Mining and Analysis of SNP in Response to Salinity Stress in Upland Cotton (Gossypium hirsutum L.).

Xiaoge Wang,Weili Fan,Wuwei Ye,Shuai Wang,Xuke Lu,Junjuan Wang,Zujun Yin,Delong Wang,Tapan Kumar Mondal

doi:10.1371/journal.pone.0158142

Xiaoge Wang, Weili Fan + Show 7 more

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https://doi.org/10.1371/journal.pone.0158142

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Abstract

Salinity stress is a major abiotic factor that affects crop output, and as a pioneer crop in saline and alkaline land, salt tolerance study of cotton is particularly important. In our experiment, four salt-tolerance varieties with different salt tolerance indexes including CRI35 (65.04%), Kanghuanwei164 (56.19%), Zhong9807 (55.20%) and CRI44 (50.50%), as well as four salt-sensitive cotton varieties including Hengmian3 (48.21%), GK50 (40.20%), Xinyan96-48 (34.90%), ZhongS9612 (24.80%) were used as the materials. These materials were divided into salt-tolerant group (ST) and salt-sensitive group (SS). Illumina Cotton SNP 70K Chip was used to detect SNP in different cotton varieties. SNPv (SNP variation of the same seedling pre- and after- salt stress) in different varieties were screened; polymorphic SNP and SNPr (SNP related to salt tolerance) were obtained. Annotation and analysis of these SNPs showed that (1) the induction efficiency of salinity stress on SNPv of cotton materials with different salt tolerance index was different, in which the induction efficiency on salt-sensitive materials was significantly higher than that on salt-tolerant materials. The induction of salt stress on SNPv was obviously biased. (2) SNPv induced by salt stress may be related to the methylation changes under salt stress. (3) SNPr may influence salt tolerance of plants by affecting the expression of salt-tolerance related genes.

Highlights

Salinity stress is a major abiotic factor that affects crop output [1], and exploring the mechanism of salt tolerance of plants is of great importance for improving their salt tolerance and creating salt tolerant germplasms
A small portion of non-coding region SNP is located in gene control region, which is known as regulatory SNP
The results showed that the number of SNPv in salt-tolerant materials was generally lower than that of salt-sensitive materials

Summary

Introduction

Salinity stress is a major abiotic factor that affects crop output [1], and exploring the mechanism of salt tolerance of plants is of great importance for improving their salt tolerance and creating salt tolerant germplasms. A small portion of non-coding region SNP is located in gene control region, which is known as regulatory SNP (rSNP) According to their different effects on genetic traits, cSNP can be divided into two types: one is synonymous cSNP, which will not change the amino acid sequence of the protein being translated; another is non-synonymous cSNP, which refers to that changes in nucleotide sequence will cause the changes of downstream protein sequence. According to the central dogma, genetic information within the gene is transcribed to mRNA, translated and transmitted to the polypeptide chain; after folding and assembly, polypeptide chain forms protein and play its functions In this process, mutation of fSNP at certain key locus may cause changes in single chain folding [6], or lead to changes in the downstream amino acid sequence and nature, or make some restriction loci disappear or reappear, or change the gene structure and regulatory loci, and affect the phenotype. Researches have shown that SNP can contribute to a phenotype directly or be associated with a phenotype [8]

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