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

Authors: RAMSAY, LARISSA - University Of Saskatchewan; KOH, CHU SHIN - University Of Saskatchewan; KAGALE, SATEESH - National Research Council - Canada; Gao, Dongying; KAUR, SUKHJIWAN - Agriculture Victoria; HAILE, TEKETEL - University Of Saskatchewan; GELA, TADESSE - University Of Saskatchewan; CHEN, LI-AN - University Of Saskatchewan; CAO, ZHE - University Of Saskatchewan; KONKIN, DAVID - National Research Council - Canada; TOEGELOVA, HELENA - Institute Of Experimental Botany; DOLEŽEL, JAROSLAV - Institute Of Experimental Botany; Rosen, Benjamin - Ben; STONEHOUSE, ROBERT - University Of Saskatchewan; HUMANN, JODI - Washington State University; MAIN, DORRIE - Washington State University; Coyne, Clarice - Clare; McGee, Rebecca; COOK, DOUGLAS - University Of California, Davis; PENMETSA, VARMA - University Of California, Davis; VANDENBERG, ALBERT - University Of Saskatchewan; CHAN, CRYSTAL - University Of Saskatchewan; BANNIZA, SABINE - University Of Saskatchewan; EDWARDS, DAVID - University Of Western Australia; BAYER, PHILLIP - University Of Western Australia; BATLEY, JACQUELINE - University Of Western Australia; UDUPA, SRIPADA - The International Center For Agricultural Research In The Dry Areas(ICARDA); BETT, KIRSTIN - University Of Saskatchewan

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 7/24/2021
Publication Date: 7/24/2021
Citation: Ramsay, L., Koh, C., Kagale, S., Gao, D., Kaur, S., Haile, T., Gela, T., Chen, L., Cao, Z., Konkin, D., Toegelova, H., Doležel, J., Rosen, B.D., Stonehouse, R., Humann, J., Main, D., Coyne, C.J., Mcgee, R.J., Cook, D., Penmetsa, V., Vandenberg, A., Chan, C., Banniza, S., Edwards, D., Bayer, P., Batley, J., Udupa, S., Bett, K.E. 2021. Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species. bioRxiv. https://doi.org/10.1101/2021.07.23.453237.
DOI: https://doi.org/10.1101/2021.07.23.453237

Interpretive Summary: Lentil (Lens culinaris) is an important grain legume for protein and other nutrients and is grown in many countries, including the United States. Despite its agronomic and economic importance, the genomic resources for lentil improvement were very limited. It has been extremely difficult to sequence as lentil has a very large genome that contains a lot of repetitive sequences or so-called "junk DNA". We overcame these challenges and developed high quality genome assemblies of cultivated lentil (L. culinaris) and its wild relative (L. ervoides). We compared the genomes of cultivated and wild lentils as well as other legumes and identified large-scale structural rearrangements that may affect DNA recombination and our ability to move unique traits from wild species into cultivated lentil. This study provides valuable resources that will enable scientists to understand the genetic and genomic basis of important agronomic traits in cultivated lentil and will enable plant breeders to efficiently transfer desirable traits, such as disease resistances, drought and heat tolerances, from lentil wild relatives.

Technical 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.