Genome-wide association mapping in hairy vetch (Vicia villosa) discovers a large effect locus controlling seed dormancy

Abstract

Hairy vetch (Vicia villosa Roth), a winter-hardy annual legume, is a promising cover crop. To fully leverage its potential, seed production and field performance of V. villosa must be improved to facilitate producer adoption. Two classic domestication traits, seed dormancy (hard seed) and dehiscence (pod shatter), are selection targets in an ongoing breeding program. This study reports a genome-wide association study of 1,019 V. villosa individuals evaluated at two sites (Knox City, Texas and Corvallis, Oregon) for the proportion of dormant seed, visual pod dehiscence scores, and two dehiscence surrogate measures (force to dehiscence and pod spiraling score). Trait performance varied between sites, but reliability (related to heritability) across sites was strong (dormant seed proportion: 0.68; dehiscence score: 0.61; spiraling score: 0.42; force to dehiscence: 0.41). A major locus controlling seed dormancy was found (q-value: 1.29 × 10−5; chromosome 1: position: 63611165), which can be used by breeding programs to rapidly reduce dormancy in breeding populations. No significant dehiscence score QTL was found, primarily due to the high dehiscence rates in Corvallis, Oregon. Since Oregon is a potentially major V. villosa seed production region, further dehiscence resistance screening is necessary

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

“…Prior to establishment, all environments were supplemented with lime, K and P based on soil test results. Additional details on the breeding program goals and methods can be found in prior publications ( Kucek et al., 2019 ; Kissing Kucek et al., 2020b ; Tilhou et al., 2023 ).…”

“…Bioinformatics processing was completed at the University of Wisconsin Biotechnology Center using the TASSEL analysis platform ( Glaubitz et al., 2014 ) in parallel with re-calling single nucleotide polymorphisms (SNPs) from the Tilhou et al., 2023 GWAS panel which are hairy vetch individuals evaluated in Oregon and Texas in 2019 (n=869). Barcoded sequence read outputs were collapsed into a set of unique sequence tags with counts.…”

“…To validate the utility of the pooled DNA samples, the pooled DNA samples were used to train genomic prediction models and predict individual plant performance in the Tilhou et al., 2023 GWAS panel. All of these models used a genomic best linear unbiased predictor (GBLUP) model:…”

“…Selection for reduced pod dehiscence and seed dormancy is challenging because both traits appear quantitative and are dependent on growing conditions ( Kissing Kucek et al., 2020a , Kissing Kucek et al., 2020b ). A recent genome wide association analysis of a breeding panel of hairy vetch found a large-effect quantitative trait loci (QTL) for seed dormancy, but no statistically significant associations for pod dehiscence ( Tilhou et al., 2023 ). In the Tilhou et al.…”

“…A recent genome wide association analysis of a breeding panel of hairy vetch found a large-effect quantitative trait loci (QTL) for seed dormancy, but no statistically significant associations for pod dehiscence ( Tilhou et al., 2023 ). In the Tilhou et al. (2023) dataset, it was difficult to determine if pod dehiscence was simply highly polygenic or if the field data was inadequate.…”