A haplotype molecular marker related to cotton fiber quality traits and application thereof
By constructing haplotype molecular markers related to cotton fiber quality and using specific SNP sites for detection, the problem of environmental influence on cotton fiber quality traits in traditional breeding has been solved, achieving rapid and accurate quality improvement and increased breeding efficiency.
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- COTTON RES INST HEBEI ACAD OF AGRI & FOREST SCI
- Filing Date
- 2026-04-30
- Publication Date
- 2026-06-09
AI Technical Summary
In traditional cotton breeding, cotton fiber quality traits such as fiber length, fiber strength, and micronaire value are greatly affected by the environment, resulting in long selection cycles, high costs, low accuracy, and a lack of stable molecular markers for genetic selection.
We provide haplotype molecular markers associated with cotton fiber quality traits. By detecting the genotype of specific SNP loci, we construct haplotype combinations to assist in the identification of fiber length, strength, and micronaire value. We use primer pairs and primer combinations for genomic DNA detection.
It enables rapid and accurate identification and improvement of cotton fiber quality, enhances breeding selection efficiency, and promotes the breeding of high-quality new cotton varieties and economic benefits.
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Figure CN122168792A_ABST
Abstract
Description
Technical Field
[0001] This invention relates to the field of molecular detection technology, and in particular to a haplotype molecular marker related to cotton fiber quality traits and its application. Background Technology
[0002] Important cotton fiber quality traits—fiber length (FL), fiber strength (FS), and micronaire (MIC)—are all complex quantitative traits controlled by multiple genes. Micronaire values are classified into three levels: A, B, and C, with level B being the standard level. Level A values range from 3.7 to 4.2, representing the best quality; level B values range from 3.5 to 3.6 and 4.3 to 4.9; and level C values range from 3.4 and below and 5.0 and above, representing the worst quality. Traditional breeding primarily focuses on phenotypic selection. However, phenotypic traits are easily influenced by external conditions such as the environment, making it difficult to break the linkage of unfavorable genes in traditional breeding. This results in long selection cycles, high costs, and low accuracy.
[0003] The development of molecular markers facilitates genetic selection of traits at the chromosomal level. Molecular markers are not limited by individual tissues or developmental stages, nor are they affected by environmental conditions, allowing for rapid and accurate detection of target genes and targeted improvement. Molecular marker-assisted selection technology is currently an effective method to overcome the bottlenecks of conventional breeding and improve the efficiency of breeding selection.
[0004] SNPs (Single nucleotide polymorphisms) refer to single nucleotide polymorphisms occurring at the same locus in the genomes of different individuals. SNPs are widely distributed in the genome, have a high density, high accuracy, and are simple and convenient to detect, and have been applied in germplasm resource analysis, molecular-assisted genetic breeding, and the construction of genetic maps. However, due to factors such as individual genetic background differences, multi-gene interactions, gene-environment interactions, and linkage disequilibrium, there is still a lack of molecular markers with clearly defined functions, significant effects, and stability in molecular breeding practices for cotton fiber quality. In recent years, with the continuous advancement of sequencing technology, the detection cost, reliability, and timeliness of SNPs have been continuously optimized, making the use of multiple SNPs to form haplotypes to improve the efficacy and stability of molecular markers a mainstream technique. Identifying SNPs and their haplotypes that are significantly associated with cotton fiber quality traits has important value for improving cotton fiber quality and for molecular breeding. Summary of the Invention
[0005] The purpose of this invention is to provide a haplotype molecular marker related to cotton fiber quality traits and its application, thereby addressing the problems existing in the prior art. The haplotype molecular marker provided by this invention can assist in identifying the levels of cotton fiber length, fiber strength, and micronaire value, which is of great significance for accelerating the breeding of high-quality cotton varieties and improving the economic benefits of cotton.
[0006] To achieve the above objectives, the present invention provides the following solution: This invention provides a haplotype molecular marker related to cotton fiber quality traits, wherein the haplotype molecular marker is any one of (1)-(3): (1) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.1, with SNP sites at the 101st and 261st bases, which are T / C and T / G mutations, respectively; (2) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.2, with SNP sites at the 101st and 168th bases, which are T / C and T / A mutations, respectively; (3) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.3, with SNP sites at the 101st and 105th bases, which are T / A and T / C mutations, respectively.
[0007] The present invention also provides a primer pair for amplifying the above-mentioned haplotype molecular markers.
[0008] The present invention also provides a combination of haplotype molecular markers related to cotton fiber quality traits, wherein the haplotype molecular markers are the haplotype molecular markers described in (1)-(3): (1) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.1, with SNP sites at the 101st and 261st bases, which are T / C and T / G mutations, respectively; (2) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.2, with SNP sites at the 101st and 168th bases, which are T / C and T / A mutations, respectively; (3) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.3, with SNP sites at the 101st and 105th bases, which are T / A and T / C mutations, respectively.
[0009] The present invention also provides a primer combination for amplifying the above-mentioned haplotype molecular marker combination.
[0010] The present invention also provides a kit for identifying cotton fiber quality traits, comprising the primer pairs or primer combinations described above.
[0011] The present invention also provides the application of the above-mentioned primer pairs, primer combinations or kits in identifying cotton fiber quality traits.
[0012] The present invention also provides a method for identifying the length of cotton fibers, comprising the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker described in (1) above was obtained by using the genomic DNA detection. Based on the genotype, the following trait was determined: individuals with the TTTT genotype had a longer fiber length than individuals with the CCGG genotype.
[0013] The present invention also provides a method for identifying the strength of cotton fibers, comprising the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker described in (2) above was obtained by using the genomic DNA detection. Based on the genotype, the following trait was determined: individuals with the CCAA genotype had higher fiber strength than individuals with the TTTT genotype.
[0014] The present invention also provides a method for identifying the micronaire value of cotton, comprising the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker described in (3) above was obtained by using the genomic DNA detection. Based on the genotype, the malclonity value of individuals with the AATT genotype is superior to that of individuals with the TTCC genotype.
[0015] This invention also provides a method for screening cotton varieties with excellent overall fiber quality traits, comprising the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker combination described above was obtained by detecting the genomic DNA. Individuals with the genotype TTTT-CCAA-AATT were selected as cotton varieties with excellent overall fiber quality traits.
[0016] The above genotype detection methods include, but are not limited to, resequencing, target fragment sequencing, and KSPA typing technology.
[0017] The present invention discloses the following technical effects: The haplotype molecular markers provided by this invention can assist in identifying the levels of fiber length, fiber strength, and micronaire value in cotton. Cotton plants carrying homozygous haplotypes TTTT (SNP1 and SNP2), CCAA (SNP3 and SNP4), and AATT (SNP5 and SNP6) exhibit superior phenotypes in fiber length, fiber strength, and micronaire value, respectively. Cotton plants carrying the SNP1-SNP6 genotype TTTT-CCAA-AATT exhibit the optimal comprehensive phenotype in fiber length, fiber strength, and micronaire value. The haplotype molecular markers disclosed in this invention have significant application value for identifying the comprehensive superior traits of cotton and are of great importance for accelerating the breeding of new high-quality cotton varieties and improving the economic benefits of cotton. Attached Figure Description
[0018] To more clearly illustrate the technical solutions in the embodiments of the present invention or the prior art, the drawings used in the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.
[0019] Figure 1 The graph shows the GWAS analysis of fiber length (FL) in natural populations; where a is the Manhattan plot of genome-wide association analysis; b, c, and d are comparison graphs of fiber length differences among different haplotypes under environmental replicates R1, R2, and R3, respectively. Figure 2 The graph shows the GWAS analysis of fiber strength (FS) in natural populations; where a is the Manhattan plot of genome-wide association analysis; b, c, and d are comparison graphs of fiber strength differences among different haplotypes under environmental replicates R1, R2, and R3, respectively. Figure 3 The graph shows the GWAS analysis of equine clonal value (MIC) in a natural population; where a is the Manhattan plot of genome-wide association analysis; b, c, and d are comparison graphs of differences in equine clonal values of different haplotypes under environmental replicates R1, R2, and R3, respectively. Figure 4 The diagram shows the haplotype effects of SNP1-SNP6 combinations in a natural population; where a is the correlation between haplotype combinations and fiber length; b is the correlation between haplotype combinations and fiber strength; and c is the correlation between haplotype combinations and micronaire value. Figure 5 Figure 1 shows the validation of SNPs and their haplotype effects in the RIL population; where a is the validation of SNP1-SNP2 haplotypes and fiber length effect; b is the validation of SNP3-SNP4 haplotypes and fiber strength effect; and c is the validation of SNP5-SNP6 haplotypes and micronaire value effect. Figure 6The diagram shows the validation of the haplotype effect of SNP1-SNP6 combinations in the RIL population; where a is the validation of the combination haplotype and fiber length effect; b is the validation of the combination haplotype and fiber strength effect; and c is the validation of the combination haplotype and micronaire value effect. Detailed Implementation
[0020] Various exemplary embodiments of the present invention will now be described in detail. This detailed description should not be considered as a limitation of the present invention, but rather as a more detailed description of certain aspects, features, and embodiments of the present invention.
[0021] It should be understood that the terminology used in this invention is merely for describing particular embodiments and is not intended to limit the invention. Furthermore, with respect to numerical ranges in this invention, it should be understood that each intermediate value between the upper and lower limits of the range is also specifically disclosed. Any stated value or intermediate value within a stated range, as well as each smaller range between any other stated value or intermediate value within said range, is also included in this invention. The upper and lower limits of these smaller ranges may be independently included or excluded from the range.
[0022] Unless otherwise stated, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. While only preferred methods and materials have been described herein, any methods and materials similar or equivalent to those described herein may be used in the implementation or testing of this invention. All references to this specification are incorporated by way of citation to disclose and describe methods and / or materials associated with those references. In the event of any conflict with any incorporated reference, the content of this specification shall prevail.
[0023] Various modifications and variations can be made to the specific embodiments described in this specification without departing from the scope or spirit of the invention, as will be apparent to those skilled in the art. Other embodiments derived from this specification will also be apparent to those skilled in the art. This specification and embodiments are merely exemplary.
[0024] The terms “include,” “including,” “have,” “contain,” etc., used in this article are all open-ended terms, meaning that they include but are not limited to.
[0025] Example 1 Mining of SNPs and their haplotypes: 1. Natural populations were constructed using 360 core germplasm accessions of modern cotton cultivars (Table 1). In 2024, three replicates (environmental replicates R1, R2, and R3) were set up in Anhui Province for planting. Cotton seedlings were collected and genomic DNA was extracted using the CTAB method.
[0026] Table 1. Core germplasm of 360 modern cotton cultivars
[0027] 2. Using Illumina HiSeq TM The sequencing platform (Illumina, Inc., San Diego, CA, USA) performed 10-fold depth paired-end PE 125bp resequencing on 360 genomic DNA samples. Following the standard workflow for cotton GWAS analysis, TM-1 was used as the reference genome (Hu et al.). Gossypium barbadense and Gossypiumhirsutum Genomes provide insights into the origin and evolution of allotetraploid cotton. Nat. Genet. 2019, 51, (4), 739-748), SNP variant detection and filtering were performed on resequencing data of 360 materials. The main software and programs involved included BWA, GATK, samtools, vcftools, plink, etc.
[0028] 3. After the cotton bolls naturally opened, 50 bolls of seed cotton were manually harvested from each material row area in each environmental replicate. The seed cotton was weighed and ginned to obtain lint. 20 grams of lint fiber samples from each material were sent to the Cotton Quality Supervision and Testing Center (Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang City, Henan Province) for fiber quality testing. Fiber length (FL; mm), strength (FS; cN / tex), and micronaire value (MIC) phenotypic values were collected. The phenotypic data from the three environmental replicates were cleaned using an R script, and the blup breeding value for each phenotype was calculated.
[0029] 4. Following the standard procedure for cotton GWAS analysis, association analysis was performed using the GEMMA program based on filtered SNP / InDel variant sites and 3-environmental phenotype blup values. A 95% confidence level screening threshold was calculated using a 10,000-permutation test to obtain genome-wide SNP signals significantly associated with FL, FS, and MIC, respectively. (See attached table.) Figure 1 a, Figure 2 a and Figure 3 a.
[0030] 5. Identification of key SNPs and their haplotypes. Based on the GWAS analysis results, two SNPs with peak association signals within the significant association intervals of each trait were selected to statistically identify haplotypes. The genetic effect of haplotypes was tested in three environmental replicates using t-tests. SNPs with the lowest allele frequency of haplotypes greater than 0.1 in all environments and with highly significant phenotypic differences (p<0.01) between haplotypes of different genotypes in all environments were selected as key candidate association sites.
[0031] The key candidate association SNP1 (A05_5386241) is located at position 101 of the haplotype molecular marker shown in SEQ ID NO.1, and contains the base polymorphism site T / C. Its genotype is homozygous TT in cotton cultivars with longer fiber length and homozygous CC in cotton cultivars with shorter fiber length. No heterozygous SNP1 material was detected in this natural population. The key candidate association SNP2 (A05_5386401) is located at position 261 of the haplotype molecular marker shown in SEQ ID NO.1, and contains the base polymorphism site T / G. Its genotype is homozygous TT in cotton cultivars with longer fiber length and homozygous GG in cotton cultivars with shorter fiber length. No heterozygous SNP2 material was detected in this natural population.
[0032] SEQ ID NO.1: ACAAGGTCAGAATGATTTCGGGTTCTCCTGTTCTGAATTTGAAAAATCATCAAAAATTGGATAAAAACAATTAGGGGCTTAAATTTATATGTTTAGAATCYTGAATGAGTCTATTTTCAAGAGAAATAAACGAGGACATCATTCGAATTCTGTACGAGAAGATAATTAATTTTTAGTGAAGAAGGGTCG GAACTGTCAGACAGCAGAACAGGGGAGATTTCAATGAGTAAACTGTATTAATTGGCCCAACCAAAAATTATKAAATTTTTATGGCAAGAAAACATATGAGCCTAGTTTCTGGGAAAATTTATGGATCTTAATTTCGAGTTCTGTAGCTCAAGATAAAAATGATTTAGTGACT; among them, Y represents T / C; K represents T / G.
[0033] The key candidate associated SNP3 (D01_45549832) is located at position 101 of the haplotype molecular marker shown in SEQ ID NO.2, and contains the base polymorphism site T / C. In cotton cultivars with high fiber strength, the genotype is homozygous CC, and in cotton cultivars with low fiber strength, the genotype is homozygous TT. Materials with the heterozygous genotype TC of SNP3 showed higher fiber strength than materials with the homozygous genotype TT of SNP3, but the significance was unstable. The key candidate associated SNP4 (D01_45549899) is located at position 168 of the haplotype molecular marker shown in SEQ ID NO.2, and contains the base polymorphism site T / A. In cotton cultivars with high fiber strength, the genotype is homozygous AA, and in cotton cultivars with low fiber strength, the genotype is homozygous TT. Materials with the heterozygous genotype TA of SNP4 showed higher fiber strength than materials with the homozygous genotype TT of SNP4, but the significance was unstable.
[0034] SEQ ID NO.2: CGAAAAGAGATGATTTGTTCTTTTTTACGAAAATCTTAATTAAAACATTAATTTTTAATAATGTTGGTATGACAACCCACATGGTAATCCATGTATAATTYATGTTAACAAGATACTATTTATCTTATATATTACGTCAATCA ATAATTTAAAAATTATAAAAATTTWAAAAAATTAAAATTTAAAAAAATATAAAAATTCATAATTAAAAAAAAACATAATATACATGTGAATTGGCATAAGGGCTAAAATGTTTAAATGTTTAACA; where W represents T / A; Y represents T / C.
[0035] The key candidate associated SNP5 (A01_21485122) is located at position 101 of the haplotype molecular marker shown in SEQ ID NO.3, and contains the base polymorphism site T / A. In cotton cultivars with lower (preferable) micronaire values, the genotype is homozygous AA, and in cotton cultivars with higher (biased) micronaire values, the genotype is homozygous TT. No heterozygous SNP5 material was detected in this natural population. The key candidate associated SNP6 (A01_21485125) is located at position 105 of the haplotype molecular marker shown in SEQ ID NO.3, and contains the base polymorphism site T / C. In cotton cultivars with lower (preferable) micronaire values, the genotype is homozygous TT, and in cotton cultivars with higher (biased) micronaire values, the genotype is homozygous CC. No heterozygous SNP6 material was detected in this natural population.
[0036] SEQ ID NO.3: ATCTGGGCTGGGTGGAGACAATACCGGAGCATTCAACAAATATTGCTTGACCTTTTCAAAAGCACTCTGGCATTCCCCCATCCCAAATACCTTGATTGTGCWTTYTAGGAGGCGAAAGATAGGATCACATTTCTCGGTTAGTTGTGAAATGAACCGAGCAATGTAATTCAACCTTCCTAGGAATCCTCGAACTTCTTTCTGAGT; among them, W represents T / A; Y represents T / C.
[0037] 7. The dominant haplotype for stable cotton fiber length enhancement constructed based on SNP1 and SNP2 was homozygous TTTT, whose fiber length (FL) was significantly higher than that of materials carrying haplotype CCGG in all three environments. SNP1 and SNP2 showed a strong linkage relationship. No samples with homozygous haplotypes TTGG and CCTT were detected. Figure 1 (middle bd); The dominant haplotype for improving cotton fiber strength based on SNP3 and SNP4 was homozygous CCAA, whose fiber strength (FS) was significantly higher than that of materials carrying haplotype TTTT in all three environments. SNP3 and SNP4 showed a strong linkage relationship. No samples with homozygous haplotypes CCTT and TTAA were detected. Figure 2 (middle bd); The dominant haplotype that stably reduces the micronaire value of cotton fibers, constructed based on SNP5 and SNP6, is homozygous AATT. Its MIC is significantly better than that of materials carrying haplotype TTCC in all three environments. SNP5 and SNP6 have a strong linkage relationship. No samples with homozygous haplotypes AACC and TTTT were detected. Figure 3 (middle bd).
[0038] 8. To ensure the representativeness and stability of haplotypes, materials with homozygous genotypes for SNP1-SNP2, SNP3-SNP4, and SNP5-SNP6 were used to construct combined haplotypes of SNP1-SNP6. The genetic effects of the combined haplotypes were then detected using the blup breeding values of the three environmental phenotypes. Figure 4In 360 natural populations, 94 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-AATT, 27 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-TTCC, 11 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-AATT, 3 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-AATT, 5 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-AATT, 9 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-AATT, 42 materials with the SNP1-SNP6 combined haplotypes TTTT-CCAA-AATT, and 83 materials with the SNP1-SNP6 combined haplotypes CCGG-CCAA-AATT, CCGG-CCAA-TTCC, CCGG-TTTT-AATT, and CCGG-TTTT-TTCC were detected. Among them, the materials carrying the combined haplotype TTTT-CCAA-AATT showed the best fiber length, the best fiber strength, and the best fiber micronaire value compared with other combined genotypes, and were identified as combined haplotypes with the best comprehensive phenotypic effect.
[0039] Example 2 Verification of SNPs and their haplotypes: By using high-generation backcrossing and self-crossing of the high-quality sea island cotton “Hai 1” and the high-yield and widely adaptable upland cotton cultivar “Zhongmian Institute 45”, a near-isogenic line (RIL) containing 550 genetically similar accessions was constructed.
[0040] Following the methods described in Example 1, the FL, FS, and MIC phenotypes of the RIL population were collected, and DNA from 550 samples was resequencing at a depth of 6-fold to complete SNP variant detection and genotyping. The significant differences in related traits among target SNPs and their haplotypes were analyzed. This example only analyzed homozygous genotype haplotypes with stable heritability and genetic effects.
[0041] FLs were clustered based on haplotypes of SNP1 and SNP2 genotypes. The results showed that in the 550 RIL population, 242 samples of homozygous haplotype CCGG and 156 samples of homozygous haplotype TTTT were detected in the SNP1-SNP2 (A05_5386241 / 5386401) group. No samples of homozygous haplotypes CCTT or GGTT were detected. The FL of individuals carrying haplotype TTTT was significantly higher than that of individuals carrying haplotype CCGG. Figure 5 (a) demonstrates that SNP1-SNP2 (A05_5386241 / 5386401) and their haplotypes play a significant role in identifying fiber length.
[0042] Based on the haplotypes of the SNP3 and SNP4 genotypes, FS were clustered. The results showed that in the 550 RIL accessions, 152 samples showed homozygous haplotype CCAA (D01_45549832 / 45549899), and 304 samples showed homozygous haplotype TTTT. No samples showed homozygous haplotypes CCTT or AATT. The FS of individuals carrying haplotype CCAA was significantly higher than that of individuals carrying haplotype TTTT. Figure 5 (b) demonstrates that SNP3-SNP4 (D01_45549832 / 45549899) and their haplotypes play a significant role in identifying fiber strength.
[0043] Based on the haplotypes of the SNP5 and SNP6 genotypes, MICs were clustered. The results showed that in the 550 RIL accessions, 198 samples showed homozygous haplotype AATT and 251 samples showed homozygous haplotype TTCC for SNP5-SNP6 (A01_21485122 / 21485125). No samples showed homozygous haplotypes AATT or TTCC. Individuals carrying haplotype AATT had significantly higher MICs than those carrying haplotype TTCC. Figure 5 (c) demonstrates that SNP5-SNP6 (A01_21485122 / 21485125) and their haplotypes play a significant role in identifying fiber micronaire values.
[0044] Based on the combined haplotypes of SNP-SNP6, FL, FS, and MIC were grouped separately. In a population of 550 RILs, the following haplotypes were detected: TTTT-CCAA-AATT (97 samples), TTTT-CCAA-TTCC (26 samples), TTTT-TTTT-AATT (15 samples), TTTT-TTTT-TTCC (4 samples), CCGG-CCAA-AATT (7 samples), CCGG-CCAA-TTCC (16 samples), CCGG-TTTT-AATT (57 samples), and CCGG-TTTT-TTCC (119 samples). Samples with any heterozygous or deleted genotypes were removed. The results showed that samples carrying the combined haplotype TTTT-CCAA-AATT exhibited the best fiber length, best fiber strength, and best fiber micronaire value compared to other combined haplotypes. Figure 6 This demonstrates that the SNP1-SNP6 combination haplotypes play a significant role in identifying FL, FS, and MIC, and that the combination haplotype TTTT-CCAA-AATT can significantly improve FL, FS, and MIC.
[0045] Improving important fiber quality traits such as fiber length, strength, and micronaire value is a crucial task in cotton breeding and production, and also a challenge in developing new cotton varieties with excellent comprehensive traits using existing breeding methods. The six SNPs and three haplotypes provided by this invention can respectively assist in identifying whether length, strength, and micronaire value are improved. Cotton plants carrying the homozygous haplotype TTTT (A05_5386241 / 5386401) have significantly increased fiber length, cotton plants carrying the homozygous haplotype CCAA (D01_45549832 / 45549899) have significantly increased fiber strength, and cotton plants carrying the homozygous haplotype AATT (A01_21485122 / 21485125) have significantly improved micronaire value. The combined haplotypes of SNP1-SNP6 provided by this invention can assist in identifying whether length, strength, and micronaire value are comprehensively improved. Cotton plants carrying the combined haplotype TTTT-CCAA-AATT have a comprehensive trait of significantly improved fiber quality. The haplotype molecular markers disclosed in this invention have significant application value for the identification of superior traits in cotton, and are of great importance for accelerating the breeding of new high-quality cotton varieties and improving the economic benefits of cotton.
[0046] The embodiments described above are merely preferred embodiments of the present invention and are not intended to limit the scope of the present invention. Various modifications and improvements made by those skilled in the art to the technical solutions of the present invention without departing from the spirit of the present invention should fall within the protection scope defined by the claims of the present invention.
Claims
1. A haplotype molecular marker associated with cotton fiber quality traits, characterized in that, The haplotype molecular marker is any one of (1)-(3): (1) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.1, with SNP sites at the 101st and 261st bases, which are T / C and T / G mutations, respectively; (2) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.2, with SNP sites at the 101st and 168th bases, which are T / C and T / A mutations, respectively; (3) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.3, with SNP sites at the 101st and 105th bases, which are T / A and T / C mutations, respectively.
2. A primer pair for amplifying the haplotype molecular marker of claim 1.
3. A haplotype molecular marker combination related to cotton fiber quality traits, characterized in that, The haplotype molecular markers are the haplotype molecular markers described in (1)-(3): (1) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.1, with SNP sites at the 101st and 261st bases, which are T / C and T / G mutations, respectively; (2) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.2, with SNP sites at the 101st and 168th bases, which are T / C and T / A mutations, respectively; (3) The nucleotide sequence is a haplotype molecular marker as shown in SEQ ID NO.3, with SNP sites at the 101st and 105th bases, which are T / A and T / C mutations, respectively.
4. A primer combination for amplifying the haplotype molecular marker combination of claim 3.
5. A reagent kit for identifying quality traits of cotton fibers, characterized in that, Includes the primer pair as described in claim 2 or the primer combination as described in claim 4.
6. The application of a primer pair as described in claim 2, a primer combination as described in claim 4, or a kit as described in claim 5 in identifying quality traits of cotton fibers.
7. A method for identifying the length of cotton fibers, characterized in that, Includes the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker described in claim 1 (1) is obtained by using the genomic DNA detection method; Based on the genotype, the following trait was determined: individuals with the TTTT genotype had a longer fiber length than individuals with the CCGG genotype.
8. A method for identifying the strength of cotton fibers, characterized in that, Includes the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker described in claim 1 (2) is obtained by using the genomic DNA detection. Based on the genotype, the following trait was determined: individuals with the CCAA genotype had higher fiber strength than individuals with the TTTT genotype.
9. A method for identifying the micronaire value of cotton, characterized in that, Includes the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker described in claim 1 (3) is obtained by using the genomic DNA detection. Based on the genotype, the malclonity value of individuals with the AATT genotype is superior to that of individuals with the TTCC genotype.
10. A method for screening cotton varieties with excellent comprehensive fiber quality traits, characterized in that, Includes the following steps: Obtain genomic DNA from the cotton sample to be tested; The genotype of the haplotype molecular marker combination described in claim 3 can be obtained by detecting the genomic DNA. Individuals with the genotype TTTT-CCAA-AATT were selected as cotton varieties with excellent overall fiber quality traits.