Dataset Information

A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton.

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.

SUBMITTER: Yasir M

PROVIDER: S-EPMC6826536 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton.

Yasir Muhammad M He Shoupu S Sun Gaofei G Geng Xiaoli X Pan Zhaoe Z Gong Wenfang W Jia Yinhua Y Du Xiongming X

Genes 20191021 10

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 (<i>Gossypium hirsutum</i> L.) comprising of 419 acc ...[more]

PMID: 31640174

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Project description:BACKGROUND: Cotton is the world's primary fiber crop and is a major agricultural commodity in over 30 countries. Like many other global commodities, sustainable cotton production is challenged by restricted natural resources. In response to the anticipated increase of agricultural water demand, a major research direction involves developing crops that use less water or that use water more efficiently. In this study, our objective was to identify differentially expressed genes in response to water deficit stress in cotton. A global expression analysis using cDNA-Amplified Fragment Length Polymorphism was conducted to compare root and leaf gene expression profiles from a putative drought resistant cotton cultivar grown under water deficit stressed and well watered field conditions. RESULTS: We identified a total of 519 differentially expressed transcript derived fragments. Of these, 147 transcript derived fragment sequences were functionally annotated according to their gene ontology. Nearly 70 percent of transcript derived fragments belonged to four major categories: 1) unclassified, 2) stress/defense, 3) metabolism, and 4) gene regulation. We found heat shock protein-related and reactive oxygen species-related transcript derived fragments to be among the major parts of functional pathways induced by water deficit stress. Also, twelve novel transcripts were identified as both water deficit responsive and cotton specific. A subset of differentially expressed transcript derived fragments was verified using reverse transcription-polymerase chain reaction. Differential expression analysis also identified five pairs of duplicated transcript derived fragments in which four pairs responded differentially between each of their two homologues under water deficit stress. CONCLUSIONS: In this study, we detected differentially expressed transcript derived fragments from water deficit stressed root and leaf tissues in tetraploid cotton and provided their gene ontology, functional/biological distribution, and possible roles of gene duplication. This discovery demonstrates complex mechanisms involved with polyploid cotton's transcriptome response to naturally occurring field water deficit stress. The genes identified in this study will provide candidate targets to manipulate the water use characteristics of cotton at the molecular level.

Project description:Cadmium (Cd), a non-essential element for plant, is a ubiquitous and highly toxic heavy metal, seriously endangering agricultural production and human health. As a nonedible economic crop, cotton (Gossypium hirsutum L.) has great potential in remediation of Cd contaminated soil, but its underlying mechanism is still unknown. Melatonin (MT), as a plant growth regulator, is involved in alleviating Cd toxicity in some plants, but the molecular mechanisms of MT-mediated Cd detoxification in cotton are largely unknown. This study investigated the possible molecular mechanisms of the MT-mediated Cd detoxification in cotton seedlings by comparative transcriptomic and metabolomic analyses. The results showed that the cotton seedlings were dwarfed and the leaves were wilted and yellow under Cd stress. The application of 50 µmol L−1 MT significantly increased the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content under Cd stress, but 100 µmol L−1 MT significantly decreased SOD activity, while increased ascorbate peroxidase (APX) activity significantly. The addition of 100 μmol L−1 MT significantly increased Cd concentration in the shoots and roots under Cd stress. RNA-seq analysis showed that 5573, 7105, 7253, 25, 198, 9 up-regulated and 6644, 7192, 7404, 9, 59, 0 down-regulated differentially expressed genes (DEGs) were identified in the comparisons of CK vs T1, CK vs T2, CK vs T3, T1 vs T2, T1 vs T3 and T2 vs T3, respectively. It was revealed that MT promoted the expression of certain related genes under Cd stress, and the effect of 100 µmol L−1 MT was better. Moreover, UPLC-MS/MS widely targeted metabolites analyses showed that 195, 150, 150, 12, 24, 59 up-regulated and 16, 11, 23, 38, 127, 66 down-regulated differentially accumulated metabolites (DAMs) were changed in the CK vs T1, CK vs T2, CK vs T3, T1 vs T2, T1 vs T3 and T2 vs T3, respectively. It was revealed that MT induced the synthesis of alkaloids and flavonoids, and inhibited or reduced the synthesis of lipids, amino acids and their derivatives. The comprehensive analyses of transcriptomic and metabolic data showed that 33 DEGs and 4 DAMs, 46 DEGs and 16 DAMs, and 1 DEGs and 1 DAMs were dominantly involved in the pathways of valine, leucine and isoleucine degradation, ABC transporter, alpha-linolenic acid metabolism, respectively. It was revealed that there were three major mechanisms involved in MT-mediated Cd detoxification in cotton, including the enhancement of antioxidant capacity regulated by APX, flavonoids and alkaloids; accumulation of secondary metabolites related to Cd chelation, such as amino acids and derivatives; and regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the MT-mediated Cd stress response.

Project description:BackgroundDue to the influence of extreme weather, the environment in China's main cotton-producing areas is prone to drought stress conditions, which affect the growth and development of cotton and lead to a decrease in cotton yield.ResultsIn this study, 188 upland cotton germplasm resources were phenotyped for data of 8 traits (including 3 major yield traits) under drought conditions in three environments for two consecutive years. Correlation analysis revealed significant positive correlations between the three yield traits. Genetic analysis showed that the estimated heritability of the seed cotton index (SC) under drought conditions was the highest (80.81%), followed by that of boll weight (BW) (80.64%) and the lint cotton index (LC) (70.49%) With genome-wide association study (GWAS) analysis, a total of 75 quantitative trait loci (QTLs) were identified, including two highly credible new QTL hotspots. Three candidate genes (Gh_D09G064400, Gh_D10G261000 and Gh_D10G254000) located in the two new QTL hotspots, QTL51 and QTL55, were highly expressed in the early stage of fiber development and showed significant correlations with SC, LC and BW. The expression of three candidate genes in two extreme materials after drought stress was analyzed by qRT-PCR, and the expression of these two materials in fibers at 15, 20 and 25 DPA. The expression of these three candidate genes was significantly upregulated after drought stress and was significantly higher in drought-tolerant materials than in drought-sensitive materials. In addition, the expression levels of the three candidate genes were higher in the early stage of fiber development (15 DPA), and the expression levels in drought-tolerant germplasm were higher than those in drought-sensitive germplasm. These three candidate genes may play an important role in determining cotton yield under drought conditions.ConclusionsThis study is helpful for understanding the regulatory genes affecting cotton yield under drought conditions and provides germplasm and candidate gene resources for breeding high-yield cotton varieties under these conditions.

Dataset Information

A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton.

Publications

A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton.

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