Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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Large-scale genome-wide association study reveals that drought-induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Theoretical and Applied Genetics ◽

10.1007/s00122-020-03665-2 ◽

2020 ◽

Vol 133 (11) ◽

pp. 3201-3215

Author(s):

Xuemin Wang ◽

Emma Mace ◽

Yongfu Tao ◽

Alan Cruickshank ◽

Colleen Hunt ◽

...

Keyword(s):

Association Study ◽

Plant Height ◽

Large Scale ◽

Genome Wide Association Study ◽

Grain Sorghum ◽

Genome Wide Association ◽

Genome Wide

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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 ◽

10.1186/s12284-019-0349-z ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 14

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.

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Genome-Wide Association Study Identifies Candidate Genes That Affect Plant Height in Chinese Elite Maize (Zea mays L.) Inbred Lines

PLoS ONE ◽

10.1371/journal.pone.0029229 ◽

2011 ◽

Vol 6 (12) ◽

pp. e29229 ◽

Cited By ~ 71

Author(s):

Jianfeng Weng ◽

Chuanxiao Xie ◽

Zhuanfang Hao ◽

Jianjun Wang ◽

Changlin Liu ◽

...

Keyword(s):

Zea Mays ◽

Association Study ◽

Candidate Genes ◽

Plant Height ◽

Genome Wide Association Study ◽

Zea Mays L ◽

Inbred Lines ◽

Genome Wide Association ◽

Genome Wide

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

Genetica ◽

10.1007/s10709-016-9932-z ◽

2016 ◽

Vol 144 (6) ◽

pp. 651-664 ◽

Cited By ~ 14

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

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

Nature Genetics ◽

10.1038/ng.1018 ◽

2011 ◽

Vol 44 (1) ◽

pp. 32-39 ◽

Cited By ~ 580

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

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Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

10.1101/865667 ◽

2019 ◽

Author(s):

Xuemin Wang ◽

Emma Mace ◽

Yongfu Tao ◽

Alan Cruickshank ◽

Colleen Hunt ◽

...

Keyword(s):

Association Study ◽

Plant Height ◽

Leaf Senescence ◽

Genome Wide Association Study ◽

Grain Sorghum ◽

Genome Wide Association ◽

Lodging Resistance ◽

Stay Green ◽

Genome Wide ◽

Selection For

AbstractSorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTL, the majority of which showed a significant association with leaf senescence and plant height (72% and 71% respectively). Only 16 lodging QTL were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTL indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se, which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots.Key messageWe detected 213 lodging QTL and demonstrated that drought induced stem lodging in grain sorghum is substantially associated with stay-green and plant height, suggesting a critical role of carbon remobilisation.

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