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.
Highlights
Soil salinization is one of the main abiotic stress factors affecting agricultural production worldwide, and salt stress has significant impacts on plant growth and development.Under salt treatment, seed germination, root length, plant height and fruit development are significantly inhibited [1]
Total of 27 single-nucleotide polymorphism (SNP) sites related to salt tolerance traits were detected (Table 2): 3 SNP sites related to 7d Radicle length; 10 SNP sites related to 7d Radicle length drop rate; 3 SNP
A total of 18,430 polymorphic SNP markers were developed and screened from natural populations using gene chip technology. These SNP markers were used to analyse the structure of the population to obtain the Q-matrix, and the salt tolerance traits and salt tolerance index data were combined to conduct a genome-wide association analysis
Summary
Soil salinization is one of the main abiotic stress factors affecting agricultural production worldwide, and salt stress has significant impacts on plant growth and development. GWAS was conducted for salt tolerance at the seedling stage using 419 upland cotton accessions and 17,264 SNPs [8]. The chip was utilized to perform a GWAS analysis of 288 upland cotton materials and found that eight SNPs were significantly associated with three salt tolerance traits. A GWAS was performed to identify marker-trait associations and 713 upland cotton accessions were phenotyped under salt stress and genotyped by the Illumina Infinium CottonSNP63K array [10]. 149 elite Gossypium hirsutum cultivar accessions (lines) were used as materials, and 70K SNP chips were used to screen SNP loci and perform genome-wide association analysis on the traits related to salt tolerance at the seedling stage to find significant association sites related to salt tolerance. This study provides a reference and basis for further theoretical studies, such as the isolation of related genes and molecular marker-assisted selection of cotton salt tolerance
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