Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage

Abstract

Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline-alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.

Keywords: GWAS; SNP; salt stress; salt tolerance gene; upland cotton.

Figure 1

Analysis of groups based on structure. (A) NJ tree; (B) A scatter plot of principal component analysis (PCA); (C) Estimated population structure.

Figure 2

Frequency distribution of plant material heterozygosity and distribution of labelled heterozygosity.

Figure 3

Heat map and cluster analysis based on the genetic relationship of 149 upland cotton varieties.

Figure 4

LD attenuation analysis of 149 cotton accessions.

Figure 5

Distribution of traits in the three environments. (A) 3d Germination potential index BLUP analyse; (B) 3d Radicle length index BLUP analyse; (C) 7d Radicle length index BLUP analyse; (D) 7d Radicle weight index BLUP analyse; (E) 7d Germination rate index BLUP analyse.

Figure 6

Manhattan and QQ charts of the 5 salt tolerance index traits. Manhattan graph: the abscissa represents the position of the chromosome, the ordinate represents the −log10(p) taking the negative logarithm based on 10, and the scattered dots (or lines) on the graph represent the corresponding data for each SNP site. The blue horizontal line is the threshold line. Scattered points (or lines) that exceed the threshold line are candidate sites. QQ chart: The abscissa represents the expected value, and the ordinate represents the observed value. The red line in the figure represents the 45° centre line, and the grey area is the 95% confidence interval of the scattered points in the figure.

Figure 7

Screening of candidate genes for salt tolerance. Manhattan diagram: The abscissa represent chromosomal positions, the ordinate represents the p-value (−log10 (p)) with a negative logarithm at 10, and the scatter (or lines) on the figure represent the −log10 (p) corresponding to each SNP site. Blue horizontal line represents the value corresponding to 0.01/marker quantity, and red horizontal line represents the value corresponding to 0.1/marker quantity. A scatter (or line) above the threshold line is the candidate site. QQ chart: The abscissa represents the expected value, and the ordinate represents the observed value. The red line in the figure represents the 45° centre line, and the grey area is the 95% confidence interval of the scattered points in the figure.

Figure 8

Transcriptome differentially expressed gene.

Figure 9

Gene sequence blast results.