Abstract
Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r2 value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants.
Highlights
It has been estimated that soil salinity has affected 80 million hectares of the world’s cultivated land [1]
Seven salt tolerance-related traits were measured to explore the level of tolerance: germination rate, relative electrical conductivity, malondialdehyde (MDA) content, fresh weight (FW), shoot length/seedling length (SL), relative water content (RWC), and chlorophyll content
The coefficient of variation (CV%) of all the traits ranged from 7.18% (RWC_150) to 51.85%
Summary
It has been estimated that soil salinity has affected 80 million hectares of the world’s cultivated land [1]. Millions of hectares of land are too saline to produce economically valuable crop yields, and this trend is on the rise every year, making the land nonproductive [2]. The problem of soil salinization is worsening in countries, such as the USA, China, Australia, Hungary and is threatening to become more intense in North and East African countries, and Middle Eastern and East Asian countries. Salt-affected areas in China constitute 4.88% of the country’s total land area, which equates to 3.6 × 107 ha of land nationwide [3]. Excessive salinity of the soil can cause ion toxicity, osmotic stress, water, and nutrient scarcity and, promptly decrease crop growth due to reduced photosynthesis [4].
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