Genome-wide association study of grain yield and related traits using a collection of advanced indica rice breeding lines for irrigated ecosystems

2016 ◽  
Vol 193 ◽  
pp. 70-86 ◽  
Author(s):  
Shanshan Liang ◽  
Liwen Wu ◽  
Guangjun Ren ◽  
Xiangqian Zhao ◽  
Meixue Zhou ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Indica Rice ◽  
Genome Wide Association ◽  
Rice Breeding ◽  
Breeding Lines ◽  
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

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 Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs

2017 ◽  
Vol 107 (1) ◽  
pp. 100-108 ◽  
Author(s):  
R. R. Burlakoti ◽  
S. Gyawali ◽  
S. Chao ◽  
K. P. Smith ◽  
R. D. Horsley ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
The United States ◽  
Genome Wide Association ◽  
Net Blotch ◽  
Upper Midwest ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Barley Breeding ◽  
Genome Wide

Pyrenophora teres f. maculata, the causal agent of spot form of net blotch (SFNB), is an emerging pathogen of barley in the United States and Australia. Compared with net form of net blotch (NFNB), less is known in the U.S. Upper Midwest barley breeding programs about host resistance and quantitative trait loci (QTL) associated with SFNB in breeding lines. The main objective of this study was to identify QTL associated with SFNB resistance in the Upper Midwest two-rowed and six-rowed barley breeding programs using a genome-wide association study approach. A total of 376 breeding lines of barley were evaluated for SFNB resistance at the seedling stage in the greenhouse in Fargo in 2009. The lines were genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Phenotypic evaluation showed a wide range of variability among populations from the four breeding programs and the two barley-row types. The two-rowed barley lines were more susceptible to SFNB than the six-rowed lines. Continuous distributions of SFNB severity indicate the quantitative nature of SFNB resistance. The mixed linear model (MLM) analysis, which included both population structure and kinship matrices, was used to identify significant SNP-SFNB associations. Principal component analysis was used to control false marker-trait association. The linkage disequilibrium (LD) estimates varied among chromosomes (10 to 20 cM). The MLM analysis identified 10 potential QTL in barley: SFNB-2H-8-10, SFNB-2H-38.03, SFNB-3H-58.64, SFNB-3H-78.53, SFNB-3H-91.88, SFNB-3H-117.1, SFNB-5H-155.3, SFNB-6H-5.4, SFNB-6H-33.74, and SFNB-7H-34.82. Among them, four QTL (SFNB-2H-8-10, SFNB-2H-38.03 SFNB-3H-78.53, and SFNB-3H-117.1) have not previously been published. Identification of SFNB resistant lines and QTL associated with SFNB resistance in this study will be useful in the development of barley genotypes with better SFNB resistance.

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 Genome Wide Association Study of Seedling and Adult Plant Leaf Rust Resistance in Elite Spring Wheat Breeding Lines

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0148671 ◽  
Author(s):  
Liangliang Gao ◽  
M. Kathryn Turner ◽  
Shiaoman Chao ◽  
James Kolmer ◽  
James A. Anderson
Keyword(s):  
Association Study ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Adult Plant ◽  
Breeding Lines ◽  
Genome Wide

scholarly journals Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Niu ◽  
Tianxiao Chen ◽  
Chunchao Wang ◽  
Kai Chen ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Candidate Genes ◽  
Grain Quality ◽  
Genome Wide Association Study ◽  
Grain Shape ◽  
Grain Weight ◽  
Genome Wide Association ◽  
Rice Grain ◽  
Genome Wide

Abstract Background Grain weight and grain shape are important agronomic traits that affect the grain yield potential and grain quality of rice. Both grain weight and grain shape are controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates the discovery of agriculturally important genetic variants and germplasm resources for grain weight and grain shape. Results Abundant natural variations and distinct phenotic differentiation among the subgroups in grain weight and grain shape were observed in a large population of 2,453 accessions from the 3 K RGP. A total of 21 stable quantitative trait nucleotides (QTNs) for the four traits were consistently identified in at least two of 3-year trials by genome-wide association study (GWAS), including six new QTNs (qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1) for grain weight and grain shape. We further predicted seven candidate genes (Os03g0186600, Os09g0544400, Os11g0163600, Os04g0580700, Os10g0399700, Os10g0400100 and Os01g0171000) for the six new QTNs by high-density association and gene-based haplotype analyses. The favorable haplotypes of the seven candidate genes and five previously cloned genes in elite accessions with high TGW and RLW are also provided. Conclusions Our results deepen the understanding of the genetic basis of grain weight and grain shape in rice and provide valuable information for improving rice grain yield and grain quality through molecular breeding.

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