Abstract
Intensive breeding of cultivated lentil has resulted in a relatively narrow genetic base, which limits the options to increase crop productivity through selection. Assessment of genetic diversity in the wild gene pool of lentil, as well as characterization of useful and novel alleles/genes that can be introgressed into elite germplasm, presents new opportunities and pathways for germplasm enhancement, followed by successful crop improvement. In the current study, a lentil collection consisting of 467 wild and cultivated accessions that originated from 10 diverse geographical regions was assessed, to understand genetic relationships among different lentil species/subspecies. A total of 422,101 high-confidence SNP markers were identified against the reference lentil genome (cv. CDC Redberry). Phylogenetic analysis clustered the germplasm collection into four groups, namely, Lens culinaris/Lens orientalis, Lens lamottei/Lens odemensis, Lens ervoides, and Lens nigricans. A weak correlation was observed between geographical origin and genetic relationship, except for some accessions of L. culinaris and L. ervoides. Genetic distance matrices revealed a comparable level of variation within the gene pools of L. culinaris (Nei’s coefficient 0.01468–0.71163), L. ervoides (Nei’s coefficient 0.01807–0.71877), and L. nigricans (Nei’s coefficient 0.02188–1.2219). In order to understand any genic differences at species/subspecies level, allele frequencies were calculated from a subset of 263 lentil accessions. Among all cultivated and wild lentil species, L. nigricans exhibited the greatest allelic differentiation across the genome compared to all other species/subspecies. Major differences were observed on six genomic regions with the largest being on Chromosome 1 (c. 1 Mbp). These results indicate that L. nigricans is the most distantly related to L. culinaris and additional structural variations are likely to be identified from genome sequencing studies. This would provide further insights into evolutionary relationships between cultivated and wild lentil germplasm, for germplasm improvement and introgression.
Highlights
IntroductionWith respect to the global production, cultivated lentil is ranked third after chickpea and pea
The genus Lens is a self-pollinating, diploid (2n = 2x = 14), cool season legume with a large genome size of c. 4 Gbp (Singh et al, 2018)
This subset of SNP markers was further filtered for percentage of missing data (50%), quality score (Q ≥ 30; 1,414,996 SNPs), and minor allele frequencies (MAF = 0.05) that resulted in a final set of 422,101 high-quality SNP markers (Supplementary Table S1), to be used in phylogenetic analysis (Table 3)
Summary
With respect to the global production, cultivated lentil is ranked third after chickpea and pea. The origin of lentil comes from the Eastern Mediterranean region, during the Neolithic age around 7000–10,000 years ago (Gupta et al, 2011). Lentil and its wild relatives are naturally distributed throughout the world especially in southwest Asia and Mediterranean regions and were later introduced into North and South America and Australia (Hamwieh et al, 2009). Lentil is produced in over 58 countries, with Canada being the largest producer, generating 48.1% of the world’s production, as well as being the world’s largest exporter accounting for 64.0% of global lentil exports. Despite being the world’s second largest producer (15.7%), India is still the world’s largest importer of lentil
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