Characterization of Genetic and Allelic Diversity Amongst Cultivated and Wild Lentil Accessions for Germplasm Enhancement

Ruwani Dissanayake; Shivraj Braich; Noel O I Cogan; Kevin Smith; Sukhjiwan Kaur

doi:10.3389/fgene.2020.00546

Characterization of Genetic and Allelic Diversity Amongst Cultivated and Wild Lentil Accessions for Germplasm Enhancement

Front Genet. 2020 Jun 10:11:546. doi: 10.3389/fgene.2020.00546. eCollection 2020.

Authors

Ruwani Dissanayake^{1

2}, Shivraj Braich^{1

3}, Noel O I Cogan^{1

3}, Kevin Smith^{2

4}, Sukhjiwan Kaur¹

Affiliations

¹ Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.
² Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
³ School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia.
⁴ Agriculture Victoria, Hamilton, VIC, Australia.

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.

Keywords: GenBank; SNP markers; allele frequency; gene annotation; introgression; pulse; sequence variant.