Hairy vetch, Vicia villosa (Roth), is a cover crop that does not exhibit a typical domestication syndrome. Pod dehiscence reduces seed yield and creates weed problems for subsequent crops. Breeding efforts aim to reduce pod dehiscence in hairy vetch. To characterize pod dehiscence in the species, we quantified visual dehiscence and force required to cause dehiscence among 606 genotypes grown among seven environments of the United States. To identify potential secondary selection traits, we correlated pod dehiscence with various morphological pod characteristics and field measurements. Genotypes of hairy vetch exhibited wide variation in pod dehiscence, from completely indehiscent to completely dehiscent ratings. Mean force to dehiscence also varied widely, from 0.279 to 8.97 N among genotypes. No morphological traits were consistently correlated with pod dehiscence among environments where plants were grown. Results indicated that visual ratings of dehiscence would efficiently screen against genotypes with high pod dehiscence early in the breeding process. Force to dehiscence may be necessary to identify the indehiscent genotypes during advanced stages of selection.

Seed dormancy complicates the agricultural use of many legume species. Understanding the genetic and environmental drivers of seed dormancy is necessary for advancing crop improvement for legumes, such as Vicia villosa. In this study, we quantify the magnitude of genetic and environmental effects on physical dormancy among 1488 maternal V. villosa plants from 18 diverse environments. Furthermore, we explore the relationship between physical dormancy and environmental conditions during seed development. Additive genetic variance (h²) accounted for 40% of the variance, while the growing environment explained 28% of the variance in physical dormancy. Maternal lines showed complete variance in physical dormancy, as one line was 100% dormant, and 56 lines were 0% dormant. Distributions of physical dormancy varied widely among seed production environments, with some site-years strongly skewed toward physically dormant seed, while other site-years exhibited little dormant seed. Twenty-three weather variables were associated with environmental and error effects of physical dormancy. High mean and minimum relative humidity, low mean and maximum temperature, and high precipitation weakly grouped with low physical dormancy. Weather variables calculated from fixed time windows approximating seed maturity to seed harvest at each site-year tended to be less predictive than biological seed drying windows calculated based on seed maturity of each maternal line. Overall, individual and cumulative effects of weather variables were poor predictors of physical dormancy. Moderate heritability indicates that breeding programs can select against physical dormancy and improve V. villosa for agricultural use. Marker-based approaches would maximize selection for physical dormancy by reducing the influence of unpredictable environmental effects.

Lotus corniculatus L., also known as birdsfoot trefoil (BFT), is a perennial, non-bloating, temperate forage legume widely grown due to its accumulation of high levels of condensed tannins (CTs) in foliage. However, variations in the CT levels and other plant metabolites in BFT genotypes in response to environmental and yearly factors under field conditions remain largely unexplored. Here, we combine conventional CT quantification and metabolome profiling with high-resolution liquid chromatography–mass spectrometry (LC-MS) to understand how environmental factors impact CT and other metabolite profiles. Eight BFT genotypes grown in Kentville, Canada, and Rhode Island and Utah in the United States were investigated, revealing significant genotypic variations in soluble CT contents. The global metabolome profiles of the eight BFT genotypes clustered predominantly based on geographical location. These results demonstrate that geographical location strongly influences CT accumulation and metabolome composition, offering potential for selecting genotypes adapted to specific environments. Our findings provide an opportunity for targeted breeding strategies to optimize CT levels, improve forage quality, and enhance stress resilience in birdsfoot trefoil.

Keymessage: Standardized microhaplotype databases for eight diverse crops enable multiallelic analyses, comparative genetics, and breeding decisions. Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multi-allelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Selected case studies with these databases highlight the operational advantages of microhaplotypes, especially for challenging, highly heterozygous, or polyploid species. They offer an informative alternative to traditional biallelic SNP analyses for resolving population structures and improving linkage map ordering. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.