]).

[0172] SIM (Single Interval Mapping) and CIM (Composite Interval Mapping) methods are commonly used approaches for detecting QTLs (Quantitative Trait Loci).

[0173] This analysis highlights three QTLs consistently identified by both methods, on chromosomes 2, 9, and 10 (reference Egu.v3), with peaks centered on SNP_6, SNP_12, and SNP_13 markers by the SIM method, and variance shares of 12%, 12%, and 12%, respectively. The confidence interval for the chromosome 2 QTL, defined by a threshold of 1.5-LOD, covers a 20.7 cM region between two SNP markers located at physical positions 67056279 and 77139690 (bp).

[0174] In a second trial in Ecuador (trial_2), 181 clones were genotyped and evaluated for resistance to heart rot across 9 separate subtrials. All clones were represented by at least 15 palms, except for two that exhibited smaller sample sizes. Monthly surveys were conducted to record the presence of symptoms of heart rot. At the end of the follow-up in May 2020, the overall rate of heart rot reached 45% in the trial (between 28% and 49% depending on the sub-trials).

[0175] The percentage of core rot per clone was used to perform QTL detection using the R / qtl package, by the SIM and CIM methods ([Fig. 7]). This analysis highlights a QTL consistently identified by both methods, on chromosome 2, which colocalizes with the QTL previously identified in assay 1.

[0176] In this analysis, the boundaries of this QTL, defined according to a threshold of 1.5 LOD, define an interval of 11.8 cM between two SNP markers at physical positions 72154369 and 77139690, which allows for a stricter delimitation of this QTL than in trial 1. The CIM method also highlights a QTL on chromosome 10, which colocalizes with the QTL identified in trial 1. The variance shares of these two QTLs are 50% and 6%, respectively.

[0177] These two analyses thus highlight three QTLs for resistance to heart rot, one of which has a potentially strong effect on chromosome 2, and indicate that there is at least partial consistency in the genetic basis of resistance between the forms of disease observed in Colombia and Ecuador. The SNPs used in the analysis are specific to the parent *E. oleifera Panama* and fixed in the species *E. guineensis*, suggesting that these are QTLs for which resistance originates from the parent *E. oleifera*. For the chromosome 2 QTL, seven SNP markers were identified at the 1.5-LOD threshold, of which five were selected as markers for use in marker-assisted selection for resistance to heart rot (SNP_5 to SNP_9).

[0178] These five markers were selected for their discriminatory character between the species E. oleifera and E. guineensis on the basis of private information from the resequencing of 32 individuals (16 E. guineensis and 16 E. oleifera') aligned to a private reference of an E. guineensis palm of Deli origin, and validated by genotyping on an SNP chip.

[0179] In order to verify whether the QTL identified on chromosome 2 is also valid for other populations within the species E. oleifera, we analyzed an interspecific pseudo-backcross 1 derived from an E. oleifera ancestor belonging to the Coari population (cross (E. oleifera Coari x E. guineensis La Mé) x E. guineensis Deli) comprising 98 individuals.

[0180] Both E. guineensis La Mé and Deli parent strains used are susceptible to heart rot. A BSA analysis was performed based on the presence or absence of symptoms for each field individual according to a monthly survey, and on SNP chip genotyping of 78K SNPs. The BSA analysis revealed a spike on the Chromosome 2 is centered on the region between positions 67435231 and 86772730 (p-value of the 4 best markers < 10⁻⁷). This region colocalizes with the chromosome 2 QTL identified in the previous examples. This result demonstrates that the identified QTL is present in highly diverse E. oleifera populations. Furthermore, the markers of SNP_5 to SNP_9 of this QTL, present in different E. oleifera populations, are discriminatory between the two species E. oleifera and E. guineensis based on private information from the resequencing of 32 individuals (16 E. guineensis and 16 E. oleifera). These results suggest that the SNP_5 to SNP_9 markers are valid for marking resistance alleles present on the QTL of chromosome 2 from various E. oleifera populations, particularly in interspecific backcross schemes aimed at introgressing resistance from an E. oleifera individual into other individuals of the species E. guineensis.

[0181] Example 3:

[0182] The results presented above demonstrate that heart rot resistance genes are present in different E. guineensis and E. oleifera populations in the same region of chromosome 2 ([Fig. 8]). The marker-assisted selection method presented here, which targets this QTL, therefore allows selection for heart rot resistance from resistant donor individuals from different populations, including the Deli, FR4, and E. oleifera populations. These results also suggest that the method could be applicable to resistant individuals from other E. guineensis palm populations. In Example 1, which yielded the narrowest QTL range, the boundary markers are located at positions 73213312 and 74028450 on chromosome 2.According to this analysis, the QTL of this chromosome would thus be located in the interval 73013312-74228450 (extreme markers + / - 200 kb, seg_2) which is centered on position 73620881. However, other studies carried out on other populations having identified wider intervals in the same region, a wider interval could be considered, between positions 71954369 and 77339690 (extreme markers of example 2 + / - 200 kb, seg_1), which would allow with a greater level of confidence to cover the area of ​​the QTL regardless of the population considered.

Claims

Demands

1. In vitro method for identifying a plant belonging to the genus Elaeis exhibiting improved resistance to heart rot, said method comprising the detection in all or part of said plant of a QTL associated with resistance to rot located on chromosome 2 between position 71954369 and 77339690 of the Egu.V3 reference genome.

2. Method according to the preceding claim, characterized in that the QTL associated with resistance to heart rot is located on chromosome 2 between position 73013312 and 74228450 of the Egu.V3 reference genome.

3. Method according to any one of the preceding claims, characterized in that said QTL can be identified by at least one marker selected from an SNP (Single Nucleotide Polymorphism) marker, an RFLP (Restriction Fragment Length Polymorphism) marker, a CPAS (Cleaved Amplified Polymorphism Sequence) marker, a RAPD (Random Amplified Polymorphism DNA) marker, an AFLP (Amplified Fragment Length Polymorphism) marker, an SSR (simple sequence repeats) marker and combinations thereof.

4. Method according to the preceding claim, characterized in that said QTL can be identified by at least one SNP marker selected from the group consisting of: - SNP_1 comprising a Cytosine at position 91 of SEQ ID NO: 1 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 1; - SNP_2 comprising a Thymine at position 91 of SEQ ID NO: 2 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 2; - SNP_3 comprising a Guanine at position 91 of SEQ ID NO: 3 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 3; - SNP_4 comprising a Cytosine at position 91 of SEQ ID NO: 4 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 4; - SNP_5 comprising an Adenine at position 91 of SEQ ID NO: 5 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 5; - SNP_6 comprising a Thymine at position 91 of SEQ ID NO: 6 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 6; - SNP_7 comprising a Thymine at position 91 of SEQ ID NO: 7 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 7; - SNP_8 comprising a Thymine at position 91 of SEQ ID NO: 8 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 8; - SNP_9 comprising a Thymine at position 91 of SEQ ID NO: 9 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 9; and - their combinations.

5. Method according to the preceding claim, characterized in that said QTL can be identified by: 1) at least one SNP marker selected from the group consisting of SNP_1, SNP_2, SNP_3 or SNP_4 and their combinations; and / or 2) at least one SNP marker selected from the group consisting of SNP_5, SNP_6, SNP_7, SNP_8, SNP_9 and their combinations.

6. A method according to any one of the preceding claims, characterized in that it also comprises the detection of at least one other QTL associated with resistance to heart rot selected from the group consisting of: *a QTL located on chromosome 5 between positions 115766007 and 116766006 of the Egu.V3 reference genome; *a QTL located on chromosome 7 between positions 119773060 and 120773059 of the Egu.V3 reference genome; *a QTL located on chromosome 9 between positions 1567660 and 2567659 of the Egu.V3 reference genome; *a QTL located on chromosome 10 between positions 11569544 and 12569543 of the Egu.V3 reference genome; and *combinations thereof

7. A method according to the preceding claim, characterized in that it comprises the detection of a QTL associated with resistance to heart rot located on chromosome 5 between positions 115766007 and 116766006 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_10 comprising an Adenine at position 91 of SEQ ID NO: 10 or at position 91 of a sequence comprising at least 90% identity with the SEQ ID NO:

10.

8. Method according to the preceding claim, characterized in that it comprises the detection of a QTL associated with resistance to heart rot located on chromosome 7 between position 119773060 and 120773059 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_11 comprising an Adenine at position 91 of SEQ ID NO: 11 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:

11.

9. Method according to the preceding claim, characterized in that it comprises the detection of a QTL associated with resistance to heart rot located on chromosome 9 between positions 1567660 and 2567659 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_12 comprising a Thymine at position 91 of SEQ ID NO: 12 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:

12.

10. Method according to the preceding claim, characterized in that it comprises the detection of a QTL associated with resistance to heart rot located on chromosome 10 between positions 11569544 and 12569543 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_13 comprising a Cytosine at position 91 of SEQ ID NO: 13 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:

13.

11. Method according to any one of the preceding claims, characterized in that said plant belonging to the genus Elaeis is chosen from Elaeis guineensis, Elaeis oleifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera.

12. Isolated nucleic acid comprising a nucleotide sequence or its complementary sequence said nucleotide sequence is selected from the group consisting of: *SEQ ID NO: 1 or a fragment consisting of at least 15 nucleotides comprising the nucleotide at position 91 of SEQ ID NO: 1; *SEQ ID NO: 2 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 2; *SEQ ID NO: 3 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 3; *SEQ ID NO: 4 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 4; *SEQ ID NO: 5 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 5; *SEQ ID NO: 6 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 6; *SEQ ID NO: 7 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 7; *SEQ ID NO: 8 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 8;*SEQ ID NO: 9 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 9; *SEQ ID NO: 10 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 10; *SEQ ID NO: 11 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 11; *SEQ ID NO: 12 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 12; and *SEQ ID NO: 13 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO:

13.

13. Use of one or more nucleotide sequences selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 13 or

14. of a fragment of these for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot in which said fragment consists of at least 15 nucleotides comprising nucleotide 91 of said nucleotide sequences selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 13 or a complementary sequence to said or said nucleotide sequences. A composition comprising at least one set of sense and antisense primers for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting resistance to heart rot, said composition comprising at least one set of sense and antisense primers selected from the group consisting of: * a sense primer comprising a SEQ ID NO: 14 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 14 and / or a sense primer comprising a SEQ ID NO: 15 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 15 and an antisense primer, comprising a SEQ ID NO: 16 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 16; * a sense primer comprising a SEQ ID NO: 17 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 17 and / or a sense primer comprising a SEQ ID NO: 18 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 18 and an antisense primer, comprising a SEQ ID NO: 19 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 19; *a sense primer comprising a SEQ ID NO: 20 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 20 and / or a sense primer comprising a SEQ ID NO: 21 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 21 and an antisense primer, comprising a SEQ ID NO: 22 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 22; *a forward primer comprising a SEQ ID NO: 23 sequence, or a sequence with at least 80% identity to SEQ ID NO: 23 and / or a forward primer comprising a SEQ ID NO: 24 sequence, or a sequence with at least 80% identity to SEQ ID NO: 24 and an antisense primer, comprising a SEQ ID NO: 25, or a sequence showing at least 80% identity with SEQ ID NO: 25; *a sense primer comprising a SEQ ID NO: 26 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 26 and / or a sense primer comprising a SEQ ID NO: 27 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 27 and an antisense primer, comprising a SEQ ID NO: 28 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 28; *a sense primer comprising a SEQ ID NO: 29 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 29 and / or a sense primer comprising a SEQ ID NO: 30 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 30 and an antisense primer, comprising a SEQ ID NO: 31 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 31; *a sense primer comprising a SEQ ID NO: 32 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 32 and / or a sense primer comprising a SEQ ID NO: 33 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 33 and an antisense primer, comprising a SEQ ID NO: 34 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 34; *a sense primer comprising a SEQ ID NO: 35 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 35 and / or a sense primer comprising a SEQ ID NO: 36 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 36 and an antisense primer, comprising a SEQ ID NO: 37 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 37; *a forward primer comprising a sequence SEQ ID NO: 38, or a sequence with at least 80% identity with SEQ ID NO: 38 and / or a forward primer comprising a sequence SEQ ID NO: 39, or a sequence with at least 80% identity with SEQ ID NO: 39 and an antisense primer comprising a sequence SEQ ID NO: 40, or a sequence with at least 80% identity with SEQ ID NO: 40; and *their combinations.

15. Composition according to the preceding claim, characterized in that it comprises at least one set of forward and reverse primers selected from the group consisting of: *a forward primer comprising a sequence SEQ ID NO: 41, or a sequence having at least 80% identity with SEQ ID NO: 41 and / or a forward primer comprising a sequence SEQ ID NO: 42, or a sequence having at least 80% identity with SEQ ID NO: 42 and a reverse primer, comprising a sequence SEQ ID NO: 43, or a sequence having at least 80% identity with SEQ ID NO: 43; *a sense primer comprising a SEQ ID NO: 44 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 44 and / or a sense primer comprising a SEQ ID NO: 45 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 45 and an antisense primer, comprising a SEQ ID NO: 46 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 46;* a sense primer comprising a SEQ ID NO: 47 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 47 and / or a sense primer comprising a SEQ ID NO: 48 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 48 and an antisense primer, comprising a SEQ ID NO: 49 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 49; and * a sense primer comprising a SEQ ID NO: 50 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 50 and / or a sense primer comprising a SEQ ID NO: 51 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 51 and an antisense primer, comprising a SEQ ID NO: 52 sequence, or a sequence exhibiting at least 80% identity with SEQ ID NO: 52; and * their combinations.;

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