Genomic-Assisted Haplotype Analysis and Trait Discovery in Soybean

Advances in next-generation sequencing generate large-scale genomic resources and enable the development of sustainable high-yield varieties that persist under biotic and abiotic stresses. The analysis of whole genome re-sequence (WGRS) data using association mapping can provide better understanding of the links with the observed phenotypic changes. In the present study, WGRS of 106 diverse soybean (cultivated, landraces and wild) germplasm collection selected for major traits including protein, soybean cyst nematode (SCN) and abiotic stress (salinity) was conducted. The genome wide association study of protein, SCN and salt-tolerance traits resulted in discovery of novel alleles and haplotypes. The major haplotype blocks were further investigated and resulted explanatory allelic variants (SNP, CNV and structural variants) within QTL and GWA loci. The genomic-assisted haplotype analysis offers an opportunity to circumvent some of the problems associated with classical mapping while increasing the efficiency of selection and crossing design. Genomic information from this study provided a valuable resource for trait dissection and facilitated genetic maker discovery that will accelerate marker-assisted selection breeding programs.