Mining And Analysis Of SNP Responsed To Salt Stress

Salinity stress is a vital abiotic factor, which influences the growth of cotton. It is of great significance for improving salt tolerance of cotton and promoting agricultural development to study salt tolerance of cotton. Researches had shown that single nucleotide polymorphism(SNP) played an important role on the resistance of plants. With the similarity of different resistance in physiological response and resistance mechanism, there may be some SNPs playing an important role in salt tolerance.We chose four salt-tolerant materials(CRI35, Kanghuangwei164, Zhong9807, CRI44) and four salt-sensitive materials(Hengmian3, GK50, Xinyan96-48, ZhongS9612) as materials. After treatment with 0.4% NaCl, the control and salt–treated materials were tested with Illumina Cotton 70 k SNP array.SNP variations(SNPv) were obtained by comparing SNP genotype of control with that of the salt-treated. And with comparing SNP genotype of different materials, we obtained polymorphic SNPs and salt-tolerant relevant candidate SNPs. Analysis of SNPv and candidate SNPs related to salt tolerance were performed with the profiles of MeDIP-Seq and transcriptome. The main results were below:(1) SNPv could be induced by salt stress, and 4971 polymorphic SNPs and1282 salt-tolerant relevant candidate SNPs in total were found. SNPv locus were those SNPs that SNP genotype of the same plant is different pre- and after- salt-treated with three biological replications. The results showed that the number of SNPv in the four salt tolerant materials were 892(CRI35), 770(Kanghuangwei164),782(Zhong9807), 891(CRI44) and the number of SNPv in four salt sensitive materials were 2546(Hengmian3), 2857(GK50), 2541(Xinyan96-48), 2838(ZhongS9612). 4971 polymorphic SNPs were detected by comparing SNP of 8 materials, and 1282 of them were different between salt-tolerant group and salt-sensitive group.(2) SNPv induced by salt stress was analyzed. SNPv may be correlated with the salt-tolerance and genetic background of materials and DNA methylation. Comparing the SNPv number of different materials, we found the SNPv number of salt tolerance materials was generally lower than that of salt sensitive materials, and negatively correlated with the salt tolerance index. GO analysis of genes including SNPv and statistics of SNPv on chromosome in different materials showed that SNPv induced by salt stress was not random, and these SNPv relatively enriched in some specific chromosomes or GO items, which may be due to the different genetic background and salt-resistance. Statistics of SNPv types indicated that the main SNPv types were G/A and C/T, similar to the mutations resulted from the CpG cytosine methylation or demethylation. And the change of methylation in the SNPv enrichment region had been observed. So, we inferred SNPv may be associated with DNA methylation.(3) 105 salt-tolerant relevant SNPs were screened, combined with differentially expressed genes(DEGs) induced by salt stress. 12556 DEGs were screened by analyzing of transcriptome data in our laboratory. Based on the relevant candidate SNPs, 105 salt-tolerant relevant SNPs were obtained; these SNPs were in or near(within 2000 bp upstream) 88 DEGs.In the study, SNPs induced by salt stress and mining of SNP responded to salt stress were analyzed,and the results could provide theoretical support for the screen of SNP markers and the function analysis of these SNPs.