Abstract
Lentil (Lens culinaris ssp. culinaris) is a nutritious and affordable pulse with an ancient crop domestication history. The genus Lens consists of seven taxa, however, there are many discrepancies in the taxon and gene pool classification of lentil and its wild relatives. Due to the narrow genetic basis of cultivated lentil, there is a need towards better understanding of the relationships amongst wild germplasm to assist introgression of favourable genes into lentil breeding programs. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows multiplexing of up to 384 samples or more per library to generate genome-wide single nucleotide Polymorphism (SNP) markers. In this study, we aimed to characterize our lentil germplasm collection using a two-enzyme GBS approach. We constructed two 96-plex GBS libraries with a total of 60 accessions where some accessions had several samples and each sample was sequenced in two technical replicates. We developed an automated GBS pipeline and detected a total of 266,356 genome-wide SNPs. After filtering low quality and redundant SNPs based on haplotype information, we constructed a maximum-likelihood tree using 5,389 SNPs. The phylogenetic tree grouped the germplasm collection into their respective taxa with strong support. Based on phylogenetic tree and STRUCTURE analysis, we identified four gene pools, namely L. culinaris/L. orientalis/L. tomentosus, L. lamottei/L. odemensis, L. ervoides and L. nigricans which form primary, secondary, tertiary and quaternary gene pools, respectively. We discovered sequencing bias problems likely due to DNA quality and observed severe run-to-run variation in the wild lentils. We examined the authenticity of the germplasm collection and identified 17% misclassified samples. Our study demonstrated that GBS is a promising and affordable tool for screening by plant breeders interested in crop wild relatives.
Highlights
Lentil (Lens culinaris ssp. culinaris) is an annual, herbaceous, self-pollinating grain legume crop
We evaluated the distribution of 5,389 single nucleotide Polymorphism (SNP) used in final phylogenetic tree which were represented in 2,120 scaffolds of the L. culinaris genome assembly (v0.6) and found them to be evenly distributed across Medicago truncatula genome version Mt4.0
We found that the biological replicates of accessions from L. culinaris and L. orientalis were closely grouped together, this was not observed in other species especially in L. nigricans, L. ervoides and L. lamottei where an accession was more closely related to other accessions from the same GBS run than to their biological replicates from a different GBS run
Summary
Lentil (Lens culinaris ssp. culinaris) is an annual, herbaceous, self-pollinating grain legume crop. Culinaris) is an annual, herbaceous, self-pollinating grain legume crop. This crop is important in cereal-based cropping systems due to its nitrogen-fixing ability. Lentil and its wild relatives are naturally distributed in South-west Asia and Mediterranean regions [1]. The genus Lens has seven closely related taxa, namely L. culinaris, L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides and L. nigricans. The most recent classification identified seven taxa grouped into four species, namely L. culinaris ssp. Odemensis, L. ervoides, L. lamottei, and L. nigricans [14, 15]. Despite the taxonomic re-organizations, all studies generally agreed that L. culinaris ssp. Orientalis is the most closely related wild progenitor of L. culinaris ssp. Culinaris while L. nigricans is the most distant relative Despite the taxonomic re-organizations, all studies generally agreed that L. culinaris ssp. orientalis is the most closely related wild progenitor of L. culinaris ssp. culinaris while L. nigricans is the most distant relative
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