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

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.

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions

“…For questions pertaining to population structure and phylogenetic relationships, filtering conditions did not affect the results. Population structure analyses and phylogenies inferred were similar to previous studies: four or five groups, when different species within Lens are considered (depending on whether orientalis and culinaris are split or not) (Alo et al, 2011;Ogutcen et al, 2018;Dissanayake et al, 2020); and three major clusters within cultivated lentils (Khazaei et al, 2016;Koul et al, 2017).…”

“…Misclassification of samples is a recurrent issue with germplasm accessions (Mason et al, 2015). In lentil studies, Dissanayake et al (2020) observed 22 misclassified accessions out of 467 lentil accessions, and 4 out of 83 accessions were identified as erroneously classified by Wong et al (2015). Less straightforward is how to deal with accessions that are putative hybrids between different groups or that could have been affected by gene flow along their evolutionary past.…”

Application of Genomics to Understand Salt Tolerance in Lentil

“…The VCF file was then filtered for a minimum read depth (DP) of 5, maximum missing data of 80%, base quality of 30 (Q30), minimum minor allelic frequency (MAF) of 5%, and heterozygosity of 20%, using VCFtools (version 0.1.16) [48] and the TASSEL software package (Trait Analysis by aSSociation, Evolution, and Linkage; version 5.2.48) [49]. Genetic diversity of the studied lentil population was also analyzed based on the method described in Dissanayake et al [38] using the StAMPP package [50] and DARwin-6.0.17 software [51] ( Figure S1).…”

“…Total RNA extraction, library preparation and quality trimming for GBS-t were performed using the method described in Dissanayake et al [38]. The remaining high-quality trimmed sequence reads were aligned to the lentil reference genome sequence of cultivar CDC Redberry (v2.0) [39] using Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.5.4a) [52].…”

“…For lentil, many complexity reduction-based GBS approaches (e.g., restriction enzymebased, transcriptome-based) have been developed and applied [30,36,37]. However, the narrow genetic diversity present within the lentil limits the number of SNPs detected and the efficiency of the approach [36,38]. Therefore, to overcome this constraint, the development of additional GBS methods is required.…”