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Molecular tools for detecting Pdh1 can improve soybean breeding efficiency by reducing yield losses due to pod shatter

Miranda, Carrie, Culp, Carolyn, Škrabišová, Mária, Joshi, Trupti, Belzile, François, Grant, David M., Bilyeu, Kristin
Molecular breeding 2019 v.39 no.2 pp. 27
Glycine max, USDA National Plant Germplasm System, alleles, breeding programs, chromosomes, computer software, genetic markers, genome-wide association study, germplasm, germplasm conservation, phenotype, plant breeding, reproductive performance, seed dispersal, soybeans, Ghana
Pod shattering is an ancestral trait that promotes seed dispersal; however, shattering can have substantial yield losses in cultivated soybean. During the improvement process, American soybean breeders virtually eliminated the shatter phenotype for released varieties, but in other countries, such as Ghana, shatter persists. The objective of our research was to find a molecular tool to implicate genetic shatter susceptibility, validate its usefulness, and apply this knowledge to identify shattering potential in parental lines. Previous research revealed the gene Pdh1 on chromosome 16 plays a crucial role in determining the shatter phenotype. A perfect molecular marker assay was developed to detect alleles of the Pdh1 gene. A genome-wide association study (GWAS) was performed using the Pdh1 allele status as a phenotype and identified a highly associated marker in the SoySNP50K array. Soybean accessions from the National Plant Germplasm System (GRIN-NPGS) with shatter score and SoySNP50K data were evaluated to determine the impact of the predicted Pdh1 alleles on early and late pod shattering. An online tool was developed to enable researchers to query the GRIN collection for the predicted Pdh1 allele status. Lines from an African soybean germplasm collection were analyzed, and it was determined that 22.5% of lines had the shatter-susceptible alleles of Pdh1; two of seven Ghanaian released soybean varieties had the shatter-susceptible alleles of Pdh1. Soybean breeding programs that access germplasm from the GRIN or the African collection can utilize these resources to eliminate the Pdh1 effects on pod shatter and thus improve yield potential.