Method for identifying oil palm plants with reduced endogenous lipase activity

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 reduced endogenous lipase activity, said method comprising the detection in all or part of said plant of a QTL (Quantitative Trait Locus) associated with the reduced endogenous lipase activity via the identification of at least one specific SNP (Single Nucleotide Polymorphism) on chromosome 3.

Description

Title of the invention: Method for identifying oil palm plants exhibiting reduced endogenous lipase activity. 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 reduced endogenous lipase activity, said method comprising the detection in all or part of said plant of a QTL (Quantitative Trait Locus) associated with the reduced endogenous lipase activity via the identification of at least one specific SNP (Single Nucleotide Polymorphism) on chromosome 3. 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. 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 oil palm, the primary supplier of vegetable fat, surpassing soybean, sunflower and rapeseed crops, 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, palm oil cultivation presents certain constraints, notably due to the acidification of the oil.

[0007] Indeed, a major problem with palm oil is its acidification, which occurs due to the rapid degradation of triglycerides caused by: *Abscission, corresponding to the process by which a ripe fruit detaches from the parent plant; and / or Bruising refers to physical damage to the fruit, usually caused by impact or excessive pressure. This can occur during harvesting, transport, or storage.

[0008] This degradation is partly due to the activation of an endogenous lipase in the mesocarp of the fruit. The degradation of triglycerides leads to the formation of free fatty acids, resulting in the acidification of palm oil.

[0009] Acidification of palm oil severely affects its quality. Indeed, acidified palm oil becomes unfit for human consumption without refining when it contains more than 5% free fatty acids. Furthermore, the free fatty acids produced are particularly susceptible to peroxidation, a process that generates co-products responsible for rancidity, thus considerably limiting the oil's shelf life.

[0010] To limit the presence of free fatty acids in palm oil, manufacturers have implemented refining processes that filter the oil and remove free fatty acids. However, in addition to being energy-intensive, these processes are not entirely satisfactory because certain undesirable by-products, such as diglycerides, are not completely eliminated.

[0011] Another solution is to regularly harvest the oil palm fruit and sterilize it within 24 hours of harvesting. However, these requirements are particularly difficult to meet for both small farms and industrial operations, since during the peak annual harvest, factories are overloaded and cannot implement such a process.

[0012] In addition, some studies have been able to develop phenotypic selection techniques for oil palms, some having a high level of lipase activity or acidity in the mesocarp and others a low lipase activity or low acidity in the mesocarp.

[0013] Phenotypic selection has the advantage of being simple insofar as it is based on the observation of the visible characteristics of individuals and does not require any knowledge of plant genetics.

[0014] However, this method has many drawbacks, including the cost and time required to obtain a population exhibiting the phenotype of interest. Furthermore, this method cannot be implemented on sterile female individuals.

[0015] In parallel with these phenotypic selection techniques, marker-assisted selection (MAS) methods have also been developed. Based on genotype observation, this method uses genetic markers identified near a gene 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 the activity of endogenous lipases in the mesocarp of oil palms.

[0016] In the context of the invention, certain markers have now been developed to identify oil palms exhibiting reduced endogenous lipase activity. These markers include mutations located around the FLL1 gene. However, these markers are not considered satisfactory because, despite having these mutations, some oil palms still exhibit an undesirable phenotype.

[0017] Indeed, the causal mutation resulting in reduced activity of endogenous lipases in the mesocarp of oil palms has not yet been identified. Consequently, the genotypic variability of oil palms according to species (Elaeis guineensis, Elaeis oleifera, or an oil palm resulting from a cross involving Elaeis guineensis and / or Elaeis oleifera) but also according to population (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) makes it difficult to select predictive markers of the phenotype of interest.

[0018] There is therefore a need to identify new markers adapted to marker-assisted selection techniques in order to identify oil palms exhibiting reduced activity of endogenous lipases while overcoming the variability between species and populations of oil palms. Summary of the invention

[0019] To meet this need, the invention proposes a new in vitro method for identifying a plant belonging to the genus Elaeis exhibiting reduced endogenous lipase activity, said method comprising the detection in all or part of said plant of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between position 70704751 and 74704750 of the Egu.V3 reference genome.

[0020] In particular, the invention relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting reduced endogenous lipase activity, said method comprising the detection in all or part of said plant of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between positions 70704751 and 74704750 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 Thymine 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 an Adenine 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 an Adenine 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 a Guanine 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 Guanine 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 Cytosine 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 Cytosine 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 Cytosine 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; - SNP_10 comprising a Cytosine 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; - 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; - 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; - SNP_13 comprising a Guanine 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; - SNP_14 comprising a Cytosine at position 91 of SEQ ID NO: 14 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 14; and - their combinations.

[0021] Advantageously, the method according to the invention makes it possible to identify oil palms belonging to the genus Elaeis exhibiting reduced activity of endogenous lipases in the mesocarp.

[0022] Indeed, surprisingly, the inventors identified particular SNPs capable of detecting a QTL (Quantitative Trait Locus) associated with reduced activity of endogenous lipases located on chromosome 3 between position 70704751 and 74704750 of the Egu.V3 reference genome.

[0023] By identifying these specific markers, the inventors have found a suitable means for identifying oil palms belonging to the genus Elaeis exhibiting reduced activity of endogenous lipases, 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 reduced endogenous lipase activity.

[0025] According to a particularly suitable embodiment, the method according to the invention also advantageously includes the detection in all or part of a plant of a QTL associated with reduced endogenous lipase activity located on chromosome 2 between position 23159847 and 24159846 of the Egu.V3 reference genome, in which said QTL can be identified by SNP_15 comprising a Thymine at position 91 of SEQ ID NO: 15 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 15.

[0026] Advantageously, the inventors have developed a method based on the detection of several QTLs in order to obtain a predictive method exhibiting optimal specificity for predicting the phenotype of interest.

[0027] According to a preferred embodiment, the method according to the invention also includes the detection in all or part of a plant of a QTL associated with reduced endogenous lipase activity located on chromosome 12 between position 3711167 and 4711166 of the Egu.V3 reference genome, in which said QTL can be identified by SNP_16 comprising a Thymine at position 91 of SEQ ID NO: 16 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 16.

[0028] Advantageously, the detection of several QTLs identified as associated with reduced endogenous lipase activity makes it possible to increase the specificity of the method according to the invention.

[0029] 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.

[0030] 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; *SEQ ID NO: 13 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 13; *SEQ ID NO: 14 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 14; *SEQ ID NO: 15 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 15; and *SEQ ID NO: 16 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 16.

[0031] Finally, the invention 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 reduced endogenous lipase activity. 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, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, and SEQ ID NO: 16, or a fragment of one of these sequences, 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, SEQ ID NO: 14, SEQ ID NO: 15, and SEQ ID NO: 16. :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, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16 or a complementary sequence to said nucleotide sequence(s).

[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]: [Fig. 1] is a graphical representation describing the relationship between the phenotype predicted using the SNP_1 to SNP_4 markers and the acidity of the oil. The graph was obtained from 225 individuals (189 with high acidity and 36 with low acidity, with an acidity threshold of 25%).

[0034] [Fig.2]: [Fig.2] is a graphical representation describing the pedigree of the pseudo- backcross 1 used in example 3. Genotypes are indicated in parentheses.

[0035] [Fig.3]: [Fig.3] is a graphical representation of a genetic map of the group homologous linkage to chromosome 3 of Egu.v3 including the position of the 4 retained SNP markers (SNP_5 and SNP_12 to SNP14).

[0036] [Fig.4]: Fig.4 is a graphical representation of the QTLs identified for the acidity character of the oil using FlexQTL software (300,000 iterations and 2 independent simulations).

[0037] [Fig. 5]: [Fig. 5] is a graphical representation showing the effect of minor QTL alleles on LG4 (left) and LG13 (right) on the acidity value of the oil in individuals of the "High Lipase" and "Low Lipase" classes. The QTL genotypes are indicated on the x-axis by a sequence of two numbers, the first indicating the major QTL genotype (0 = homozygous LL / LL, 1 = heterozygous and 2 = homozygous HL / HL) and the second the minor QTL genotype (0 = homozygous REF, 1 = heterozygous, 2 = homozygous ALT). Detailed description of the invention

[0038] Definitions:

[0039] 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 oleifer a.

[0040] 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.

[0041] 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 encodes at least one gene whose expression, alone or in combination with other genes, results in the expression of the phenotypic trait, or encodes 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. A QTL can be defined by indicating its genetic location in the genome of the introgression donor containing the QTL using one or more molecular genomic markers.

[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] By "trait" in the sense of the invention, we mean a phenotype of the plant.

[0044] By "locus" or "loci" in the sense of the invention, one means one or more places specific on a chromosome, where, for example, a gene or a genetic marker is located.

[0045] 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").

[0046] 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.

[0047] 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.

[0048] To calculate the sequence identity, the following procedure is generally used:

[0049] 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.

[0050] 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.

[0051] 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%.

[0052] 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.

[0053] 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.

[0054] By "phenotype of interest" in the sense of the invention, we mean an oil palm exhibiting reduced activity of endogenous lipases within the mesocarp.

[0055] 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.

[0056] In vitro method for identifying a plant belonging to the genus Elaeis exhibiting reduced activity of endogenous lipases

[0057] The invention therefore relates to an in vitro method for identifying a plant belonging to the genus Elaeis exhibiting reduced endogenous lipase activity, said method comprising the detection in all or part of said plant of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between position 70704751 and 74704750 of the Egu.V3 reference genome, in which said QTL can be identified by at least one SNP marker chosen from the group consisting of: - SNP_1 comprising a Thymine 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 an Adenine 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 an Adenine 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%, especially at least 98%, even more preferably at least 99% identity with SEQ ID NO: 4; - SNP_5 comprising a Guanine 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%, especially at least 98%, even more preferably at least 99% identity with SEQ ID NO: 5; - SNP_6 comprising a Guanine 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 Cytosine 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 Cytosine 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%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO:8; - SNP_9 comprising a Cytosine 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%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 9; - SNP_10 comprising a Cytosine 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; - 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; - 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; - SNP_13 comprising a Guanine 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; - SNP_14 comprising a Cytosine at position 91 of SEQ ID NO: 14 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 14, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 14; and - their combinations.

[0058] 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.

[0059] Preferably, the method according to the invention comprises the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between position 72389708 and 73008701 of the Egu.V3 reference genome, more preferably between position 72638099 and 72801079 of the Egu.V3 reference genome.

[0060] Advantageously, SNPs 1 to 14, taken individually or in combination, allow the detection of a QTL on chromosome 3 of the Egu.V3 reference genome. associated with alleles causing the phenotype linked to reduced activity of endogenous lipases present in the mesocarp of 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

[0061] 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 that phenotype. Indeed, one of the key aspects of the method according to the invention is to provide markers capable of detecting all the alleles responsible for the phenotype of interest in order to overcome inter-species and inter-population genotypic variability.

[0062] Preferably, the method according to the invention comprises the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between position 70704751 and 74704750 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, 10, 11, 12, 13, 14 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, SNP_10, SNP_11, SNP_12, SNP_13, SNP_14, and any combinations thereof.

[0063] According to a particular embodiment, the method according to the invention comprises the detection of a QTL associated with reduced activity of endogenous lipases located on chromosome 3 between position 70704751 and 74704750 of the Egu.V3 reference genome, wherein 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, SNP_9, SNP_10, SNP-H, SNP_12, SNP_13 and SNP_14.

[0064] Advantageously, when the method according to the invention combines all the markers SNP_1 to SNP_14, the accuracy of detection of the phenotype of interest is greater than 90%, in particular greater than 95%.

[0065] Advantageously, the method according to the invention is thus able to identify oil palms belonging to the genus Elaeis exhibiting reduced activity of endogenous lipases by overcoming the variabilities between species and populations of oil palms.

[0066] 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.

[0067] 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.

[0068] According to another embodiment, the method according to the invention comprises the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between positions 70704751 and 74704750 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, SNP_4, SNP_5 and their combinations; and / or 2) at least one SNP marker chosen from the group consisting of SNP_6, SNP_7, SNP_8, SNP_9, SNP_10, SNP_11 and their combinations; and / or 3) at least one SNP marker chosen from the group consisting of SNP_5, SNP_11, SNP_12, SNP_13, SNP_14 and their combinations.

[0069] Advantageously, the combination of markers belonging to groups 1), 2) and 3) makes it possible to identify 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, and this regardless of the population to which they belong.

[0070] 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 exhibiting the phenotype of interest.

[0071] 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.

[0072] 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.

[0073] Preferably, the plant belonging to the genus Elaeis belongs to a population of oil palms chosen from La mé or Deli.

[0074] According to one embodiment, the method according to the invention also comprises the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 2 between positions 23159847 and 24159846 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_15 comprising a Thymine at position 91 of SEQ ID NO: 15 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 15, preferably at less than 95%, in particular at least 98%, even more preferentially at least 99% identity with SEQ ID NO: 15.

[0075] According to another embodiment, the method according to the invention also includes the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 12 between position 3711167 and 4711166 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_16 comprising a Thymine at position 91 of SEQ ID NO: 16 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 16, preferably at least 95%, in particular at least 98%, even more preferably at least 99% identity with SEQ ID NO: 16.

[0076] Thus, according to a particular embodiment, the method according to the invention comprises detection in all or part of said plant: * of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between positions 70704751 and 74704750 of the Egu.V3 reference genome, wherein said QTL can be identified by at least one SNP (nucleotide polymorphism) marker selected from the group consisting of SNP_1, SNP_2, SNP_3, SNP_4, SNP_5, SNP_6, SNP_7, SNP_8, SNP_9, SNP_10, SNP_H, SNP_12, SNP_13 or SNP_14 and any combination thereof; and * of a QTL associated with reduced endogenous lipase activity located on chromosome 2 between positions 23159847 and 24159846 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_15 comprising a Thymine at position 91 of SEQ ID NO: 15 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 15, preferably at least 95%, in particular at least 98%, and even more preferably at least 99% identity with SEQ ID NO: 15; and / or * of a QTL associated with reduced endogenous lipase activity located on chromosome 12 between position 3711167 and 4711166 of the Egu.V3 reference genome, in which said QTL can be identified by SNP_16 comprising a Thymine at position 91 of SEQ ID NO: 16 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 16, preferably at least 95%, notably at least 98%, even more preferably at least 99% identity with SEQ ID NO: 16.

[0077] Isolated nucleic acid

[0078] 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. 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: 16. Most advantageously the fragment of said nucleotide sequence consists of 15 nucleotides, including the nucleotide in position 91 of one of the sequences SEQ ID NO: 1 to SEQ ID NO: 16.

[0079] 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; *SEQ ID NO: 13 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 13; *SEQ ID NO: 14 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 14; *SEQ ID NO: 15 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 15; and *SEQ ID NO: 16 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 16.

[0080] 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, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16.

[0081] 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, 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, SEQ ID NO:14, SEQ ID NO:15 and SEQ ID NO:16.

[0082] 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, SEQ ID NO: 14, SEQ ID NO: 15, and SEQ ID NO: 16 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, SEQ ID NO: 14, SEQ ID NO: 15, and SEQ ID NO: 16 :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 , SEQ ID NO :14 , SEQ ID NO :15 and SEQ ID NO :16 or complementary nucleotide sequences of these.

[0083] 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, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16 or a nucleotide sequence complementary thereto.

[0084] Use of at least one nucleic acid according to the invention

[0085] 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 reduced endogenous lipase activity.

[0086] 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.

[0087] 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, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16, 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, SEQ ID NO: 14,SEQ ID NO: 15 and SEQ ID NO: 16 or a complementary sequence to said nucleotide sequence(s). Examples

[0088] Example 1: Preliminary study on the identification of alleles responsible for the phenotype of interest

[0089] Previous work has demonstrated that mesocarp lipase activity in Elaeis guineensis is predominantly under the control of a major QTL in or near the EgLIPl gene (Domonhedo et al. 2018, doi: 10.1007 / sl 1295-018-1284-7).

[0090] A BLAST analysis made it possible to position this gene around position 72703000 on chromosome 3 of the public reference Egu.V3.

[0091] Phenotypic evaluation of a panel of 1183 palm trees from various populations revealed the presence of individuals exhibiting reduced activity of endogenous lipases. These individuals are designated "LL" for Low Lipase, compared to "HL" for "High Lipase" individuals.

[0092] The phenotypic identification of the LL and HL individuals was carried out as described in Morcillo et al. 2013 (doi: 10.1038 / ncomms3160), by titration of the acidity on ripe fruit pulp one hour after grinding.

[0093] The individuals analyzed are adult palm trees planted at the Centre de Recherches Agricoles Plantes Pérennes (CRA-PP) in Pobè, in the South East of Benin and determined by the coordinates 2° 15" - 2° 45" E and 6° -7+ 45" N.

[0094] The panel consists of 1002 Elaeis guineensis individuals, 50 Elaeis oleifera (from 7 different populations), 35 hybrid individuals from crosses between the two species and 96 individuals from first generation backcrosses ([backcrossl or BC1], (Elaeis guineensis x Elaeis oleifera) x Elaeis guineensis, with their hybrid parents and Elaeis guineensis included in the sample).

[0095] The results are presented in Table 1 below.

[0096] [Tables 1] Plant material studied (species and their hybrids) Number of individuals Class HL Number of individuals Class LL Total First backcross (BC1) E. oleifera H 50 50 E. guineensis, group A 530 797 E. guineensis, group B 103 112 215 Hybrids Interspecies S 35 Total / 446 1183

[0097] These results indicate that there are two segregating "LL" alleles in Elaeis guineensis, one from group A and the other from group B, and that a third "LL" allele is present in a fixed form in the species Elaeis oleifera. The study of the segregation of the trait within the cross also indicates that the "LL" alleles are recessive.

[0098] Example 2:

[0099] To identify specific markers of the LL allele present in group B, 20 KASP (competitive allele-specific PCR) SNP markers were chosen in the major QTL area around the EgLIPl gene based on 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 belonging to the Deli population.

[0100] These markers were tested on a panel of 382 individuals from various populations, including 269 of known phenotype, including 83 individuals from group B of phenotypic class "LL", chosen from the panel of 1183 palm trees already phenotyped described in Example 1.

[0101] The test panel for carrying out Example 2 is presented in Table 2 below.

[0102] [Tables2] Group Population Number of individuals Number of individuals HL Number of individuals LL A Deli 35 8 8 B La Mé, Yangambi, Nifor, Yocoboué, Pobè, La Mé x C 328 170 83 ameroun, La Mé x Nifor, La Mé x Si biti AxB Deli x La Mé 25

[0103] The ability of each marker to predict the presence of the "LL" allele in homozygous form in group B was evaluated as a percentage of correctly predicted individuals (HL individuals of genotype HL / HL or HL / LL, and LL individuals of genotype LL / LL, with an acidity threshold of 25%).

[0104] The 5 most predictive markers are described in Table 3.

[0105] [Tables3] Accuracy (%) SNP_1 87 SNP_2 89 SNP_3 87 SNP_4 88 SNP_5 87

[0106] The analysis of the combined information of several of these 5 markers also makes it possible to increase the accuracy of the prediction of LL individuals.

[0107] For example, the combined use of markers SNP_1 to SNP_4, on 225 individuals for whom the information from the 4 markers is consistent and without missing data, increases the prediction accuracy to 91%. [Fig. 1] thus shows the relationship between the measured oil acidity and the genotype determined from the combination of the 4 markers, thereby demonstrating the relevance of using these markers.

[0108] Example 3:

[0109] Markers have been developed to identify the LL allele belonging to the species Elaeis oleifera and present in an interspecific pseudo-backcross 1 derived from an E. oleifera ancestor belonging to the Panama population (cross (E. oleifera Panama x E. guineensis 1) x E. guineensis 2).

[0110] This backcross population was planted as embryo clones at different sites.

[0111] Four SNP markers (SNP_5 and SNP_12 to SNP_14) were chosen in the major QTL area around the EgLIPl gene.

[0112] These markers were selected from a panel of ~50 SNPs located on the same chromosome as EgLIPl, discriminating between the ancestor E. oleifera and E. guineensis on the private information basis of the resequencing of 32 individuals (16 E. guineensis and 16 E. oleifera) aligned to a private reference of an E. guineensis palm belonging to the Deli population, and validated by genotyping on an SNP chip.

[0113] The genetic positioning of these markers was verified using a genetic map established on the chromosome homologous to chromosome 3 of Egu.v3 from a population of 187 clones from the interspecific pseudo-backcross described above using SNP chip genotyping.

[0114] The pedigree of pseudo-backcross 1 is described in [Fig.2].

[0115] The map includes 179 independent SNP markers on a linkage group of 48.067 cM homologous to chromosome 3 of Egu.v3. All selected markers localize at 21.011 cM on this linkage group. Figure 3 presents a schematic representation of chromosome 3 including the linkage group containing the markers of interest (SNP5 and SNP12 to SNP14).

[0116] Acidity was measured in 8 clones from pseudo-backcross 1, with between 1 and 6 measurements per clone. This is consistent with the genotype deduced from the four SNP markers (SNP5 and SNP12 to SNP14) shown in Table 6.

[0117] [Tables4] Clone number of measurements, acidity (%) Genotype deduced from markers #1 2 47.9 HL / LL #2 2 1.87 HL / LL #3 6 46.24 HL / LL #4 1 1.28 HL / LL #5 2 4.89 HL / LL #6 1 45.71 HL / LL #7 1 28.81 HL / LL #8 1 38.71 HL / LL

[0118] Thus, the use of SNP5 and SNP_12 to SNP_14 markers is relevant for identifying the phenotype of interest in plants belonging to the genus Elaeis.

[0119] Example 4:

[0120] A mapping population of 380 individuals from a single oil palm plant of the species E. guineensis and belonging to the Deli population was genotyped on a 67K SNP chip, which made it possible to construct a genetic map of 9547 markers located at 3451 unique positions using the Lepmap3 software (Rastas et al. 2017), i.e. about 1 SNP every 0.54 cM.

[0121] Of these 380 individuals, 334 were phenotyped for the oil acidity trait. This population shows segregation for this trait, with individuals exhibiting very low, low, high, and very high acidity.

[0122] These data were used for QTL detection using the FlexQTL software (Bink et al, 2008).

[0123] This made it possible to detect several QTLs involved in the acidity character of the oil.

[0124] Of the 3 QTLs identified, these data show in [Fig. 4] that there is 1 major QTL and 2 minor QTLs. The major QTL is located in the region of the EgLIPl gene, the major determinant of acidity, on linker group 1 (LG1), homologous to chromosome 3 in the Egu.v3 reference.

[0125] The two minor QTLs are located on linkage groups 4 (LG4) and 13 (LG13), which are homologous to chromosomes 2 and 12 of the Egu.v3 reference, respectively. The results are illustrated in [Fig. 4], allowing visualization of QTLs identified for the oil acidity trait using the FlexQTL software (300,000 iterations and 2 independent simulations). The significance level is indicated by the intensity; the presence of two bars observed one above the other reveals the presence of a QTL, highlighted with two independent simulations. The linkage group numbering is analogous to that of the genetic map of Billotte et al. 2005 (doi: 10.1007 / s00122-004-1901-8).

[0126] In the context of the invention, a so-called major QTL, also called a strong effect QTL, is a QTL that explains a large part of the phenotypic variance, whereas a so-called minor QTL, also called a weak effect QTL, explains only a small part of the phenotypic variance.

[0127] An analysis of the relationship between the predicted alleles at the minor QTLs LG4 and LG13 revealed a modulating role of the identified regions on the acidity value of the oil within individuals of the "High Lipase" and "Low Lipase" classes. The results of this analysis are presented in [Fig. 5].

[0128] At the QTL LG4 level, the presence of one of the two alleles leads to a significant decrease in the acidity value of the oil, with an additive effect between the heterozygous and homozygous form.

[0129] Thus, for LL individuals, the acidity value decreases from approximately 12% to 7.5% in the presence of the modulator allele in its heterozygous form, and only 6% in its homozygous form, representing a 50% reduction in acidity. A significant decrease is also observed in HL individuals, which can drop to less than 45% acidity in individuals heterozygous for LG1 and homozygous for the moderator allele at the LG4 QTL. Regarding the effect of the minor QTL on LG13, a difference in effect is observed depending on the class of individuals concerned.

[0130] The results thus show that a decrease in acidity value is observed when the moderator allele of the LG 13 QTL is in its homozygous form. The acidity in this case is 50% compared to approximately 65% ​​for the alternative allele in the homozygous or heterozygous state.

[0131] The analysis from the FlexQTL software also made it possible to identify the most predictive marker for each of the two minor QTLs, among the 9547 SNP markers used during QTL detection (SNP 15 and SNP 16).

Claims

1. Demands In vitro method for identifying a plant belonging to the genus Elaeis exhibiting reduced endogenous lipase activity, said method comprising the detection in all or part of said plant of a QTL associated with reduced endogenous lipase activity located on chromosome 3 between position 70704751 and 74704750 of the Egu.V3 reference genome, in which said QTL can be identified by at least one SNP marker selected from the group consisting of: - SNP_1 comprising a Thymine 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 an Adenine 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 an Adenine 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 a Guanine 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 Guanine 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 Cytosine 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 Cytosine 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 Cytosine 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; - SNP_10 comprising a Cytosine 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; - 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; - 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; - SNP_13 comprising a Guanine 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; - SNP_14 comprising a Cytosine at position 91 of SEQ ID NO: 14 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO: 14; and - their combinations.

2. Method according to claim 1, 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, SNP_4, SNP_5 and their combinations; and / or 2) at least one SNP marker selected from the group consisting of SNP_6, SNP_7, SNP_8, SNP_9, SNP_10, SNP_H and their combinations; and / or 3) at least one SNP marker selected from the group consisting of SNP_5, SNP_11, SNP_12, SNP_13, SNP_14 and their combinations.

3. A method according to any one of the preceding claims, characterized in that it also comprises the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 2 between positions 23159847 and 24159846 of the Egu.V3 reference genome, wherein said QTL can be identified by SNP_15 comprising a Thymine at position 91 of SEQ ID NO: 15 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:

15.

4. A method according to any one of the preceding claims, characterized in that it also comprises the detection of a QTL associated with reduced endogenous lipase activity located on chromosome 12 between positions 3711167 and 4711166 of the reference genome Egu.V3, wherein said QTL can be identified by SNP_16 comprising a Thymine at position 91 of SEQ ID NO: 16 or at position 91 of a sequence comprising at least 90% identity with SEQ ID NO:

16.

5. 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 o leifera or a plant resulting from a cross involving Elaeis guineensis and / or Elaeis o leifera.

6. 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 comprising the nucleotide at position 91 of SEQ ID NO: 1; *SEQ ID NO: 2 or a fragment consisting of at least 15 nucleotides comprising the nucleotide at position 91 of SEQ ID NO: 2; *SEQ ID NO: 3 or a fragment consisting of at least 15 nucleotides comprising the nucleotide at position 91 of SEQ ID NO: 3; *SEQ ID NO: 4 or a fragment consisting of at least 15 nucleotides comprising 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; *SEQ ID NO: 13 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 13; *SEQ ID NO: 14 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 14; *SEQ ID NO: 15 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO: 15; and *SEQ ID NO: 16 or a fragment consisting of at least 15 nucleotides including the nucleotide at position 91 of SEQ ID NO:

16.

7. Use of at least one isolated nucleic acid according to the preceding claim, for marker-assisted selection of a plant belonging to the genus Elaeis exhibiting reduced endogenous lipase activity.

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