Understanding the extent and consequences of structural variation in genomes of Lens species

Long-read sequencing technologies have considerably improved the Lcu assembly by allowing us to sequence through the many repeat-heavy regions, correcting orientation and scaffold order, and pulling apart collapsed regions. A completed long-read assembly for Lcu and all other Lens species will be available in the first year of this grant. Further exploration of long-read data will greatly facilitate our understanding of the variation outside the genic regions in both cultivated lentil and its wild relatives and enhance our ability to harness adaptive variation lurking in the dark corners of the Lens genepool. It will also help better resolve quantitative trait loci (QTL) and facilitate the design of markers useful for marker-assisted selection. Emerging research suggests that, like SNPs, structural variations are not evenly distributed throughout plant genomes, but instead elevated in regions of high recombination where uneven crossing over is most likely to occur. It has been hypothesized that many structural variants that segregate in wild taxa are fixed during domestication Understanding lentil phenotypes in the context of these structural variations will help us design better crossing strategies for harnessing existing variation.

This activity will look into structural variation in the genus Lens, comparative genomics and explore genome graphs for variant calling.