Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species

Larissa Ramsay,  View ORCID ProfileChu Shin Koh,  View ORCID ProfileSateesh Kagale, Dongying Gao, Sukhjiwan Kaur,  View ORCID ProfileTeketel Haile, Tadesse S. Gela, Li-An Chen, Zhe Cao, David J. Konkin, Helena Toegelová, Jaroslav Doležel, Benjamin D. Rosen, Robert Stonehouse,  View ORCID ProfileJodi L. Humann,  View ORCID ProfileDorrie Main,  View ORCID ProfileClarice J. Coyne, Rebecca J. McGee, Douglas R. Cook,  View ORCID ProfileR. Varma Penmetsa,  View ORCID ProfileAlbert Vandenberg, Crystal Chan,  View ORCID ProfileSabine Banniza, David Edwards,  View ORCID ProfilePhilipp E. Bayer,  View ORCID ProfileJacqueline Batley,  View ORCID ProfileSripada M. Udupa,  View ORCID ProfileKirstin E. Bett

Abstract

Understanding the genomic relationship between wild and cultivated genomes would facilitate access to the untapped variability found in crop wild relatives. We developed genome assemblies of a cultivated lentil (Lens culinaris) as well as a wild relative (L. ervoides). Comparative analyses revealed large-scale structural rearrangements and additional repetitive DNA in the cultivated genome, resulting in regions of reduced recombination, segregation distortion and permanent heterozygosity in the offspring of a cross between the two species. These novel findings provide plant breeders with better insight into how best to approach accessing the novel variability available in wild relatives.