Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy

Authors: ALI, SHAHJAHAN - Orise Fellow; Kissing Kucek, Lisa; Riday, Heathcliffe; KROM, NICK - Noble Research Institute; KROGMAN, SARAH - Noble Research Institute; COOPER, KIMBERLY - Noble Research Institute; JACOBS, LYNNE - Noble Research Institute; MEHTA, PERDEEP - Noble Research Institute; TRAMMELL, MICHAEL - Oklahoma State University; BHAMIDIMARRI, SURESH - Corteva Agriscience; BUTLER, TWAIN - Noble Research Institute; SAHA, MALAY - Noble Research Institute; MONTEROS, MARIA - Bayer Cropscience

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2023
Publication Date: 6/1/2023
Citation: Ali, S., Kucek, L.K., Riday, H., Krom, N., Krogman, S., Cooper, K., Jacobs, L., Mehta, P., Trammell, M., Bhamidimarri, S., Butler, T., Saha, M.C., Monteros, M.J. 2023. Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy. The Plant Genome. 16(2). Article e20330. https://doi.org/10.1002/tpg2.20330.
DOI: https://doi.org/10.1002/tpg2.20330

Interpretive Summary: Hairy vetch, a relatively new plant species introduced in the cropping system, has characteristics of quick growth habit, high biomass yield and winter hardiness. It has the potential to grow as a cover and a fodder crop. However, seed hardness and pod shattering are major constraints for growing hairy vetch commercially. Furthermore, cultivars with hard seed can lead to uneven strand establishment due to variable germination rates and seedling emergence. Hard seed can become a weed for the next crop in rotation system. Gene sequencing helps to identify internal factors associated with seed hardness and pod shattering. Manipulating these genes or internal factors help to develop improved hairy vetch cultivars in a shorter time with the characteristics of soft seeded, low shatter and high biomass production.

Technical Abstract: Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield and winter hardy characteristics. Seed hardness and pod shattering are major constraints for growing hairy vetch commercially. Seed hardness affects the ability of the seed to imbibe water and germinate. Hard-seeded cultivars are valuable as forages, while soft-seeded and shatter resistant cultivars provide advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with seed hardness in hairy vetch. RNA was extracted from contrasting soft and hard seeded ‘AU Merit’ plants from leaves, flowers, immature pods, seed coats and cotyledons. A range of 31.22 to 79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1,040 X to 2,639X. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome resulted in identification of 76,422 gene transcripts across all tissues. A total of 24,254 transcripts were constitutively expressed in hairy vetch based on the sequenced RNA seq libraries from multiple tissues. Differential gene expression analysis between hard vs. soft-seeded types, enabled identification of genes up- and down- regulated in seed coats compared to other plant tissues. Key candidate genes with a potential role in seed hardness were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of genetic determinants of seed hardness in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.