Genome‐wide association study identifies QTLs conferring salt tolerance in rice

2019 ◽  
Vol 139 (1) ◽  
pp. 73-82 ◽  
Author(s):  
Hongzhou An ◽  
Kai Liu ◽  
Baoxiang Wang ◽  
Yunlu Tian ◽  
Yuwei Ge ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

2018 ◽  
Vol 19 (10) ◽  
pp. 3145 ◽  
Author(s):  
Jie Yu ◽  
Weiguo Zhao ◽  
Wei Tong ◽  
Qiang He ◽  
Min-Young Yoon ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Genome Wide Association ◽  
Phenotypic Correlation ◽  
Genome Wide ◽  
A Genome ◽  
Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

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

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 829 ◽  
Author(s):  
Muhammad Yasir ◽  
Shoupu He ◽  
Gaofei Sun ◽  
Xiaoli Geng ◽  
Zhaoe Pan ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Stress Tolerance ◽  
Salinity Stress ◽  
Upland Cotton ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Salinity Stress Tolerance

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.

scholarly journals Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Chen Liu ◽  
Kai Chen ◽  
Xiuqin Zhao ◽  
Xiaoqian Wang ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Field Conditions ◽  
Genome Wide Association ◽  
Saline Stress ◽  
Rice Breeding ◽  
Genome Wide

Abstract Background Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

scholarly journals Genome‐wide association study dissects the genetic bases of salt tolerance in maize seedlings

2019 ◽  
Vol 61 (6) ◽  
pp. 658-674 ◽  
Author(s):  
Xi Luo ◽  
Bingcai Wang ◽  
Shan Gao ◽  
Fei Zhang ◽  
William Terzaghi ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Maize Seedlings ◽  
Genome Wide ◽  
Genetic Bases

scholarly journals Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 559
Author(s):  
Ashutosh Kumar Yadav ◽  
Aruna Kumar ◽  
Nitasha Grover ◽  
Ranjith Kumar Ellur ◽  
Haritha Bollinedi ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide ◽  
Trait Associations

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

scholarly journals Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

2020 ◽  
Author(s):  
Pan Hu ◽  
Qi Zheng ◽  
Qiaoling Luo ◽  
Wan Teng ◽  
Hongwei Li ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Genome Wide Association Study ◽  
High Salinity ◽  
Wheat Yield ◽  
Snp Array ◽  
Soil Salinization ◽  
Genome Wide Association ◽  
Salt Tolerant ◽  
Genome Wide

Abstract Background Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield. Result In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTL were significantly associated with traits under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14–50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding. Conclusion Utilizing a Wheat660K SNPs chip, QTL for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

scholarly journals Genome-wide association study of salt tolerance at the seed germination stage in rice

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Yingyao Shi ◽  
Lingling Gao ◽  
Zhichao Wu ◽  
Xiaojing Zhang ◽  
Mingming Wang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Seed Germination ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Germination Stage
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