SNP molecular markers associated with cotton fiber strength and quality traits and their applications

Abstract

The present invention discloses SNP molecular markers associated with cotton fiber strength quality traits and their applications, belonging to the fields of molecular biology and bioinformatics. The SNP molecular marker is at least one of the nucleotide sequences shown in SEQ ID NO.1-SEQ ID NO.126. The present invention provides the SNP molecular markers associated with upland cotton fiber strength, which can be detected in various tissues and developmental stages of cotton, are not restricted by the environment and season, are not affected by expression, do not need to analyze the length of the fragment, only need + / - analysis, are suitable for rapid, large-scale, and automated screening, and can be used alone or in combination to assist in identifying high- and low-strength fiber germplasm materials, which can greatly save the work of breeding and improvement.

Description

Technical Field

[0001] The present invention relates to SNP molecular markers associated with cotton fiber strength quality traits and applications, and belongs to the fields of molecular biology and bioinformatics. Background Art

[0002] Fiber strength refers to the maximum load that a fiber can withstand when it is broken, expressed in g and cN. It is one of the indicators that reflect the quality of cotton fiber. With the rapid development of the textile industry, the speed of cotton variety improvement lags behind the development of textile technology. At present, the quality of cotton fiber in my country can meet the requirements of spinning medium and low-grade cotton yarn ( Count yarn) requirements, but spinning high count yarn ( In recent years, my country has approved several new upland cotton varieties with lengths exceeding 31mm and fiber strengths exceeding 30 cN / tex. However, these varieties have a limited range of qualities, and most upland cotton cultivars have low fiber strengths. Therefore, cultivating high-quality cotton varieties, especially those with high fiber strengths, has become a top priority in cotton breeding.

[0003] Traditional breeding methods for improving fiber quality first require a series of hybridizations and backcrosses between germplasm with high-fiber-strength genes and existing upland cotton varieties to break the negative correlation between fiber quality and yield traits. However, fiber quality testing is required in each round of backcrossing, which is costly and labor-intensive, and results are only available some time after flowering. Furthermore, environmental factors also affect fiber quality. This necessitates a larger breeding population, which can lead to increased blindness, time-consuming and labor-intensive work, and increased costs, slowing progress in quality breeding. Therefore, early identification of high- and low-strength fiber germplasm through marker-assisted identification can significantly reduce the effort required for breeding improvements.

[0004] Molecular marker technology allows for rapid population testing and identification of genotypes. By leveraging the linkage relationship between target traits and molecular markers, selection can be performed for the target trait, significantly improving selection efficiency.

[0005] A single nucleotide polymorphism (SNP) marker is a single nucleotide mutation at the same genomic site between closely related species or individuals of the same species. It represents a difference in base type at a single site in homologous sequence alignment. SNPs are widely distributed, densely distributed, and numerous throughout the genome, making them a powerful genomic tool for improving the efficiency and accuracy of breeding practices. Summary of the Invention

[0006] In view of the deficiencies of the prior art, the present invention aims to provide SNP molecular markers associated with cotton fiber strength quality traits and their applications.

[0007] In order to achieve the above object, the technical solution of the present invention is:

[0008] A SNP molecular marker associated with cotton fiber strength quality traits, wherein the SNP molecular marker is at least one of the nucleotide sequences shown in SEQ ID NO.1-SEQ ID NO.126.

[0009] The SNP molecular site mutated at the 51 bp position of the sequence, and the mutation form of the SNP molecular marker is as follows:

[0010]

[0011]

[0012]

[0013]

[0014]

[0015] An application of the SNP molecular marker in identifying cotton fiber strength quality traits.

[0016] An application of the SNP molecular marker in cotton assisted breeding.

[0017] An application of the SNP molecular marker in improving cotton germplasm resources.

[0018] A primer or reagent for detecting the SNP molecular marker.

[0019] A kit for detecting the SNP molecular marker.

[0020] A gene chip containing the SNP molecular marker.

[0021] A method for analyzing cotton fiber strength using the SNP molecular marker comprises the following steps:

[0022] (1) Extracting genomic DNA from the sample to be tested;

[0023] (2) Using the extracted DNA as a template, primers were designed based on the SNP molecular markers and PCR amplification was performed respectively;

[0024] (3) Analyze the cotton fiber strength based on the PCR amplification products.

[0025] Beneficial effects of the present invention:

[0026] The present invention provides the SNP molecular marker associated with upland cotton fiber strength, which can be detected in various tissues and developmental stages of cotton, is not restricted by environment and season, is not affected by expression, does not require analysis of fragment length, and only requires + / - analysis. It is suitable for rapid, large-scale, and automated screening. When used alone or in combination, it can assist in identifying high- and low-strength fiber germplasm materials, which can greatly save the work of breeding and improvement. DETAILED DESCRIPTION

[0027] The specific embodiments of the present invention are further described in detail below with reference to the examples.

[0028] Example 1. Acquisition of SNP molecular markers

[0029] (1) Determination of fiber strength

[0030] The population was tested with 2 replicates at 5 sites (1 replicate at some sites) in 2017 and 2018. A total of 1,799 progeny and 13 parents, totaling 1,812 materials, were randomly arranged within and between subpopulations. The parents of the subpopulation were randomly added to the subpopulation. Three controls were set up for the entire population, namely the parents of the population, ZZM3, Lumianyan 28, and Jinke 178. The three controls appeared in the population every 15 materials and eventually evenly covered the entire population. The five experimental sites are: Anyang, Henan, China (AY), Anqing, Anhui, China (AQ), Xingtai, Hebei, China (XT), Shihezi, Xinjiang, China (SHZ), and Alaer, Xinjiang, China (ALE). Each test site was planted in a single row (except for Alaer, Xinjiang Uyghur Autonomous Region, China, which was double row) with a row length of 2m. The number of plants per row ranged from 10 to 30 (depending on the local cultivation pattern). The sampling period varied from September 20 to October 20 (depending on the local frost period and cultivation pattern). Except for the two plants at the two ends, bolls were collected from the middle of the remaining plants close to the main stem in each plot. 1-2 bolls were collected from each plant, for a total of 20 bolls. To reduce errors, the unique barcode numbering system of the present invention was used, and the number plate was placed in the boll weight bag. To reduce errors, all boll weight materials from various locations were ginned at the Anyang Farm of the Cotton Research Institute of the Chinese Academy of Agricultural Sciences using the Xinxiang MPSY-20A leather gin. 20 boll samples from each harvested plot were ginned and lint samples were obtained. The HFT9000 (HVICC calibration level) instrument of the Cotton Fiber Quality Supervision and Inspection Center (Anyang) of the Ministry of Agriculture and Rural Affairs was used to measure the cotton fiber strength according to the instructions. The R software package lme4 was used.

[0031] (https: / / github.com / lme4 / lme4) Estimates the best linear unbiased predictor (two replicates over two years).

[0032] (2) Extraction of genomic DNA from the sample to be tested (CTAB method)

[0033] ① Place approximately 3g of fresh leaves in a 2ml centrifuge tube with steel balls, snap-freeze in liquid nitrogen, and grind into powder using a sample grinder. Add 800μl of preheated (65°C) CTAB lysis buffer (add 0.8% β-mercaptoethanol before use and preheat in a 65°C water bath for 30 minutes). Shake vigorously and place in a 65°C water bath for 30-40 minutes, shaking up and down every 10 minutes. Cool to room temperature after the water bath.

[0034] ② Add 800 μl of a mixture of chloroform and isoamyl alcohol in a volume ratio of 24:1, and slowly invert the tube until it is mixed and no layers are separated.

[0035] ③Centrifuge at 12000rpm for 10 minutes.

[0036] ④ Use a blunt tip to aspirate the supernatant and transfer it to another 1.5ml centrifuge tube.

[0037] ⑤ Add 1 volume of anhydrous ethanol and slowly invert several times until flocculent DNA appears. Let it stand for 10 minutes.

[0038] ⑥ Use a small gun tip to pick out the DNA into a 1.5ml centrifuge tube (or centrifuge at 12000rpm for 1.5min and remove the supernatant), and add 70% (v / v) ethanol solution to wash once.

[0039] ⑦ Dry overnight, add ddH2O to dissolve the DNA until it is completely dissolved, and store at -20℃ until use.

[0040] (3) SNP detection

[0041] A total of 1,812 upland cotton samples were collected, and genomic DNA was extracted for genome resequencing, including 13 parents and 1,799 recombinant inbred lines (RIL). When collecting samples, seeds of each line were sown in an incubator, and young leaves of the cotton plants were collected. 5 μg of high-quality cotton genomic DNA was extracted from all samples using the above-mentioned CTAB method. The extracted genomic DNA was sent to Shenzhen BGI Genomics Technology Co., Ltd. for genome resequencing. High-quality clean data was obtained by sequencing, with a data volume of 20.47 Gb. The average sequencing depth of the parents was 35X, and the average sequencing depth of the offspring was more than 4X. Sequence positioning was performed using the genome of high-quality tetraploid cotton (G. hirsutum'Texas Marker 1') as the reference genome. Before mapping, all unassembled contigs were connected to a pseudo-chromosome (named "ChrUN"). The short sequences of 1,812 samples were mapped to the reference genome using BWA (v.0.7.12) software, and all unaligned reads and low-quality reads (mapping quality less than 20) were removed. Then, variants were identified for each sample using GATK UnifiedGenotyper (v.3.8.0), and the variant files of all samples (n=1,812) were merged into a single VCF file. Finally, 11,856,129 and 4,543,742 high-quality SNPs and Indels were identified, respectively. Based on the minor allele frequency greater than 0.05 and the deletion rate less than 0.2, the variant sites were further filtered using VCFtools to screen out 1,855,955 high-quality SNPs and Indels, respectively, for subsequent genome-wide association analysis. The effects of all variants were annotated by ANNOVAR.

[0042] (4) Genome-wide association analysis of fiber strength traits in upland cotton

[0043] The upland cotton trait results obtained in step (1) and the genotype data obtained in step (3) were statistically analyzed using a mixed linear model using the Efficient Mixed-Model Association Expedited (EMMAX) statistical analysis software. For details, please refer to: http: / / csg.sph.umich.edu / kang / emmax / download / index.html. The statistical model is:

[0044] y=Xα+Zβ+Wμ+e

[0045] y is the phenotypic trait, X is the indicator matrix of fixed effects, α is the estimated parameter of fixed effects; Z is the indicator matrix of SNPs, β is the effect of SNPs, W is the indicator matrix of random effects, μ is the predicted random individual, e is the random residual, and it obeys e~(0,δ e 2 In this model, a kinship matrix was added to μ to correct for population analysis. The analysis revealed that a total of 126 SNPs were significantly associated with fiber strength in upland cotton. The allele loci for these SNP markers are shown in Table 1. The reference sequence was the upland cotton cultivar TM-1, with the reference genome version number G.hirsutum_TM-1_ICR (http: / / grand.cricaas.com.cn / page / download / download). The nucleotide sequences 50 bp upstream and downstream of these SNP sites are shown in SEQ ID NO. 1 to SEQ ID NO. 126.

[0046] Table 1 SNP molecular markers associated with upland cotton fiber strength

[0047]

[0048]

[0049]

[0050]

[0051]

[0052]

[0053]

[0054] (5) Verification: The effects of the above SNPs were verified using the fiber strength BLUP values ​​(best linear unbiased prediction values) of 1812 cotton multi-parent populations under 10 environments with 5 points over 2 years. The results showed that 97.58% of the SNPs showed a significant effect on the variation of fiber strength traits in upland cotton. SEQUENCE LISTING <110> Cotton Research Institute, Chinese Academy of Agricultural Sciences <120> SNP molecular markers associated with cotton fiber strength and quality traits and their applications <160> 126 <170> PatentIn version 3.5 <210> 1 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 1 agctgcaatt ggagtggact gagaaacaga ttctgccaat cccaatgcaa gtctaaggtc 60 ctgtgtcaac attagcttct gttacaacat gaaatattaa c 101 <210> 2 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 2 ccgtcaagac acttcttaca ctcagtgctg gaaaggtccc tggtgcactg agtcaacccg 60 taaagtttgt tcgatccgta cagctccgtt tctccaacgg c 101<## <210> 3 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 3 tgctggaaag gtccctggtg cactgagtca acccgtaaag tttgttcgat ccgtacagct 60 ccgtttctcc aacggcatac attttgggat ttgaataagc t 101 <210> 4 <211> 101 <212> DNA <213> Cotton (Gossypium spp)<## <400> 4 aaatactcgg tttgggtttt gacctatggc atggcgcccg aaccctgatg aaggagtttg 60 actggagagg tactcaatga cttggtttaa gttggcttca t 101 <210> 5 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 5 ctgtggcggc aatgtctgag atggaggtgg aggaatatcg gcagcggagg gaaattacag 60 ttgaaggtcg tgatgttcca aagcctgtga agagttttgc t 101 <210> 6 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 6 ctcatagaga ttccataaca gcattaggtt ctttgaatgg tcaaggtgaa agagaatcaa 60 gagggatagc tcccgtgatg tttaatggat gttctccaac t 101 <210> 7 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 7 gaatgaatct tcgatttaac agttcttata tttgagcttt taactcaact aactcattca 60 gtgccatcct ataaggagcg atggacactg gagctgctcc a 101 <210> 8 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 8 tatgcatgca tattgcacct tacttcaatc aggtgaacgc ttttttgtcc attctgccta 60 aggcaataca agggttttta gcacctggag tgtaccttta t 101 <210> 9 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 9 cttgtatttg gtcatgaatt gtcaggattt gctatttgga tgtatagtgt ggttacccac 60 aattggtcga aatgccccct aatgaatttg cctcgttgtc t 101 <210> 10 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 10 aaaaggctca attcgtctca ttgatttgcg gcagtcagct ttgtgtgatt ttcatgccaa 60 attgtaagtg tcttactttt ttggtttttt ttttttgctg a 101 <210> 11 <211> 101 <212> DNA[[ID=X]] <213> Cotton (Gossypium spp) <400> 11 ggattcgggt tgtgaaatgg atcagagttc gggtggggac ccgcgattcg tagagagcag 60 taaaaacgga gagagttatt tggatgcaca gggcggtagg g 101 <210> 12 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 12 taatgggtac gctaagaaca attgctttga aaaagctgtt gaattgtttc agatactaaa 60 agataaaggg attaaagcta atgaaactgt tatggttagt g 101 <210> 13 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 13 agaacaattt gagtttgaat gtgattcttg ggacggcttt agtagatatg tatgcaagat 60 gtgggagtat tgagaaagct attaaagtgt ttgatcaaat g 101 <210> 14 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 14 gatgaaaccg aatttgggtt ttcgataacc ccacgaacca atgccaagga gcttgagttt 60 atagaacaat ctttggctag aaggccaggt gtttgtccaa a 101 <210> 15 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 15 acaatcaaag ctgtgattct tgacgcagaa gagcgatccg cgaccagcca actggtcaaa 60 gattggcttg aaaagctgaa agatgtactt tacgatgctg a 101 <210> 16 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 16 atcaaagctg tgattcttga cgcagaagag cgatccgcga ccagccaact ggtcaaagat 60 tggcttgaaa agctgaaaga tgtactttac gatgctgacg a 101 <210> 17 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 17 caaaaggaag taggataata gtaactactc gttcttctaa ggtagccaag gtcactagta 60 aatgtcagcc ttatgttctg aaaggcttgt ctgataatga t 101 <210> 18 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 18 gtgtattgga tttgcattct ttaggtagtc agatgatttc accctccatt gacaagttga 60 aacatttgag gtaccttgat ctttcttata atctccgtct t 101 <210> 19 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 19 gggattcgta aaaaatgcaa aagaggagtt taaggctgct aatttgaaag cgaagcaaca 60 tttgagatcg ttggttttag aatggaatgc tgatattgat g 101 <210> 20 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 20 tgctcacaaa tctcgtttat atgagaatat atcggggtaa tttcaaacaa gtcccgtcct 60 ttgtgcaatt tccctgtctt aaagggctgg agatatatga t 101 <210> 21 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 21 ttaaagcaga ctatcaagat gaacatcaat gctaatgccc catcaacttc aacctcttct 6​​​​​​​​​​​​​​​​​​​​​​​​​​​ctggagttat ctggagctgg catccaaata ttccaagatc atacaagcct gcgctctcta 60 tggctgcaaa atattccaaa gtgtcggcat cttccggagt g 101 <210> 24 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 24 agatcataca agcctacgct ctctaaggct gcgaaatatt ccaaagtgtc ggcatcttcc 60 ggagtggctt caacatctaa caaatctgca acggctttat c 101 <210> 25 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 25 agcaaattaa gcaatgttca gctgctatac tatttttgaa gtgaagaaat ggagctggtc 60 cgattgaagc aacctatttt ggatgatttg ttcctatata a 101 <210> 26 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 26 tggagaaaat tacaacattt gggcagtgaa aataaggaca tacctgcagg tgcatgacct 60 gtggaatgtt gttctcaatg acactgagcc accaccactg a 101 <210> 27 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 27 aagaagcaga gagagctcag gttcaaattc gagtgccaaa tgcaagaagc cttggacaga 60 aaagaagaag aaagaaccta ccagaaagaa gtttccacct t 101 <210> 28 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 28 agctcaggct gctgaagatg ttgaaacaca agaagagcat gttttttcag tatcatgctt 60 tgcaagctca agcaaggtta gcaaaatttg gttaattgac a 101 <210> 29 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 29 attgtcgtaa aatataaaaa attcatttcc aatacacgca agcatctaca gtttccaatt 60 atcgtattcc aagtttcatc gctcaaatgg tatctcgctt t 101 <210> 30 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 30 aaagagcaaa gcaatgcttc aaatgggatg ggagatgatc ataactcaac ttaagtgtag 60 gtagaatttc tccgtcaatt tgtgatattt tagcaagttc a 101 <210> 31 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 31 tccgcggggc gatcacgcgg aatgaagcca aaagtgttgg cctcactttc aattgaagct 60 aacctcgcct taatggccct cattttccga cccattttga g 101 <210> 32 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 32 agcggtaatg atgatgatga tgatgacaag tcacttgaag acctccggcc ccatcccaat 60 ctcaaggagc tctttattgg aggatggagg agtgatgcca a 101 <210> 33 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 33 aatgatgatg atgatgatga caagtcactt gaagacctcc ggccccatcc caatctcaag 60 gagctcttta ttggaggatg gaggagtgat gccaagtttc c 101 <210> 34 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 34 ctttgcggaa agatctattg ggtgggagca agctgacgaa agaggtacgc attttcttct 60 caagctcaaa ccagtttgct tacagtctca aaatgggtcg t 101 <210> 35 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 35 gaatgaggag tgggaagaat gggttagttt aaaagagtta ttagtaggtg ggggtaaagg 60 aagtaggata atagtaacta ctcactcttt gagagtagca a 101 <210> 36 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 36 tggtctttgt tcaaagaaat agtatttgag caaagatcta taaacccaac ttttgtgaaa 60 atagggaaac agatcttgga aaggtgtggt ggggttccct t 101 <210> 37 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 37 gcgaagaatg ttatggctta actcatatgc cacgtggaat agggaagctg acttcccttg 60 agacgttaag cgactttgta gttgacaaag atggctcaca t 101 <210> 38 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 38 tgggattcgt aaaaaatgca aaagagaagt ttaaagctgc taattttaaa aagaagcaac 60 atttgagatt gttggactta gtatggaatg attatggtga t 101 <210> 39 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 39 tctttgctca caaacctcgt cgtgattaca atacggggtc ctagtaattt ttaacaaatc 60 ccatccttgg cgcaattgcc ttgtcttcaa aagctgttaa t 101 <210> 40 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 40 ctttgctcac aaacctcgtc gtgattacaa tacggggtcc tagtaatttt taacaaatcc 60 catccttggc gcaattgcct tgtcttcaaa agctgttaat t 101 <210> 41 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 41 gaaactgaaa aggagtggcg ttctttcaaa gataatgaac ttgctagact gtctgtacat 60 caagatgaaa ttttacctac acttaggttg agctacaatc a 101 <210> 42 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 42 tcacaaatct cgtccatatt aaaatatggg gtcttggtag taaattcaaa catctcccgt 60 cctttgctca atttccttgt cttcaagatt tggtaatttg t 101 <210> 43 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 43 ggacacaagg tgggaacttc cttttgacag gttctttctt cttcttctca gtccagggct 60 tcttgccttt ggcatttaag tttgcacttg agctttctct g 101 <210> 44 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 44 tatacttctt ggcacagtct tcattgtgct gcctaatctg ggctatagtc gggttggctc 60 ttagtggtgg tggctcagtg tcattgagaa caacattcca c 101 <210> 45 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 45 tcattgtgct gcctaatctg ggctatagtc gggttggctc ttagtggtgg tggctcagtg 60 tcattgagaa caacattcca caggtcgtgt gcctgcaggt a 101 <210> 46 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 46 accaacctgt agctatatga gcaatcttat gccaatcggc cccaatgtcc ttccgacatc 60 tttcctccaa ctggggagtt tgtcgtatgc ataactcctc c 101 <210> 47 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 47 ctgtagctat atgagcaatc ttatgccaat cggccccaat gtccttccga catctttcct 60 ccaactgggg agtttgtcgt atgcataact cctccaaact g 101 <210> 48 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 48 ctccttgtct tccattgggg ccatgatctt ccatgcactc gagctcagtt gaattagata 60 tcttcagctg ttgaagacaa ggcaattgag caatggatga g 101 <210> 49 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 49 caaattttgc atattgcaaa tactctttgg gaggatctta agattgggat tgtcggaaag 60 atctagatac ctcaaatgtt tcaatttatg aatggaacgt g 101 <210> 50 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 50 gcaagcatct acatcttgaa attactaaat cccatgtttc gtcctcgctc ttaatttggc 60 tttgctcgct ctcttttgga aaacaaagta aagttcgcaa c 101 <210> 51 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 51 atcttgaaat tactaaatcc catgtttcgt cctcgctctt aatttggctt tgctcgctct 60 cttttggaaa acaaagtaaa gttcgcaact tctttccctt a 101 <210> 52 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 52 ccttaagcaa aggaattaat aaaggactaa ttgatacatg acgacatttt tcactgacct 60 cacttgcact tgaatttgaa tctaccaaac tactctctgt c 101 <210> 53 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 53 attgaacaag tgttcgtaca tcaattttat gatcttttgg atataaccga taataagcaa 60 aacaatgctt caaatgggat ggaagatgat cataactcaa g 101 <210> 54 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 54 tgatacaaac attctcttca ctttgaaact ctaagatgag ttttagaaga gctgctttat 60 catcttccct ccctattatc tcatctttat gagcaaaaga g 101 <210> 55 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 55 ccgatctcac cggaatattc cgtcgcattg ggtgctgaac agatggccgg aagtgttttt 60 ttggtgatca agattgatgg acggttgaga tggaaagttg g 101 <210> 56 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 56 gatcaagatt gatggacggt tgagatggaa agttgggact tttgtaactg ggaggtatca 60 tattcatgca aggtgtccgg cttatattac gtttggggaa c 101 <210> 57 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 57 atcatattca tgcaaggtgt ccggcttata ttacgtttgg ggaacaaagc cacggcgttt 60 tggtcggaga aaatgctgta aagtttcagt tctatagtag a 101 <210> 58 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 58 attacgtttg gggaacaaag ccacggcgtt ttggtcggag aaaatgctgt aaagtttcag 60 ttctatagta gatgcagtgt tagcttgtga agaagaagaa g 101 <210> 59 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 59 ttggtcggag aaaatgctgt aaagtttcag ttctatagta gatgcagtgt tagcttgtga 60 agaagaagaa gcaagtaacg ccgttaagta tatggttttg t 101 <210> 60 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 60 agacaccagc tgtggaatat taataatctc caaatgagag agattcttaa tggcttgcca 60 ttgcatgccc tctaaatcaa cctccttgca atctcctatt g 101 <210> 61 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 61 tggaatatta ataatctcca aatgagagag attcttaatg gcttgccatt gcatgccctc 60 taaatcaacc tccttgcaat ctcctattgt taattttttg a 101 <210> 62 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 62 tcttaatggc ttgccattgc atgccctcta aatcaacctc cttgcaatct cctattgtta 60 attttttgag gccggtgaaa tgtttcaagt actcatctag c 101 <210> 63 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 63 tcttcaccaa ccttagatca tcatcgagtg aaggatacaa cggcattgaa gtcaaagggc 60 aatttgcaat ttctaaggag gaaagacaag gaaatgccat g 101 <210> 64 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 64 agtgaaggat acaacggcat tgaagtcaaa gggcaatttg caatttctaa ggaggaaaga 60 caaggaaatg ccatggttga tgttcctata acagttgtgt c 101 <210> 65 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 65 ctcccaccca atagatcttt ccgcaaagct tcggtagaga aatcatcaag taagtcgtcg 60 gcatcataaa gtacatcttt cagcttttca agccaatctt t 101 <210> 66 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 66 cccaatagat ctttccgcaa agcttcggta gagaaatcat caagtaagtc gtcggcatca 60 taaagtacat ctttcagctt ttcaagccaa tctttgacgc g 101 <210> 67 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 67 acgagatttg tgagcaaaga aagccaaatt ggaaacttgg catcacccct tcatcctcga 60 atccagagct tcttgagatt aggatggggc tggagatctt c 101 <210> 68 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 68 ttacgaatgc caaatttgtt attattaact ctccccttat gttgttaagc agtctcaatt 60 cacttagatc tgcaccacca tgggacccat ctttatccac t 101 <210> 69 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 69 gatctgcacc accatgggac ccatctttat ccactacaaa catgcttaac atctcaagtg 60 aagtcagctt ccctattcca cgtggcatat gagttaaact a 101 <210> 70 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 70 tgaagtcagc ttccctattc cacgtggcat atgagttaaa ctactacaat gttcacacgc 60 aagatgggta agattcacca atttttcaat cttctttggc a 101 <210> 71 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 71 gtaagaaaga tcaaggtacc tcaaatgttt caacttgtaa atggagggtg aaatcatctg 60 aatacctaac aaattagtca atttcaatac acgcaagcat c 101 <210> 72 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 72 tttctcctat gtttaaatac tccaaactgg ttaggcaacg catctcgtcc agaagagatg 60 ttaaattggg caaattaacc agataaagcc cttgcagatt t 101 [[ID=⑧]]<210> 73 <211> 101 <212> DNA[[ID=⑨]] <213> Cotton (Gossypium spp) <400> 73 ccggcccatt ttgagaccat aagcaaattg gtttgaggtt gagaagaaaa tgcgtacctc 60 tttcgtcagc ttgttcccac ccgatagatc tttccgcaaa g 101 <210> 74 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 74 ttgagtctgc agatctttgt tcaaatgcta tctctttgaa caaagaccaa gcatcattat 60 cagacaagcc tttcagaaca taaggctgac atttactagt a 101 <210> 75 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 75 ctcttctgcg tcaagaagca cagctttgat tgtagagaca gtgcttttga agttgtcgag 60 gtcatttttg acattccaac acagtctaat ttgagagagc g 101 It should be noted that in the above translation, the numbers in - are kept as they are because they are specific tags that need to be preserved exactly. And the text within <213> is translated as "Cotton (Gossypium spp)" which is the common English name for cotton plants in the context of biological or scientific texts. The nucleotide sequences within <400> are also kept as they are since they are likely genetic code sequences that are not typically translated in a patent text context. If there are specific requirements for handling these nucleotide sequences further, additional information would be needed. Also, some of the numbers like <210>, <211>, <212> seem to be some kind of identifiers within the patent text structure and are left as they are for translation. The overall translation aims to follow the rules of preserving tags and maintaining the original line breaks as closely as possible while presenting the text in English.<210> 76 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 76 catcaaaata aataaataac aaagacagac caacctgtta ctaccaaatg tgggggatgt 60 gagcaatctt atgccaatca gcgccaatgt ccttccgaca t 101 <210> 77 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 77 aataacaaag acagaccaac ctgttactac caaatgtggg ggatgtgagc aatcttatgc 60 caatcagcgc caatgtcctt ccgacatctt tcctccaact g 101 <210> 78 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 78 atgtggggga tgtgagcaat cttatgccaa tcagcgccaa tgtccttccg acatctttcc 60 tccaactgag gaattccatt tatgtctaaa atttgcaatt t 101 <210> 79 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 79 cttggcatca cccctccatc ctgcaatatg gagctgcttg agattaggat ggggttggag 60 gtcttcaagt gacttctcat catcataatc atcatcagaa t 101 <210> 80 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 80 aagttgtttt tgcaattgat ccatttcaag attttgatca ggtgcttgat tagtcacaga 60 tttgataatg ttcgctacaa taactttcac atcaaaatca t 101 <210> 81 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 81 caaagacttg tttctatacc aatattgaca ccaaaatctg agttcttcaa ctgaaacctt 60 gttcttctcc actgttttaa agcattcaat agctggaaat c 101 <210> 82 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 82 accaatgaaa actaaaataa aacaaaaaga aaaaaggtga cttacacaag tactctagta 60 atgaattcac ccaacatttc ttctttcctt cttaaaagtt t 101 <210> 83 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 83 gccagattat taaagctgcc aaatgtaata aaaccattgg caagagcagg ggttggtgat 60 acaggtccag cctcaggtga aggggtataa caaaggaagc a 101 <210> 84 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 84 ataagacacg gaatgagtga aataatcggg agaaatatat ccaatcacta gaggtcgttc 60 tggatctttt ggattgtccc atgaattgta ttgcgaatat a 101 <210> 85 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 85 gaatgagtga aataatcggg agaaatatat ccaatcacta gaggtcgttc tggatctttt 60 ggattgtccc atgaattgta ttgcgaatat aacctcataa a 101 <210> 86 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 86 ataagttcta actttgatga actaacagga attcccccgg accaacaacg gttaattttt 60 gctggtaaac aacttgaaga tggccgtaca ttggctgatt a 101 <210> 87 <211> 101 <212> DNA[[ID=5l]] <213> Cotton (Gossypium spp) <400> 87 cgagttagct cctgaccaat ttgcaaacgg tgctcaggaa agacaggtga taatttcatg 60 gcttgaatat cagtgttaac aatccagaac tctacaccct t 101 <210> 88 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 88 cttattttga tacggactaa cgctatggga gttggtggaa catctaaaat aaggcatatt 60 agacctttgg ctcggactcg aagacccgca cctaagtttc c 101 <210> 89 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 89 aagctaatgg cttgccccag caactcatac atctaaagtc atgggaacct gaattcaaaa 60 gaataaagca agacatcgca agtatcccgt atttaccaga a 101 <210> 90 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 90 actcatacat ctaaagtcat gggaacctga attcaaaaga ataaagcaag acatcgcaag 60 tatcccgtat ttaccagaat cacaggcgag gctgaaactg c 101[[ID=~]] <210> 91 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 91 ctgaattcaa aagaataaag caagacatcg caagtatccc gtatttacca gaatcacagg 60 cgaggctgaa actgctcgaa gtagaacggt ccttgaagca a 101 <210> 92 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 92 tcccgtattt accagaatca caggcgaggc tgaaactgct cgaagtagaa cggtccttga 60 agcaatgcct aaaactacta tcacaggtac gcagagaact a 101 <210> 93 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 93 taccagaatc acaggcgagg ctgaaactgc tcgaagtaga acggtccttg aagcaatgcc 60 taaaactact atcacaggta cgcagagaac tatcaaaagc a 101 <210> 94 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 94 taagtctcta atttaattcg gtttttcagg tccataaact tggtgaagtc ttccttaata 60 atgaggtacg cagatttctt atcattgaca ttaagcaacg a 101 <210> 95 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 95 taattcggtt tttcaggtcc ataaacttgg tgaagtcttc cttaataatg aggtacgcag 60 atttcttatc attgacatta agcaacgata acatttctca t 101 <210> 96 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 96 tctttctgtg atgccaacta tggaagaaat tgctgcaagt ttgccatctc ctgaagcatt 60 accacctcct tctagtgatt gtgacaacga caaaggtctc c 101 <210> 97 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 97 atggaatgct tcaacagggt gggagtgagg tgtttggagc acaaaacatc atgaacgcac 60 caccattgtc gcagagtgat aattggatga acttaatgct c 101 <210> 98 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 98 acatcatgaa cgcaccacca ttgtcgcaga gtgataattg gatgaactta atgctcagtg 60 caagcaacaa aagagatggg gaattggttt tccgtaactt g 101 <210> 99 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 99 catgaacgca ccaccattgt cgcagagtga taattggatg aacttaatgc tcagtgcaag 60 caacaaaaga gatggggaat tggttttccg taacttgtca g 101 <210> 100 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 100 ttgcgatatc gtgatgatac ctacacctaa agccccaaat ggtgctaatg tacaaccatc 60 gcctgatgat aatctggtca attcctcaaa cttgatgttg a 101 <210> 101 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 101 tggtgctaat gtacaaccat cgcctgatga taatctggtc aattcctcaa acttgatgtt 60 gaccggaccc aagaaaagaa atcgggaagc tgaaggagaa g 101 <210> 102 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 102 caaccatcgc ctgatgataa tctggtcaat tcctcaaact tgatgttgac cggacccaag 60 aaaagaaatc gggaagctga aggagaaggc atcaagaaac a 101 <210> 103 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 103 tcgcctgatg ataatctggt caattcctca aacttgatgt tgaccggacc caagaaaaga 60 aatcgggaag ctgaaggaga aggcatcaag aaacagagcc g 101 <210> 104 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 104 tctggtcaat tcctcaaact tgatgttgac cggacccaag aaaagaaatc gggaagctga 60 aggagaaggc atcaagaaac agagccggcc ccggctaacg g 101 <210> 105 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 105 aaggagaagg catcaagaaa cagagccggc cccggctaac ggttgaatca ccaaatttgg 60 gagaagagaa tactgaagag catattcagg tgaaaactca a 101 <210> 106 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 106 catcaagaaa cagagccggc cccggctaac ggttgaatca ccaaatttgg gagaagagaa 60 tactgaagag catattcagg tgaaaactca aaccttgata t 101 <210> 107 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 107 agccggcccc ggctaacggt tgaatcacca aatttgggag aagagaatac tgaagagcat 60 attcaggtga aaactcaaac cttgatatgt tgaattattt t 101 <210> 108 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 108 ccggctaacg gttgaatcac caaatttggg agaagagaat actgaagagc atattcaggt 60 gaaaactcaa accttgatat gttgaattat ttttctaaat t 101 <210> 109 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 109 ttttaatgaa gacaatgaca gctttcctgc cttagaacaa gcaccgcaag gtactgagtt 60 tctccgtcaa aatattgaag ttttggtttc cggtacaatc a 101 <210> 110 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 110 ttaatgcttt tttttttttt gtgatttgct tttgtttaca ggtaaactat agtaacttca 60 tgcatggact gatgaaagag aacatacaat tgaacaggaa a 101 <210> 111 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 111 agcgaaaggt ccttgaaatc gagctcgagt tcaaggacac tggtttgaca gatgaggcaa 60 agtggagatt gctcgaatta gaagaagagt ttaagagatt g 101 <210> 112 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 112 gacactggtt tgacagatga ggcaaagtgg agattgctcg aattagaaga agagtttaag 60 agattggata aaaaatggat gaaggtatgg tattgtttac a 101 <210> 113 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 113 gacaatattg tgctataggc tcgacaccag aatcgcaatt ttcgccggga aaccaatcta 60 gaaaaatgtc ggtgaaaaaa ctgtcttcgt tgctcatgtt g 101 <210> 114 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 114 atattcaagc tcaatacgtt gttgtattct tgcatatgtt tctctttcta gccgtacaat 60 tactagtaca cctattatga ttccgaatac aagagtcaaa a 101 <210> 115 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 115 tgaaaaccat atttcttagc gtaattaagc gtagcgcccc actttttcaa cgtatcccag 60 tccaaatcct caaccggaaa atcttccatc tctttgatcg c 101 <210> 116 <211> 101<00​​​​​​​​​ <210> 117 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 117 ggcctgttcc aagcctagga aatctttgta ttccactttg ttgttgtcct tgtcgtgaag 60 ttggttttcc aaatcacgca atttagatag tacttcttca c 101 <210> 118 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 118 cgtcttgaag atttcactct gcgggcctct aagcatgatt aaaagaacaa caaaggtgat 60 tgcaaaagtc aagaccccct ctgcaaaggc tccagtgtgc g 101 <210> 119 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 119 gtgatcacta tcgcaaatgc agtatttggc tcaaaccctt ccattaatgc agatattctt 60 gccaaggctt ttaatctgga taggaaaatg gtgaagaatc t 101 <210> 120 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 120 ctccaaagac aatataatgg aaggaatacc taaagaggtg cagtcaaaac catcggtcga 60 ttccttcaaa gatttgcaag gagaagagat gttgaaagag a 101 <210> 121 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 121 gaaagaggat gtgatccttt ttggttcaga cttaagcatg catggaggcc gaactgccat 60 ggaaagtaaa gtgaaaaagc ctgtagctcc agtgggtgat a 101 <210> 122 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 122 attaaattga agatcgagaa ttggagtaca aggtttctat cacaaggggg caaagaggtt 60 tttataaaat ctgttcttca ggctatacca acttatgcta t 101 <210> 123 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 123 atgggatata gagatatggc tcagtttaat atttctttac ttgctaagca aggttggaga 60 attatcaata atcaggatgc tcttgttatg caagttctta a 101 <210> 124 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 124 ttatgcaagt tcttaaagcg aaatattttc caaatgatca ttttttaaat gctcgtttgg 60 gaaattccgg ctcttatgta tggaaaagta tttgggcagc g 101 <210> 125 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 125 gcaagttctt aaagcgaaat attttccaaa tgatcatttt ttaaatgctc gtttgggaaa 60 ttccggctct tatgtatgga aaagtatttg ggcagcgaag g 101 <210> 126 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 126 agaagtagta gaaagatggg ccttgaatga aaaacctacc atatgattct cccattataa 60 tggacaattt ttcatccaag tatttgataa ctgcagcatt a 101

Claims

1. A SNP molecular marker combination associated with upland cotton fiber strength quality traits, characterized in that: The SNP molecular marker combination includes SNP molecular markers of nucleotide sequences shown in SEQ ID NO.1 to SEQ ID NO.126; the SNP molecular site mutates at the 51 bp position of the sequence, and the mutation form of the SNP molecular marker is as follows:

2. Use of the SNP molecular marker combination according to claim 1 in identifying fiber strength quality traits of upland cotton.

3. Use of the SNP molecular marker combination according to claim 1 in upland cotton assisted breeding.

4. Use of the SNP molecular marker combination according to claim 1 in improving upland cotton germplasm resources.

5. A primer or reagent for detecting the SNP molecular marker combination according to claim 1.

6. A kit for detecting the SNP molecular marker combination according to claim 1.

7. A gene chip containing the SNP molecular marker combination according to claim 1.

8. A method for analyzing upland cotton fiber strength using the SNP molecular marker combination according to claim 1, characterized in that: The following steps are involved: (1) Extracting genomic DNA from the sample to be tested; (2) Using the extracted DNA as a template, primers were designed according to the SNP molecular marker combination and PCR amplification was performed separately; (3) Analyze the fiber strength of upland cotton based on the PCR amplification products.

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