Skip to main content
ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #352621

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

item MIRANDA, CARRIE - University Of Missouri
item CULP, CAROLYN - University Of Missouri
item SKRABISOVA, MARIA - Palacky University
item JOSHI, TRUPTI - University Of Missouri
item BELZILE, FRANCOIS - Laval University
item Grant, David
item Bilyeu, Kristin

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2019
Publication Date: 2/9/2019
Citation: Miranda, C., Culp, C., Skrabisova, M., Joshi, T., Belzile, F., Grant, D.M., Bilyeu, K.D. 2019. Molecular tools for detecting Pdh1 can improve soybean breeding efficiency by reducing yield losses due to pod shatter. Molecular Breeding. 39:27.

Interpretive Summary: Soybean can be an important economic food crop because of its low cost and high protein content. Soybean was initially domesticated in East Asia as a food crop, and diverse soybean accessions are currently curated by the USDA National Plant Germplasm System (NPGS). While the accessions in the NPGS collection are available for research and selection of beneficial traits, the lines also contain undesirable traits. In cultivars and landraces from Asia ,the pods often shatter early, resulting in a significant drop in available harvest. A shatter gene was recently identified on chromosome 16 that contributes to pod shatter. U.S. soybeans are fixed for shatter resistance, but the Asian accessions are susceptible to shattering, particularly landraces from Japan and Korea. The objective of this research was to develop tools and resources to improve soybean breeding for programs that need higher yield alongside the diversity and beneficial traits from Asian accessions. We used association analysis (GWAS) to find the most significantly associated SNP on chromosome 16 that contributes to pod shatter. We aim to provide resources to reduce the potential of shattering, allowing researchers to more efficiently breed for increased yield.

Technical Abstract: 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 over time 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 that underlies a major QTL for pod shatter on chromosome 16 and plays a crucial role in determining the shatter phenotype. We developed a perfect molecular marker assay to detect alleles of the Pdh1 gene. In addition, we performed a Genome Wide Association Analysis Study using the Pdh1 allele status as a phenotype and identified a highly associated marker in the SoySNP50K array. Soybean accessions from the GRIN National Plant Germplasm System (GRIN-NPGS) with recorded shatter scores and SoySNP50K data were evaluated to determine the impact of the predicted Pdh1 alleles on early and late pod shattering. We developed an online tool to enable researchers to query the GRIN collection for the predicted Pdh1allele status. We analyzed lines from an African soybean germplasm collection and determined ~20% of all 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 Pdh1effects on pod shatter and thus improve yield potential.