SNP Molecular Markers Associated with the Quality Trait of Cotton Fiber Elongation Rate and Their Applications

Abstract

The present invention discloses SNP molecular markers associated with the quality trait of cotton fiber elongation rate and their applications, belonging to the fields of molecular biology and bioinformatics. The SNP molecular markers are at least one of the nucleotide sequences shown in SEQ ID NO.1 - SEQ ID NO.39, and the SNP molecular locus has a mutation at the 51st bp of the sequence. The SNP molecular markers provided by the present invention are SNPs detected using the largest population in cotton to date. Compared with other populations, there are more accurate and novel signal sites. It can be used for more accurate and comprehensive prediction and screening of cotton fiber elongation rate at an early stage. It is embodied in the form of DNA, is not affected by factors such as sampling sites and environments, and can be directly analyzed based on the presence or absence of the marker.

Description

Technical Field

[0001] The present invention relates to a SNP molecular marker associated with the cotton fiber elongation quality trait and an application thereof, and belongs to the fields of molecular biology and bioinformatics. Background Art

[0002] Cotton fiber, formed by the elongation and thickening of epidermal cells from the fertilized ovule, is a high-quality natural fiber and a major raw material for the textile industry, playing a crucial role in both the global and domestic economies. Fiber quality is a complex quantitative trait controlled by multiple genes, with components including fiber length, strength, fineness, elongation, uniformity, and maturity. Phenotypic values ​​of cotton fiber quality are not only controlled by genetic factors within the cultivar, but also by a combination of environmental factors and the interaction between cultivar and environment. Cotton fiber elongation is also a key indicator of fiber quality. Elongation at break is the percentage ratio of the fiber's elongation at break to its original length. Greater elongation indicates greater deformability and decreased rigidity. Phenotypic variation in cotton fiber elongation is primarily driven by cultivar effects, environmental effects, and the interaction between cultivar and environment. Multiple studies have demonstrated a significant correlation between fiber elongation and both fiber length and strength. Therefore, in-depth research on fiber elongation is crucial for understanding the mechanisms underlying the formation of cotton fiber length and strength.

[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 requires a larger breeding population, which increases blindness, time-consuming efforts, and costs, leading to slow 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] SNPs (single nucleotide polymorphisms) refer to DNA sequence polymorphisms caused by variations in a single nucleotide at the genomic level. As an important genetic tool, SNPs offer advantages such as widespread distribution, large numbers, and ease of batch detection. They are also a key focus of functional genomics research. SNPs are suitable for genetic analysis of complex traits and for identifying genes that cause population differences. They are crucial for constructing high-density genetic maps of plants, cloning new genes, and studying their function. Summary of the Invention

[0005] In view of the deficiencies of the prior art, the present invention aims to provide a SNP molecular marker associated with the cotton fiber elongation quality trait and its application.

[0006] In order to achieve the above object, the technical solution of the present invention is:

[0007] A SNP molecular marker associated with the cotton fiber elongation quality trait, wherein the SNP molecular marker is at least one of the nucleotide sequences shown in SEQ ID NO.1-SEQ ID NO.39.

[0008] The SNP molecular marker is a combination of two or more of the nucleotide sequences shown in SEQ ID NO.1 to SEQ ID NO.39.

[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] An application of the SNP molecular marker in identifying the quality trait of cotton fiber elongation.

[0013] An application of the SNP molecular marker in cotton assisted breeding.

[0014] An application of the SNP molecular marker in improving cotton germplasm resources.

[0015] A primer or reagent for detecting the SNP molecular marker.

[0016] A kit for detecting the SNP molecular marker.

[0017] A method for analyzing cotton fiber elongation using the SNP molecular marker comprises the following steps:

[0018] (1) Extracting genomic DNA from the sample to be tested;

[0019] (2) Using the extracted DNA as a template, primers were designed based on the SNP molecular markers and PCR amplification was performed respectively;

[0020] (3) Analyze the cotton fiber elongation based on the PCR amplification products.

[0021] Beneficial effects of the present invention:

[0022] The SNP molecular markers provided by this invention are the largest SNP population detected to date in cotton. Compared to other populations, they have more accurate and novel signal loci. They can be used for more accurate and comprehensive prediction and screening of cotton fiber elongation at an early stage. Since they are expressed in DNA, they are not affected by factors such as sampling location and environment, allowing direct analysis based on the presence of the marker. DETAILED DESCRIPTION

[0023] The specific embodiments of the present invention are further described in detail below with reference to the examples.

[0024] Example 1. Acquisition of SNP molecular markers

[0025] (1) Determination of fiber elongation

[0026] 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 (AY), Anqing, Anhui (AQ), Xingtai, Hebei (XT), Shihezi, Xinjiang (SHZ), and Alaer, Xinjiang (ALE). Each test site was planted in single rows (except for Alaer, Xinjiang, which had double rows) with a row length of 2 m. The number of plants per row ranged from 10 to 30 (depending on the local cultivation pattern). Sampling time varied from September 20 to October 20 (depending on the local frost period and cultivation pattern). Except for two plants at the ends, bolls were sampled from the middle of the remaining plants, close to the main stem, in each plot, with 1 to 2 bolls per plant, for a total of 20 bolls. To reduce errors, the unique barcode numbering system of the present invention was used, and the number plates were placed in the boll weight bags. To reduce errors, all boll weight materials from various locations were ginned at the Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang Farm, Henan Province, using a Xinxiang MPSY-20A leather gin. Lint samples were obtained from 20 harvested boll samples. Cotton fiber elongation was measured using an HFT9000 (HVICC calibration level) instrument from the Cotton Fiber Quality Supervision and Inspection Center (Anyang) of the Ministry of Agriculture and Rural Affairs according to the instructions. The best linear unbiased predictor (two replicates over two years) was estimated using the R package lme4 (https: / / github.com / lme4 / lme4).

[0027] (2) Extract genomic DNA from the sample to be tested

[0028] 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.

[0029] 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.

[0030] ③Centrifuge at 12000rpm for 10 minutes.

[0031] ④ Use a blunt tip to aspirate the supernatant and transfer it to another 1.5ml centrifuge tube.

[0032] ⑤ Add 1 volume of anhydrous ethanol and slowly invert several times until flocculent DNA appears. Let it stand for 10 minutes.

[0033] 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 to wash once.

[0034] ⑦ Dry overnight, add ddH2O to dissolve the DNA until it is completely dissolved, and store at -20℃ until use.

[0035] (3) SNP detection

[0036] 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 (RILs). 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, an average sequencing depth of 35X for parents, and an average sequencing depth of more than 4X for offspring. 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.

[0037] (4) Genome-wide association analysis of fiber elongation traits in upland cotton

[0038] 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:

[0039] y=Xα+Zβ+Wμ+e

[0040] 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, the population analysis was corrected by adding the kinship matrix to μ. The analysis found that a total of 39 SNPs were significantly associated with fiber elongation in upland cotton. The allele loci of the SNP markers are shown in Table 1. The reference sequence is the upland cotton cultivar TM-1, and the reference genome version number is G.hirsutum_TM-1_ICR.

[0041] (http: / / grand.cricaas.com.cn / page / download / download) The nucleotide sequences of the 50 bp upstream and downstream of these SNP sites are shown in SEQ ID NO. 1 to SEQ ID NO. 39.

[0042] Table 1 SNP molecular markers associated with upland cotton fiber elongation

[0043]

[0044]

[0045] (5) Verification: The effects of the above SNPs were verified using the fiber elongation 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 100% of the SNPs showed a significant effect on the variation of the fiber elongation trait in upland cotton. SEQUENCE LISTING <110> Cotton Research Institute, Chinese Academy of Agricultural Sciences <120> SNP molecular markers associated with cotton fiber elongation quality traits and their application <160> 39 <170> PatentIn version 3.5 <210> 1 <211> 101 <212> DNA <213> Cotton (Gossypium spp.) <400> 1 tgttgaggag ttgccgaagg tcccggtgct gctatactgt aatgtatggt cagaggttgc 60 tctggttgag gagctgtgga aggtcccgga tctacgctgt a 101 <210> 2 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 2 tcattgaacc gtatctgata gccattgctg aatacgtagg gctgcgcact tatcagaaag 60 acactcttga atccaattcc tgcaaagaaa acataataca t 101 <210> 3 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 3<​​​​​​​​​​​​​​​​​​​​​​​​​​​​tatcttcgtt ccttaatgtt gtttctaata accctttaga ccatgggttt gatttgggtg 60 aaattgggtt ccttgacaac caagcaacga caaatgctac t 101 <210> 6 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 6 ggttcgccgg ttttcaaggg tttaatgaga atccaggtaa tcctctgttt ctaaataggt 60 ctaagctgct aagaccattg gatagcttcc cttcagtggg a 101 <210> 7 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 7 tatggtatac gcacctagag agttaccctg aacaattctt tgcactagat gctgatggac 60 agtttacttc ttttgcaact gtaccctctg agggaactgg a 101 <210> 8 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 8 cgctagcaca ccaagatgca tgctatgact tgatataacc gatgaaggaa cgttgccctg 60 ctgtctcaat gctcgccgta caccaacgcg caattctcca t 101 <210> 9 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 9 gtttcttgct tattttctga attgtcattt tcaaaatgaa cttgcaggat tgtccattag 60 tgatagagtg ttttaacttc aacagcaatg gcaaacacga t 101 <210> 10 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 10 tcaaccggac gtgttgcttc ccgtgatatc gttcaatttg ttccatttag ggatgtacaa 60 agtaagtcat ctacacactc tgatatttcg gaaatgtttt g 101 <210> 11 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 11 tagtagatca tgaagacggc attgtttaac tctgtcgttg acactccatt tggctacttg 60 aaccatgttt ctctcgatta actcattcaa gtaatcctct g 101 <210> 12 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 12 caacctttct ggcgtaattc caaaatcctt ggaaaaactc cattacctta catattttaa 60 tgtgtctttt aatcaactcg aaggggagat acccggtgcg g 101 <210> 13 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 13 ggatgctgca gtgcaaacaa tgaccatggc cactattggg tacatggcac caggtacaaa 60 tgtttgtatt tgtattttga tttatgtgca taatttctct g 101 <210> 14 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 14 agcagctaaa gcaacatgca taaaatcaat catggaactt gcatgttttt gtactgctga 60 ctcattttct aagaggaaga ctatggaaaa agttgagatc g 101 <210> 15<7-digit tag 0000204<211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 15 gaactctgaa aggcgacgtt gttgcgataa agatttttaa gctacagaaa ggagggttag 60 aaagttttga agttaactgt caagcattgt catttattcg t 101 <210> 16 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 16 gcccaattct tagacaaagg cagtgctgaa acaataacca ctacaatggc agaaagtcct 60 It should be noted that the 7-digit tag in the original text was misspelled as in the translation of line 1. It should be corrected to in the translation to be completely consistent with the original text. Also, the 7-digit tag in the original text was misspelled as in the translation of line 28. It should be corrected to in the translation. After correction, the translation is as follows: <210> 13 <211> 101 <212> DNA <000,0192> <213> Cotton (Gossypium spp) <400> 13 ggatgctgca gtgcaaacaa tgaccatggc cactattggg tacatggcac caggtacaaa 60 tgtttgtatt tgtattttga tttatgtgca taatttctct g 101 <210> 14 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 14 agcagctaaa gcaacatgca taaaatcaat catggaactt gcatgttttt gtactgctga 60 ctcattttct aagaggaaga ctatggaaaa agttgagatc g 101 <210> 15 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 15 gaactctgaa aggcgacgtt gttgcgataa agatttttaa gctacagaaa ggagggttag 60 aaagttttga agttaactgt caagcattgt catttattcg t 101 <210> 16 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 16 gcccaattct tagacaaagg cagtgctgaa acaataacca ctacaatggc agaaagtcct 60 ggttatatgg caccaggtga tctaatttct tgggtttagt t 101 <210> 17 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 17 ggacaagatt tgagtttggt gttcagggta gtgaataaat acgaggctgc tggatattca 60 ctgtccaagg ctatttatga cgggattcat cgttctttaa c 101 <210> 18 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 18 gcaggcatac catatctgct tcagattcac taagtggttt cccacaatca actgtttcaa 60 gtttcgcaag tactggtttt ctctccttta tctgcattat t 101 <210> 19 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 19 caagtcataa tagctagcgc tggataatac atagaattcc cgtatataat ttgtttgtct 60 aaatcctttc tcaagtccgt atatccaaca gcagagacat a 101 <210> 20 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 20 agtgaaaaga acaagtaggc attaccaact gctggaaata tcgatataaa gccggtgaca 60 tactagcagg agatttccac aatttctgat aactaggcag t 101 <210> 21 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 21 atttcggatg ggttcacttt tggaatcgcg ttcgcatcga gacaatcatt attcttcaac 60 agctcacttc agttgtcgcc ttgcgatcgc cggctctctt t 101 [[ID=第十八条]]<210> 22[[ID=第十九条]] [[ID=第二十条]]<211> 101[[ID=第二十一条]] [[ID=第二十二条]]<212> DNA[[ID=第二十三条]] [[ID=第二十四条]]<213> Cotton (Gossypium spp)[[ID=第二十五条]] [[ID=第二十六条]]<400> 22[[ID=第二十七条]] [[ID=第二十八条]]tattcttcaa cagctcactt cagttgtcgc cttgcgatcg ccggctctct ttgtcaaacg 60[[ID=第二十九条]] [[ID=第三十条]]ccaactctcg cctcgctctg tttagaccta aagttgatga g 101[[ID=第三十一条]] [[ID=第三十二条]]<210> 23[[ID=第三十三条]] [[ID=第三十四条]]<211> 101[[ID=第三十五条]] [[ID=第三十六条]]<212> DNA[[ID=第三十七条]] [[ID=第三十八条]]<213> Cotton (Gossypium spp)[[ID=第三十九条]] [[ID=第四十条]]<400> 23[[ID=第四十一条]] [[ID=第四十二条]]caagaacttc ctagttttag tcacggacat tattcttttg gtgatcaagt agtcagcaag 60[[ID=第四十三条]] [[ID=第四十四条]]aaccccaccg atatttgaga atatgaacat gttgaaatac g 101[[ID=第四十五条]] [[ID=第四十六条]]<210> 24[[ID=第四十七条]] [[ID=第四十八条]]<211> 101[[ID=第四十九条]] [[ID=第五十条]]<212> DNA[[ID=第五十一条]] It should be noted that in the above translation, the content of some line numbers such as "第十八条", "第十九条", etc. seems to be incorrect or inconsistent with the original intention. It is recommended to double-check and correct according to the actual situation to ensure the accuracy of the translation.<213> Cotton (Gossypium spp) <400> 24 ttttaatgga caagctatta acccgtattt ggataatact ttaattgtcc atattccaaa 60 gagcattagc cctgtgagtt ttgcccattt caggctaatc a 101 <210> 25 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 25 agggcgaata attttcaaaa aaaactcgat aggaaacctt atccaccttc caaaagtgac 60 tgcgaaacca tgctaaaagg aggtgcgtgc atccaatgaa t 101 <210> 26 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 26 caaatttctt ttaattcctg taagttattc tgagtcacgc taacacgagt gaagtcccat 60 aactctgaca catatccctc ggccaaacta tcgcctttct c 101 <210> 27 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 27 tttgatggtc atggaaatta ttacaacaaa gaatgggatc taattgaagg caatggcaag 60 cagttttgtt ggtaccatgt tgagcttcct aaagggaaac a 101 <210> 28 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 28 tggttttccg tctacgacac gaatcccagt aatgtttttg cccgaaagta cgtcgtgtaa 60 gtagaagtga aggtgggata acttttcttg cttgagccct a 101 <210> 29 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 29 tgcccgaaag tacgtcgtgt aagtagaagt gaaggtggga taacttttct tgcttgagcc 60 ctagtgatga tggagatatg tatttaccga aaagctcgga a 101 <210> 30 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 30 gatttgagtg attgaatgag tctttgcttg agcataacct cgagcgaatc agaaaacacc 60 gctcccacca acaatcggca tctctctcac ggcggaaaga a 101 <210> 31 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 31 atgatccttg cgcttttccc accatttttg agttgacatc gggctcgatc atcaaagggt 60 catcgacaac atatacatct ccgaagatca atggtgagga a 101 <210> 32 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 32 gtatttgcca aaaacctcag aatccgaccg acgaccagcg atgacagtga tgaagaagag 60 aataaggaat aagatgaagc tatgggtttt gagcattgac g 101 <{210}> 33 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 33 atggttgttt gttttgtact gatttaggct aaccagattg ctgggatggc caataaccct 60 caggtctact ggtagcatgt gattgaaata atgtttttct g 101 <210> 34 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 34 tagatgctaa ttgcttcact tttcttgaat tagcctcacc cgtctcctag tgttggctca 60 atggaccctt ctcaaaattt tcccccacct atgtctggtc a 101 <210> 35 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 35 tgtcattttt tatcagattc ttttttgaac attgcaggta ttactacaac aaggttacaa 60 atctatcaac atggtcactc cctgaagagc tgaaggtctc c 101 <210> 36 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 36 gaagacttga aggctgccat tttggaggat attagctctc cacctatatc ggatgttaac 60 ttgaaggtat atacatgttt ttgatagttc tcatttgttt a 101 <210> 37 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 37 aagaagctaa gaagcgtaaa cgtcttgctg atgacttctt tgatttattg tattctatga 60 aggtaaggca ggctttcctt aaaatttgat ctaatagttt a 101 <210> 38 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 38 [[ID=4,2]]gatggatccg gacttcaaat cacctggtgg gataaaacaa tcaaccgaaa tgcctggtac 60 attgaaggca acctcctcga tcgtccaagc ttcttccatc t 101 <210> 39 <211> 101 <212> DNA <213> Cotton (Gossypium spp) <400> 39 acctcttata cgaagcagta acggaagggt tcctcgataa ctgcccctta acccattgtc 60 ctatacccga cccgactcgt ttcgagtccc cgatttcgac t 101

Claims

1. SNP molecular marker combination associated with the fiber elongation quality trait of upland cotton, characterized in that, The SNP molecular marker combination includes SNP molecular markers with nucleotide sequences shown in SEQ ID NO.1 - SEQ ID NO.39; The SNP molecular locus has a mutation at the 51st bp of the sequence, and the mutation form of the SNP molecular marker is shown as follows:

2. Use of the SNP molecular marker combination according to claim 1 in identifying the quality trait of fiber elongation rate of upland cotton.

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

4. Use of the SNP molecular marker combination according to claim 1 in the improvement of 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 method for analyzing the fiber elongation rate of upland cotton by using the SNP molecular marker combination described in claim 1, characterized in that Comprising the following steps: (1) Extract genomic DNA of the sample to be tested; (2) Using the extracted DNA as a template, design primers according to the SNP molecular marker combination and perform PCR amplification respectively; (3) Analyze the fiber elongation rate of upland cotton according to the PCR amplification product.

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