Bhat, J A and Adeboye, K A and Ganie, S A and Barmukh, R and Hu, D and Varshney, R K and Yu, D (2022) Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.). Frontiers in Genetics (TSI), 13. 01-19. ISSN 1664-8021
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Abstract
Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production and productivity. Here, 211 soybean genotypes were evaluated across six environments for four yield-related traits, including seed yield per plant (SYP), number of pods per plant number of seeds per plant and 100-seed weight (HSW). Genome-wide association study (GWAS) and genomic prediction (GP) analyses were performed using 12,617 single nucleotide polymorphism markers from NJAU 355K SoySNP Array. A total of 57 SNPs were significantly associated with four traits across six environments and a combined environment using five Genome-wide association study models. Out of these, six significant SNPs were consistently identified in more than three environments using multiple GWAS models. The genomic regions (±670 kb) flanking these six consistent SNPs were considered stable QTL regions. Gene annotation and in silico expression analysis revealed 15 putative genes underlying the stable QTLs that might regulate soybean yield. Haplotype analysis using six significant SNPs revealed various allelic combinations regulating diverse phenotypes for the studied traits. Furthermore, the GP analysis revealed that accurate breeding values for the studied soybean traits is attainable at an earlier generation. Our study paved the way for increasing soybean yield performance within a short breeding cycle.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | haplotype-based breeding, GWAS, legumes, seed yield, candidate genes, crop improvement |
| Subjects: | Others > Crop Improvement Others > Crop Yield Others > Legume Crops |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 05 Dec 2023 04:51 |
| Last Modified: | 05 Dec 2023 04:51 |
| URI: | http://oar.icrisat.org/id/eprint/12323 |
| Official URL: | https://www.frontiersin.org/articles/10.3389/fgene... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | This work was supported in part by National Natural Science Foundation of China (No. 32090065, and Ministry of Science and Technology (No. 2017YFE0111000). JB also thank International Genome Center, Jiangsu University for their research assistance and facilities provided. RKV is thankful to Food Futures Institute, Murdoch University for supporting this research in part. |
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