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Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean

Bhat, J.A., Karikari, B., Adeboye, K.A., Ganie, S.A., Barmukh, R., Hu, D., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Yu, D. (2022) Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean. Theoretical and Applied Genetics, 135 . pp. 2407-2422.

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Genetic variation is pivotal for crop improvement. Natural populations are precious genetic resources. However, efficient strategies for the targeted utilization of these resources for quantitative traits, such as plant height (PH), are scarce. Being an important agronomic trait associated with soybean yield and quality, it is imperative to unravel the genetic mechanisms underlying PH in soybean. Here, a genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with PH in a natural population of 211 cultivated soybeans, which was genotyped with NJAU 355 K Soy SNP Array and evaluated across six environments. A total of 128 SNPs distributed across 17 chromosomes were found to be significantly associated with PH across six environments and a combined environment. Three significant SNPs were consistently identified in at least three environments on Chr.02 (AX-93958260), Chr.17 (AX-94154834), and Chr.19 (AX-93897200). Genomic regions of ~ 130 kb flanking these three consistent SNPs were considered as stable QTLs, which included 169 genes. Of these, 22 genes (including Dt1) were prioritized and defined as putative candidates controlling PH. The genomic region flanking 12 most significant SNPs was in strong linkage disequilibrium (LD). These SNPs formed a single haplotype block containing five haplotypes for PH, namely Hap-A, Hap-B, Hap-C, Hap-D, and Hap-E. Deployment of such superior haplotypes in breeding programs will enable development of improved soybean varieties with desirable plant height.

Item Type: Journal Article
Murdoch Affiliation(s): Centre for Crop and Food Innovation
Western Australian State Agricultural Biotechnology Centre
Publisher: Springer Verlag
Copyright: © 2022 The Authors.
United Nations SDGs: Goal 12: Responsible Consumption and Production
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