Molecular marker associated with salt tolerance and relative survival seedling rate of cotton as well as KASP detection primer and application of molecular marker

Abstract

The invention discloses a molecular marker associated with salt tolerance and relative survival seedling rate of cotton as well as a KASP detection primer and application of the molecular marker. 39 SNP loci significantly associated with the RSR and ST characters of upland cotton are obtained through whole genome association analysis of the relative emergence rate (RSR) and the salt tolerance grade (ST) characters of 373 core germplasm under salt stress, D11: 10968079 is jointly associated with the RSR and ST characters, and the optimal genotype of D11: 10968079 is AA / TT; the KASP detection primer for predicting the salt tolerance of the upland cotton under the salt stress is developed, and consists of two competitive upstream primers as shown in SEQ ID NO.1-2 and a common downstream primer as shown in SEQ ID NO.3. The detection primer can be used for predicting the salt tolerance or the relative survival seedling rate of the cotton under the salt stress. The method has application prospects in the aspects of salt tolerance prediction of cotton germplasm or salt tolerance germplasm cultivation and the like.

Description

Technical Field

[0001] The present invention relates to molecular markers and detection primers associated with cotton salt tolerance and relative survival rate, in particular to SNP molecular markers associated with cotton salt tolerance and relative survival rate and KASP detection primers thereof, and applications of the SNP molecular markers and KASP detection primers thereof in predicting cotton salt tolerance, belonging to the field of molecular markers related to cotton salt tolerance, KASP detection primers and applications thereof. Background Art

[0002] Cotton, a key fiber and oilseed crop, is also a pioneer crop cultivated on saline-alkali land. In recent years, the cotton acreage has drastically decreased, impacting the industry's security and necessitating structural adjustments. Given cotton's strong tolerance to salt and alkali, and the fact that significant saline-alkali land remains underdeveloped, developing cotton cultivation on saline-alkali land is not only crucial for the safety of the cotton industry but also represents a crucial step in the more scientific development and utilization of saline-alkali land reserves.

[0003] Salt tolerance of cotton (threshold is 7.7dSm -1 ) is stronger than corn (1.7dSm -1 ), rice (3.0dSm -1 ), wheat (6.0dSm -1 ) are major food crops, but are most sensitive to salt stress during the germination and seedling stages. Therefore, improving cotton seedling survival under salt stress is of great significance for the structural adjustment of the cotton industry, food security, and the scientific development and utilization of saline-alkali land. It is also a key breeding goal for cotton.

[0004] As the genomes of major agricultural crops are continuously deciphered and data quality continues to improve, it has become possible to explore the control sites of major breeding target traits at the whole genome level, develop whole genome selection breeding markers and accurately apply them in breeding.

[0005] Studies have shown that genome-wide association studies (GWAS) are currently one of the best methods for identifying loci controlling important crop traits across the entire genome and are widely used. The principle is to select case and control groups within a population (for quantitative traits, this can be a continuously distributed population) and compare the allele or genotype frequencies of all SNPs across the genome between the case and control groups. If the allele or genotype frequency of a particular SNP is significantly higher or lower in the case group than in the control group, the locus is considered to be associated with the trait. Subsequently, the possible trait-associated gene is inferred based on the locus's location in the genome and linkage disequilibrium.

[0006] Through genome-wide association analysis, SNP molecular markers associated with cotton salt tolerance and relative survival rate were obtained, and KASP detection primers for predicting cotton salt tolerance were developed based on them. This has important application prospects in predicting cotton germplasm salt tolerance or breeding salt-tolerant germplasm. Summary of the Invention

[0007] One of the purposes of the present invention is to provide a SNP molecular marker associated with cotton salt tolerance and relative survival rate.

[0008] The second object of the present invention is to provide KASP detection primers for detecting the genotype of SNP molecular markers associated with cotton salt tolerance and relative survival rate.

[0009] The third purpose of the present invention is to apply the SNP molecular marker or KASP detection primer to predict the salt tolerance of cotton.

[0010] In order to achieve the above objectives, the main technical solutions adopted by the present invention include:

[0011] One aspect of the present invention is to provide a SNP molecular marker associated with cotton salt tolerance and relative survival rate, wherein the SNP molecular marker is selected from any one of the following 39 SNP molecular markers: A01:85660976[C / A]; A05:41279075[C / T]; A07:52601100[C / T]; A09:20316137[C / T]; A10:9609390[C / T]; A10:67334353[C / T]; A11:432162[G / A]; A12:432163[C / T]; A13:432164[C / T]; A14:432166[C / A]; A15:432167[C / T]; A16:432167[C / T]; A17:432167[C / A]; A18:432167[C / T]; A19:432167[C / T]; A20:432167[C / T]; A21:432167[C / A]; A22:432167[C / T]; A23:432167[C / T]; A24:432167[C / T]; A25:432167[C / T]; A26:432167[C / T]; A27:432167[C / T]; A28:432167[C / A]; A29:432167[C / T]; A30:432167[C / T]; A31:432167[C / 3:1627727[T / C]; A13:1627728[C / T]; A13:11620626[T / C]; D01:43350000[C / T]; D03:5757725[G / A]; D03:140834 74[A / G]; D04:6101995[C / G]; D04:6116865[T / A]; D07:11309925[C / T]; D07:11309938[C / T]; D07:11309950[C / T]; D07:11309951[A / G]; D07:11418694[C / A]; D07:11418706[T / C]; D07:11418711[T / C]; D07:11418715[A / T]; D07:1 1418726[A / T]; D07:11418765[A / C]; D07:11418769[C / T]; D07:11418770[A / C]; D07:27801321[C / T]; D10:5068946 5[A / T]; D11:10968079[G / A]; D11:37241865[T / C]; D11:37241900[C / A]; D11:37241910[G / A]; D11:37241911[T / C] ; D11:37241920[T / G]; D11:37241922[A / C]; D11:37241928[A / G]; D11:65026765[C / G]; scaffold17685:660[A / G].

[0012] In a preferred embodiment of the present invention, the SNP molecular marker is D11:10968079[G / A].

[0013] In a preferred embodiment of the present invention, the dominant genotype of the SNP molecular marker D11:10968079 is AA / TT.

[0014] Another aspect of the present invention is to develop KASP detection primers for predicting the salt tolerance or relative survival rate of cotton germplasm under salt stress based on the SNP molecular marker D11:10968079[G / A] associated with cotton salt tolerance and relative survival rate.

[0015] In a preferred embodiment of the present invention, the KASP detection primers are composed of two competitive upstream primers carrying fluorescent groups and a common downstream primer; preferably, the nucleotide sequences of the two competitive upstream primers carrying fluorescent groups are shown in SEQ ID NO.1 and SEQ ID NO.2, respectively; the nucleotide sequence of the common downstream primer is shown in SEQ ID NO.3; more preferably, the nucleotide sequence shown in SEQ ID NO.1 carries a FAM fluorescent group; and the nucleotide sequence shown in SEQ ID NO.2 carries a HEX fluorescent group.

[0016] Another aspect of the present invention is to apply SNP molecular markers or KASP detection primers associated with cotton salt tolerance and relative survival rate to predict the salt tolerance or relative survival rate of cotton germplasm under salt stress.

[0017] For reference, the present invention provides a method for predicting the salt tolerance of cotton germplasm based on SNP molecular markers, comprising: (1) extracting genomic DNA of the cotton germplasm to be tested as a PCR amplification template, and using the KASP detection primers to establish a PCR amplification system for PCR amplification; (2) using a fluorescence signal detector or a fluorescence quantitative PCR instrument to read the signal, and collecting the signal to identify the type of allele; (3) if the allele type of the cotton germplasm to be tested is AA / TT, the salt tolerance of the cotton germplasm to be tested is high; if the allele type of the cotton germplasm to be tested is AG / TC or GG / CC, the salt tolerance of the cotton germplasm to be tested is low.

[0018] In a preferred specific embodiment of the present invention, if the allele type of the cotton germplasm to be tested is AA / TT, the salt tolerance of the cotton germplasm to be tested is high salt tolerance, and the relative survival seedling rate under salt stress is higher than the relative survival seedling rate of the germplasm with the genotype of AG / TC or the genotype of GG / CC.

[0019] The present invention also provides a KASP detection kit for predicting the salt tolerance of cotton germplasm, comprising KASP detection primers; the KASP detection primers are composed of two competitive upstream primers and a common downstream primer; preferably, the nucleotide sequences of the two competitive upstream primers are shown in SEQ ID NO.1 and SEQ ID NO.2, respectively; the nucleotide sequence of the common downstream primer is shown in SEQ ID NO.3; more preferably, the nucleotide sequence shown in SEQ ID NO.1 carries a FAM fluorescent group; and the nucleotide sequence shown in SEQ ID NO.2 carries a HEX fluorescent group.

[0020] A preferred embodiment of the present invention is the use of the KASP detection kit in predicting the salt tolerance of cotton germplasm.

[0021] The present invention obtains 39 SNP sites significantly associated with the RSR and ST traits of upland cotton through genome-wide association analysis (GWAS) of the relative emergence rate (RSR) and salt tolerance grade (ST) traits of 373 core germplasms under salt stress, among which the site D11:10968079 on chromosome D11 is jointly associated with the RSR and ST traits and further determines that the optimal genotype of the D11:10968079 site is AA / TT. Based on the SNP site, KASP detection primers for predicting the salt tolerance of upland cotton under salt stress were developed. The present invention further uses KASP detection primers to predict the salt tolerance of 54 newly bred new lines. The results show that the use of the KASP detection primers can accurately predict the salt tolerance of different cotton germplasms under salt stress or the relative survival rate of seedlings under salt stress. The present invention has application prospects in predicting the salt tolerance of cotton or cultivating salt-tolerant germplasms. BRIEF DESCRIPTION OF THE DRAWINGS

[0022] Figure 1 Manhattan plot obtained for the identification of salt tolerance, RSR and ST traits GWAS analysis of some germplasms; Figure 1 -A is the result of identification of surviving seedlings of highly salt-resistant germplasm Taiyuan4 under salt stress; Figure 1 -B is the result of identification of surviving seedlings of salt-resistant germplasm Jianian8 under salt stress;

[0023] Figure 1 -C is the result of identification of surviving seedlings of salt-tolerant germplasm Ekangmian10 under salt stress; Figure 1 -D is the result of identification of surviving seedlings of salt-sensitive germplasm Lumian6 under salt stress; Figure 1 -E is the Manhattan plot obtained from the GWAS analysis of RSR traits; Figure 1 -F is the Manhattan plot obtained from the GWAS analysis of ST traits. DETAILED DESCRIPTION

[0024] The present invention will be further described below in conjunction with specific embodiments, and the advantages and features of the present invention will become clearer as the description proceeds. However, it should be understood that the embodiments are merely exemplary and do not limit the scope of the present invention in any way. It should be understood by those skilled in the art that the details and forms of the technical solutions of the present invention may be modified or replaced without departing from the spirit and scope of the present invention, but such modifications or replacements fall within the scope of protection of the present invention.

[0025] Experimental materials and methods

[0026] 1.1 Test materials

[0027] The GWAS analysis was conducted using 373 core accessions of upland cotton collected and preserved in the China Cotton Germplasm Bank, including 101 international accessions and 272 domestic accessions. International accessions included 5 from Australia, 8 from Pakistan, 1 from Brazil, 2 from Bulgaria, 2 from Russia, 1 from France, 55 from the United States, 1 from Mexico, 17 from the Soviet Union, 1 from Japan, 1 from Sudan, 1 from Turkey, 3 from Uganda, 1 from Uzbekistan, 1 from Spain, and 1 from Chad. Domestic accessions included 8 from Beijing, 2 from Anhui, 2 from Gansu, 4 from Guangxi Zhuang Autonomous Region, 2 from Guizhou, 26 from Hebei, 65 from Henan, 24 from Hubei, 6 from Hunan, 34 from Jiangsu, 5 from Jiangxi, 13 from Liaoning, 14 from Shandong, 13 from Shanxi, 8 from Shaanxi, 6 from Shanghai, 9 from Sichuan, 24 from Xinjiang Uyghur Autonomous Region, 3 from Yunnan, 3 from Zhejiang, and 1 from Chongqing.

[0028] The verification test used 54 new upland cotton breeding lines bred by the inventor's laboratory over the years as materials. These lines have excellent comprehensive agronomic traits.

[0029] 1.2 Test methods

[0030] 1.2.1 Determination of salt concentration

[0031] The 0.3% NaCl salt concentration determined by the present inventors' laboratory in the early stage was used as the identification salt concentration for the germination and seedling stage of upland cotton core germplasm and verification population (Li Hanli, Wang Shengfen, Wang Guoning, Li Zhikun, Wu Liqiang, Zhang Yan, Wu Jinhua, Zhang Guiyin, Ma Zhiying. Identification of salt tolerance of low-phenol cotton germplasm resources. Journal of Plant Genetic Resources, 2016, 17(6): 1099-1105).

[0032] 1.2.2 Growth of cotton seedlings under salt stress

[0033] 373 core collections of upland cotton and new lines of the verification population were delinted with concentrated sulfuric acid, and 400 plump and consistent seeds were selected from each material for salt tolerance identification and cultivation. In this study, cotton seedlings of the test varieties were cultivated by sand culture. Three replicates were set for each material, and the sowing amount for each replicate and water treatment was 100 seeds. The test varieties were evenly placed in a prepared germination box containing 800g of dry quartz sand, covered with 250g of dry quartz sand on the surface of the seeds, and then evenly poured with 250mL of water with a salt concentration of 0.3%, covered with moisture, and placed in a constant temperature and humidity culture room at 28°C and 12h light / 12h dark conditions for cultivation. No further treatment was performed during the period.

[0034] 1.3 Salt tolerance identification indicators and grading standards

[0035] 1.3.1 Salt tolerance identification indicators

[0036] According to the cotton seedling cultivation method described in 1.2.2, 7 days after sowing, the number of seedlings and the survival rate (SR) of 373 core collections of upland cotton and new lines of the verification population were counted. Since the seed emergence rate is affected by the vitality of the seeds themselves, it is necessary to calculate the relative survival rate (RSR) as the basis for the salt tolerance identification of the 373 core collections of upland cotton and new lines of the verification population. The calculation formula is as follows (Liu Guoqiang, Lu Liming, Liu Jinding. Research on the identification of salt tolerance of cotton variety resources. Crop Variety Resources, 1993, (2): 21-22):

[0037] Survival rate (%) = number of surviving seedlings / total number of seedlings × 100%;

[0038] Relative survival rate (%) = survival rate of seedlings / survival rate of control × 100%.

[0039] 1.3.2 Salt tolerance identification and grading standards

[0040] The salt tolerance of cotton is divided into four levels (Table 1). Considering that the vitality of the seeds themselves will affect the germination rate of the seeds, the relative germination rate is used as the basis for grading the salt tolerance of cotton: when the relative germination rate is between 0.0% and 49.9%, the salt tolerance level is level 4, which belongs to salt-sensitive germplasm (Salt Sensitivity, S); when the relative germination rate is between 50.0% and 74.9%, the salt tolerance level is level 3, which belongs to salt-tolerant germplasm (Salt Tolerance, T); when the relative germination rate is between 75.0% and 89.9%, the salt tolerance level is level 2, which belongs to salt-resistant germplasm (Resistance, R); when the relative germination rate is between 90.0% and 100.0%, the salt tolerance level is level 1, which belongs to highly resistant germplasm (Highly Resistance, HR) (Ye Wuwei, Lin Jinding. Technology and Application of Salt Tolerance Identification of Cotton Germplasm Resources. China Cotton, 1998, (09): 34-38).

[0041] Table 1 Salt tolerance grading standards for cotton seedlings

[0042]

[0043] 1.4 Data Processing

[0044] Using Excel statistical analysis software, the number of surviving seedlings of 373 upland cotton core collections and new lines in the validation population was counted, and the surviving seedling rate and relative surviving seedling rate were calculated according to the method described in 1.3.1.

[0045] Experimental Example 1 Screening experiment of SNP molecular markers and KASP breeding markers related to cotton salt tolerance 1 Screening experiment of SNP molecular markers related to cotton salt tolerance

[0046] 1.1 Genome-wide association analysis

[0047] The 3,596,291 SNP sites obtained by the inventors' research group in the early stage of resequencing 373 core collections (Ma, Z., He, S., Wang, X., Sun, J., Zhang, Y., Zhang, G., Wu, L., Li, Z., Liu, Z., et al. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nature Genetics, 2018, 50(6), 803-813) and the relative emergence rate and salt tolerance grade traits of the 373 core collections identified in this experiment were used for genome-wide association analysis using the mixed linear model (MLM) program in TASSE software. The reference genome was TM-1 (Zhang T, HuY, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L.acc.TM-1) provides a resource for fiber improvement. Nat Biotechnol, 2015, 33: 531-537), the associated SNP sites were located on chromosomes within 100kb when the threshold was 5.

[0048] 1.2 39 SNP molecular markers associated with relative emergence rate and salt tolerance grade

[0049] The results of the relative emergence rate (RSR) and salt tolerance grade (ST) of 373 core accessions of upland cotton are shown in Table 2, including 42 high salt-resistant accessions, 105 salt-resistant accessions, 151 salt-tolerant accessions, and 75 salt-sensitive accessions. 76 of the foreign accessions reached the salt tolerance grade or above; 106 of the domestic accessions reached the salt tolerance grade or above, and these accessions came from the cotton-growing areas of the Yellow River Basin and 75 from the cotton-growing areas of the Yangtze River Basin. The growth of different salt-tolerant accessions under salt stress is shown in Table 2. Figure 1 As shown, the relative survival rate of Taiyuan4 was 93.67%, and the salt tolerance grade was 1 ( Figure 1 -A); the relative survival rate of Jiamian8 was 78.87%, and the salt tolerance grade was 2 ( Figure 1 -B); the relative survival rate of Ekangmian10 was 60.10%, and the salt tolerance grade was 3 ( Figure 1-C); the relative survival rate of Ekangmian10 was 17.68%, and the salt tolerance grade was 4 ( Figure 1 -D).

[0050] Table 2 Identification results of RSR and ST of 373 core collections of upland cotton

[0051]

[0052]

[0053]

[0054]

[0055]

[0056]

[0057]

[0058]

[0059]

[0060]

[0061]

[0062] GWAS analysis identified 39 SNPs significantly associated with RSR and ST traits on 13 chromosomes (At01, At05, At07, At09, At10, At11, At13, Dt01, Dt03, Dt04, Dt07, Dt10, and Dt11) and one scaffold (17685:660) in upland cotton (Table 3). Among them, site D11:10968079 was a pleiotropic association site for RSR and ST traits ( Figure 1 -E, Figure 1 -F).

[0063] Table 3 39 SNP molecular markers associated with RSR and ST

[0064]

[0065]

[0066] 1.3 KASP detection primer design

[0067] Based on the information of SNP site D11:10968079, a set of KASP detection primers was designed to predict the salt tolerance of cotton under salt stress (Table 4).

[0068] The KASP detection primers are composed of two competitive upstream primers and a common downstream primer; preferably, the nucleotide sequences of the two competitive upstream primers are shown in SEQ ID NO.1 and SEQ ID NO.2 respectively; the nucleotide sequence of the common downstream primer is shown in SEQ ID NO.3.

[0069] Table 4 KASP detection primers used for screening RSR and ST traits

[0070]

[0071]

[0072] Note: The amplification primer shown in SEQ ID NO.1 carries a FAM fluorescent group; the amplification primer shown in SEQ ID NO.2 carries a HEX fluorescent group.

[0073] Test Example 2D11: Verification of the optimal genotype at locus 10968079

[0074] 1 Test method

[0075] To further determine and verify the accuracy of the optimal genotype at this locus, 54 new upland cotton breeding lines were selected for RSR and ST trait identification and genotype identification at this locus. The salt stress treatment of the 54 new upland cotton germplasms and the determination of RSR and ST were the same as those described in 1.2 and 1.3 of the experimental materials and methods.

[0076] 2× Master Mix for ASPCR V1 (Cat. No. 102001000059) used for KASP amplification was purchased from Chengdu Hanchen Guangyi Technology Co., Ltd. The reaction system was as follows: 1.5 μL of DNA at a concentration of 30 ng / μL; 1.5 μL of 2× Master Mix for ASPCR V1; and 0.04 μL of primers. The primers used were the same as those in Table 4 of Experimental Example 1. The KASP amplification reaction procedure is shown in Table 5.

[0077] Table 5 Reaction procedures for KASP amplification

[0078]

[0079] Fluorescence signal detection was performed using an LGC SNP typing detector (LGC-Pherastar SNP). In the genotype detection of the D11:10968079 site, the amplification product of the primer SEQ ID NO.1 stimulated a FAM signal, and the amplification product of the primer SEQ ID NO.2 stimulated a HEX signal.

[0080] 2 Test results

[0081] Table 6 RSR and ST identification results and genotypes of 54 new upland cotton lines

[0082]

[0083]

[0084]

[0085] The experimental results are shown in Table 6. Among them, there were 5 new lines with high salt tolerance, 15 new lines with salt tolerance, 12 new lines with salt tolerance, and 22 accessions with salt sensitivity. A one-way analysis of variance showed that the mean RSR of accessions with the AA / TT genotype at this locus was greater than that of accessions with the AG / TC genotype or the GG / CC genotype, with a P-value of 0.0011 < 0.05 for the inter-group difference. The salt tolerance rate was 88.9% in the AA / TT group, 60.0% in the AG / TC group, and 38.5% in the GG / CC group. This further confirmed that the optimal genotype for the association of this locus with both RSR and ST traits was AA / TT; that is, when the AA / TT genotype at this locus was present, the accession was likely to be salt tolerant.

Claims

1. A SNP molecular marker associated with cotton salt tolerance and relative survival rate, characterized in that: The SNP molecular marker is selected from any one of the following 39 SNP molecular markers: A01:85660976[C / A]; A05:41279075[C / T]; A07:52601100[C / T]; A09:20316137[C / T]; A10:9609390[C / T]; A10:67334353[C / T]; A11:432162[G / A]; A13:1627727[T / C]; A13:1627728 [C / T]; A13:11620626[T / C]; D01:43350000[C / T]; D03:5757725[G / A]; D03:14083474[A / G]; D04:6101995[C / G]; D04:6116865[T / A]; D07:11309925[C / T]; D07:11309938[C / T]; D07:11309950[C / T]; D07:11309951[A / G]; D07:11418694[C / A]; D07:11418706[T / C]; D07:11418711[T / C]; D07:11418715[A / T]; D07:11418726[A / T]; D 07:11418765[A / C]; D07:11418769[C / T]; D07:11418770[A / C]; D07:27801321[C / T]; D10:50689465[A / T]; D1 1:10968079[G / A]; D11:37241865[T / C]; D11:37241900[C / A]; D11:37241910[G / A]; D11:37241911[T / C]; D11 :37241920[T / G]; D11:37241922[A / C]; D11:37241928[A / G]; D11:65026765[C / G]; scaffold17685:660[A / G].

2. The SNP molecular marker according to claim 1, characterized in that The SNP molecular marker is D11:10968079[G / A].

3. The SNP molecular marker according to claim 2, characterized in that The dominant genotype of the SNP molecular marker D11:10968079 is AA / TT.

4. A KASP detection primer for detecting the genotype of the SNP molecular marker according to claim 2 or 3, wherein the KASP detection primer consists of two competitive upstream primers with fluorescent groups and a common downstream primer, characterized in that: The nucleotide sequences of the two competitive upstream primers with fluorescent groups are shown in SEQ ID NO.1 and SEQ ID NO.2 respectively; the nucleotide sequence of the common downstream primer is shown in SEQ ID NO.3; preferably, the nucleotide sequence shown in SEQ ID NO.1 carries a FAM fluorescent group, and the nucleotide sequence shown in SEQ ID NO.2 carries a HEX fluorescent group.

5. Use of the SNP molecular marker according to any one of claims 1 to 3 in predicting the salt tolerance of cotton.

6. Use of the KASP detection primers according to claim 4 in predicting the salt tolerance of cotton germplasm.

7. The use according to claim 6, characterized in that include: (1) extracting genomic DNA from the cotton germplasm to be tested as a PCR amplification template, and using the KASP detection primers described in claim 4 to establish a PCR amplification system for PCR amplification; (2) Using a fluorescence signal detector or a fluorescence quantitative PCR instrument to read the signal, the signal is collected to determine the type of allele; (3) If the allele type of the cotton germplasm to be tested is AA / TT, the cotton germplasm to be tested has a high salt tolerance; if the allele type of the cotton germplasm to be tested is AG / TC or GG / CC, the cotton germplasm to be tested has a low salt tolerance.

8. The use according to claim 7, characterized in that If the cotton germplasm to be tested has an allele type of AA / TT, the relative survival rate of the cotton germplasm to be tested under salt stress is higher than the relative survival rate of the germplasm with a genotype of AG / TC or a genotype of GG / CC.

9. A KASP detection kit for predicting the salt tolerance of cotton germplasm, comprising KASP detection primers; characterized in that: The KASP detection primer is the KASP detection primer according to claim 4.

10. Use of the KASP detection kit according to claim 9 in predicting the salt tolerance of cotton germplasm.

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