Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

2011 ◽  
Vol 44 (1) ◽  
pp. 32-39 ◽  
Author(s):  
Xuehui Huang ◽  
Yan Zhao ◽  
Xinghua Wei ◽  
Canyang Li ◽  
Ahong Wang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Yield Traits ◽  
Rice Germplasm ◽  
Genome Wide

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.

Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Genetica ◽  
2016 ◽  
Vol 144 (6) ◽  
pp. 651-664 ◽  
Author(s):  
Gabriel Feresin Pantalião ◽  
Marcelo Narciso ◽  
Cléber Guimarães ◽  
Adriano Castro ◽  
José Manoel Colombari ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Water Deficit ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0145577 ◽  
Author(s):  
Xianjin Qiu ◽  
Yunlong Pang ◽  
Zhihua Yuan ◽  
Danying Xing ◽  
Jianlong Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Indica Rice ◽  
Genome Wide Association ◽  
Milling Quality ◽  
Rice Germplasm ◽  
Genome Wide

scholarly journals Genome-wide association study of flowering time reveals complex genetic heterogeneity and epistatic interactions in rice

2020 ◽  
Author(s):  
Chang Liu ◽  
Yuan Tu ◽  
Shiyu Liao ◽  
Xiangkui Fu ◽  
Xingming Lian ◽  
...  
Keyword(s):  
Association Study ◽  
Flowering Time ◽  
Genetic Heterogeneity ◽  
Mixed Models ◽  
Genome Wide Association Study ◽  
Heading Date ◽  
Genome Wide Association ◽  
Epistatic Interactions ◽  
Genome Wide ◽  
Wide Range

AbstractSince domestication, rice has cultivated in a wide range of latitudes with different day lengths. Selection of diverse natural variations in heading date and photoperiod sensitivity is critical for adaptation of rice to different geographical environments. To unravel the genetic architecture underlying natural variation of rice flowering time, we conducted a genome wide association study (GWAS) using several association analysis strategies with a diverse worldwide collection of 529 O. sativa accessions. Heading date was investigated in three environments under long-day or short-day conditions, and photosensitivity was evaluated. By dividing the whole association panel into subpopulations and performing GWAS with both linear mixed models and multi-locus mixed-models, we revealed hundreds of significant loci harboring novel candidate genes as well as most of the known flowering time genes. In total, 127 hotspots were detected in at least two GWAS. Universal genetic heterogeneity was found across subpopulations. We further detected abundant interactions between GWAS loci, especially in indica. Functional gene families were revealed from enrichment analysis of the 127 hotspots. The results demonstrated a rich of genetic interactions in rice flowering time genes and such epistatic interactions contributed to the large portions of missing heritability in GWAS. It suggests the increased complexity of genetic heterogeneity might discount the power of increasing the sample sizes in GWAS.

scholarly journals Genome-wide association study for grain yield and related traits in elite wheat varieties and advanced lines using SNP markers

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0188662 ◽  
Author(s):  
Sheng-Xing Wang ◽  
Yu-Lei Zhu ◽  
De-Xin Zhang ◽  
Hui Shao ◽  
Peng Liu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Wheat Varieties ◽  
Genome Wide

scholarly journals Quantile regression for genome-wide association study of flowering time-related traits in common bean

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0190303 ◽  
Author(s):  
Moysés Nascimento ◽  
Ana Carolina Campana Nascimento ◽  
Fabyano Fonseca e Silva ◽  
Leiri Daiane Barili ◽  
Naine Martins do Vale ◽  
...  
Keyword(s):  
Quantile Regression ◽  
Association Study ◽  
Common Bean ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide
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