ArticleThe plant genome2025
BIGapp: A user-friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.).
Article in The plant genome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- DNA extraction from sweetpotato (Molecular breeding : new strategies in plant improvement · 2026Article
- Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Enhancing alfalfa breeding through genomic prediction with exotic germplasm resources.BMC plant biology · 2026Article
- BIGapp: A user-friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.).The plant genome · 2025Article
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12 authors.
Funding
Abstract
Alfalfa (Medicago sativa L.) is a globally vital forage crop valued for its perennial growth and multiple annual harvests. A breeding effort is underway to improve the crop for productivity and persistence against biotic and abiotic stresses using "creeping rootedness," a trait where plants exhibit horizontal root growth, similar to rhizomes, with increased vegetative ground surface area. In this study, we genotyped a breeding population of 648 alfalfa lines segregating for creeping rootedness using the 3K DArTag marker panel to identify trait-associated genomic loci and evaluate the feasibility of genomic prediction to accelerate breeding cycles. Using genome-wide association studies (GWAS), we identified three quantitative trait loci (QTLs), with one major QTL located on chromosome 6.1 associated with this trait. Genomic prediction showed moderate predictive ability (r = 0.68) for creeping rootedness. A significant advancement in this study was the development and utilization of the Breeding Insight Genomics Application (BIGapp), an R Shiny application designed to streamline the processing of genomic data through an intuitive interface. This tool makes integrating genomics into existing breeding programs accessible, regardless of species ploidy or the researcher's coding proficiency. The identified QTL will be essential in future efforts to develop new alfalfa cultivars with the creeping rootedness trait and accelerate the breeding cycle, with BIGapp playing a pivotal role in these advancements.
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