scholarly journals Genome-Wide Association Study Identifies Loci for Salt Tolerance during Germination in Autotetraploid Alfalfa (Medicago sativa L.) Using Genotyping-by-Sequencing

2016 ◽  
Vol 7 ◽  
Author(s):  
Long-Xi Yu ◽  
Xinchun Liu ◽  
William Boge ◽  
Xiang-Ping Liu
Keyword(s):  
Salt Tolerance ◽  
Medicago Sativa ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Medicago Sativa L

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 Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

2021 ◽  
Author(s):  
Dong Cao ◽  
Dongxia Wang ◽  
Shiming Li ◽  
Yun Li ◽  
Ming Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Energy Crop ◽  
Hexaploid Triticale ◽  
Genome Wide ◽  
Genetic Mechanisms

Abstract Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

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
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