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.

Spanish Melon Landraces: Revealing Useful Diversity by Genomic, Morphological, and Metabolomic Analysis

“…These genes (SAUR) are part of an important family related to auxin signal transduction, usually employed as marker genes [28]. Recent analysis have identified cotton, an SNP locus (Gh_D08G1308) associated to plant salt tolerance which resulted to belong to SAUR-like auxin-responsive protein family [29]. Tzuri et al [30] found that SNPs CmOr (MELO3C005449) related to fruit quality and responsible for fruit flesh colour was not detected in our sample.…”

Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)

“…In-depth phenotyping is a key part of a GWAS procedure [ 29 ]. Herein, a total of 25 seedling-linked traits were evaluated that have been previously employed for QTL mapping of salinity tolerance at the seedling stage in cotton, rice, and maize [ 7 , 9 , 10 ]. Similar to our observations, previous reports have also shown that salinity negatively affects seedling-related traits [ 29 – 32 ].…”

“…The second biggest abiotic factor affecting agricultural productivity worldwide is salinity/salt stress, which damages numerous physiological, biochemical, and molecular processes [ 5 , 6 ]. Salinity is one of the important abiotic stresses that can seriously disrupt wheat production [ 7 ]. Generally speaking, when neutral soluble salts (chlorine, calcium, sodium, etc.)…”

“…QTL mapping has been used for detecting genes/genomic regions linked to salt tolerance traits, such as bio-physiological (e.g., Na + /K + ratio) and agronomical traits (e.g., grain yield) in the salt-stressed wheat fields [ 7 , 15 , 19 ]. Importantly, these endeavors have relied on mapping populations of small size and a low number of SSRs markers, reflecting a limited resolution of QTLs, which cannot be reliably adopted in the marker-assisted selection.…”

“…Interestingly, ZmCLCg was found as a chloride transport in maize. By using 18,430 polymorphic SNPs on 149 cotton genotypes, Zheng et al [ 7 ] found six seedling salt tolerance genes, including Gh_D08G1309 , Gh_D08G1308 , Gh_A01G0908 , Gh_A01G0906 , Gh_D01G0945 , and Gh _D01G0943 , which were found to be responsible for cell amplification, auxin response, N-glycosylation, transmembrane transport, osmotic pressure balance, sucrose synthesis, and intracellular transport, respectively. Thabet et al [ 28 ] evaluated 121 barley accessions for seedling salt tolerance by using 9 K SNPs and revealed around 1500 candidate genes, which encode potassium channels mapped on Ch.1H.…”