Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence

Authors: Tilhou, Neal; Kissing Kucek, Lisa; CARR, BRANDON - Natural Resources Conservation Service (NRCS, USDA); DOUGLAS, JOEL - Natural Resources Conservation Service (NRCS, USDA); ENGLERT, JOHN - Natural Resources Conservation Service (NRCS, USDA); ALI, SHAHJAHAN - Oak Ridge Institute For Science And Education (ORISE); Raasch, John; BHAMIDIMARRI, SURESH - Corteva Agriscience; Mirsky, Steven; MONTEROS, MARIA - Bayer Cropscience; Hayes, Ryan; Riday, Heathcliffe

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2024
Publication Date: 4/4/2024
Citation: Tilhou, N.W., Kucek, L.K., Carr, B., Douglas, J., Englert, J., Ali, S., Raasch, J.A., Bhamidimarri, S., Mirsky, S.B., Monteros, M.J., Hayes, R.J., Riday, H. 2024. Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2024.1384596.
DOI: https://doi.org/10.3389/fpls.2024.1384596

Interpretive Summary: Cover crops are grown to improve soil, water, and air quality between cash crops. Use of cover crops is increasing, but remains around 5% of non-alfalfa cropland. Hairy vetch (Vicia villosa) is an aggressive legume which can produce nitrogen and supress weeds. However, hairy vetch releases seed early (pod shatter or dehiscence) and has dormant (hard) seed. This causes weedy hairy vetch populations in later cash crop fields. Plant breeding can eliminate these traits. This study used a novel pooled DNA method to economically survey the genetics influencing these traits at four breeding environments (Maryland 2020; Wisconsin 2021; Maryland 2022; Wisconsin 2022). These DNA pools confirmed that genetic patterns which reduced dormant seed and pod dehiscence were consistent across all environments, with the exception of seed dormancy in the Maryland sites. In addition this study found multiple potential regions in the genome which control seed dormancy, but a smaller number of weaker regions which influence pod dehiscence.

Technical Abstract: Hairy vetch (Vicia villosa) is a promising legume cover crop, but it’s use is limited by high rates of pod dehiscence and seed dormancy. We used contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. In addition, we combined pooled DNA sample genetic association results with a prior genome-wide association study. Genomic prediction indicated generally positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but poor predictive ability for seed dormancy in the Maryland environments (0.07-0.15). Independently, the pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dormancy and four significant QTL for pod dehiscence. Unfortunately, the pod dehiscence QTL increased the rate of pod dehiscence and are not useful for marker-assisted selection. When combined with a prior association study, sixteen seed dormancy QTL and zero pod dehiscence QTL were significant. Unfortunately, combining the association studies did not greatly improve the detection of strong QTL.