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. 2016 Jun 29;11(6):e0158142.
doi: 10.1371/journal.pone.0158142. eCollection 2016.

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

Xiaoge Wang  1 , Xuke Lu  1 , Junjuan Wang  1 , Delong Wang  1 , Zujun Yin  1 , Weili Fan  1 , Shuai Wang  1 , Wuwei Ye  1
Affiliations

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

Xiaoge Wang et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Salt tolerance index and numbers of SNPv in different varieties.
Fig 2
Fig 2. Distribution on the chromosomes of SNPv of eight varieties and chip SNP.
1~4: the salt sensitive varieties: Hengmian3, GK50, Xinyan96-48, ZhongS9612; 5~8: the salt tolerant varieties: CRI35, Zhong9807, CRI 44, Kanghuangwei164; 9: Illumina Cotton SNP 70K Chip.
Fig 3
Fig 3. GO analysis of genes containing chip-SNP, SS-SNPv and ST-SNPv.
Fig 4
Fig 4. Numbers of methylation reads in SNPv rich region.
Fig 5
Fig 5
Locations (a) and distribution (b) of SNPr in different chromosomes. The boxes in Fig 5A are the rich region of SNPr.
Fig 6
Fig 6. GO analysis of genes neighboring SNPr rich regions.
Fig 7
Fig 7. The possible relation of ROS, DNA methylation, SNPv and SNPr.
See this image and copyright information in PMC

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