A low-coverage skim-sequencing and imputation pipeline for genomic selection.

ABSTRACT: Genomic selection (GS) can accelerate plant breeding gains by reducing breeding cycle times, reducing phenotyping costs, or improving selection accuracy. GS is especially promising for perennial crops such as intermediate wheatgrass (IWG, Thinopyrum intermedium) that may require multiple years of evaluation under phenotypic recurrent selection. A major obstacle in implementing GS is the need for an affordable, high-density, genetic marker system that is scalable to thousands or tens-of-thousands of samples in breeding programs, especially in emerging or minor crop species. As sequencing costs continue to decrease, low-coverage whole genome skim-sequencing (skim-seq) has become an attractive method for GS. Using commercial laboratory products and open-source software, we implemented whole g

SUBMITTER: Sthapit SR 

PROVIDER: S-EPMC12547641 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature