scholarly journals Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

2019 ◽  
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Fengmin Wang ◽  
Yan Feng ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Candidate Genes ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide

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.

scholarly journals Genome-wide association study and genomic selection for yield and related traits in soybean

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255761
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Qijian Song ◽  
Jin Yuan ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci (E2, E4, and Dt1) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.

scholarly journals Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

2020 ◽  
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Fengmin Wang ◽  
Yan Feng ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Study ◽  
Genomic Selection ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide

Abstract BackgroundSoybean [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 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). Population structure was inferred using STRUCTURE 2.3.4, 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 (if no annotated genes found close the top one) 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 in soybean through marker-assisted selection (MAS) and GS in breeding programs. After validation, the candidate genes can be transferred to new cultivars using the linked SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e29229 ◽  
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

Genome‑wide association study dissects the genetic control of plant height and branch number in response to low‑phosphorus stress in Brassica napus

2021 ◽  
Author(s):  
Haijiang Liu ◽  
Jingchi Wang ◽  
Bingbing Zhang ◽  
Xinyu Yang ◽  
John P Hammond ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Study ◽  
Candidate Genes ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Branch Number ◽  
P Deficiency ◽  
Genome Wide ◽  
P Supply

Abstract Background and Aims Oilseed rape (Brassica napus) is one of the most important oil crops worldwide. Phosphorus (P) deficiency severely decreases the plant height (PH) and branch number (BN) of B. napus. However, the genetic bases controlling PH and BN in B. napus under P deficiency remain largely unknown. This study aims to mine candidate genes for PH and BN by genome-wide association study (GWAS) and determine low-P tolerance haplotypes. Methods An association panel of B. napus were grown in the field with a low P supply (P, 0 kg/ha) and a sufficient P supply (P, 40 kg/ha) across two years and PH and BN were investigated. More than five million single-nucleotide polymorphisms (SNPs) were used to conduct GWAS of PH and BN at two contrasting P supplies. Key Results A total of 2127 SNPs were strongly associated (P < 6.25×10 −07) with PH and BN at two P supplies. There was significant correlation between phenotypic variation and the number of favorable alleles of associated loci on chromosomes A10 (chrA10_821671) and C08 (chrC08_27999846), which will contribute to breeding improvement by aggregating these SNPs. BnaA10g09290D and BnaC08g26640D were identified to be associated with the chrA10_821671 and chrC08_27999846, respectively. Candidate gene association analysis and haplotype analysis showed that the inbred lines carrying ATT at 'BnaA10g09290Hap1' and AAT at 'BnaC08g26640Hap1' had higher PH than lines carrying other haplotype alleles at low P supply. Conclusion Our results demonstrate the power of GWAS in identifying genes of interest in B. napus and provided insights into the genetic basis of PH and BN at low P supply in B. napus. Candidate genes and favorable haplotypes may facilitate marker-based breeding efforts aimed at improving P use efficiency in B. napus.

scholarly journals A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0171105 ◽  
Author(s):  
Rodrigo Iván Contreras-Soto ◽  
Freddy Mora ◽  
Marco Antônio Rott de Oliveira ◽  
Wilson Higashi ◽  
Carlos Alberto Scapim ◽  
...  
Keyword(s):  
Association Study ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

2020 ◽  
Vol 13 (9) ◽  
pp. 1311-1327 ◽  
Author(s):  
Yunlong Pang ◽  
Chunxia Liu ◽  
Danfeng Wang ◽  
Paul St. Amand ◽  
Amy Bernardo ◽  
...  
Keyword(s):  
High Resolution ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Genomic Regions
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