Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a Forage breeding program

Abstract

Most orphan crops have not been fully sequenced, hence we rely on genome sequences of related species to align markers to different chromosomes. This hinders their utilisation in plant population improvement programs. Utilising the advances in the science of sequencing technologies, the population structure, relatedness, and genetic diversity among accessions can be assessed quickly for better exploitation in forage breeding programs. Using DArTseq technology, we studied the genetic and structural variation in 65 Lablab purpureus (L.) Sweet conserved gene-bank accessions using 9320 DArTseq-based SNPs and 15,719 SilicoDart markers. These markers had a low discriminating ability with mean polymorphic information content (P.I.C.) of 0.14 with DArTseq-based SNPs and 0.13 with SilicoDart markers. However, the markers had a high mean call rate of 73% with DArTseq-based SNPs and 97% with SilicoDart markers. Analysis of molecular variance revealed a high within populations variance (99.4%), indicating a high gene exchange or low genetic differentiation (PhiPT = 0.0057) among the populations. Structure analysis showed three allelic pools in variable clusters of ΔK = 3 and 6. Phylogenetic tree of lablab accessions showed three main groups with variable membership coefficients. Most pairs of accessions (40.3%) had genetic distances between 0.10 and 0.15 for SilicoDart markers, while for DArTseq-based SNPs, (46.5%) had genetic distances between 0.20 and 0.25. Phylogenetic clustering and minimum spanning analysis divided the 65 accessions into three groups, irrespective of their origin. For the first time, this study produced high-density markers with good genom coverage. The utilisation of these accessions in a forage program will base on the information from molecular-based grouping. The outcomes uncovered the presence of noteworthy measure of variety in Uganda, CIAT and ILRI accessions, thus demonstrating an opportunity for further marker-trait-association studies.

A population genomics approach to unlock the genetic potential of lablab (Lablab purpureus), an underutilized tropical forage crop

“…Table 5) which is a much higher SNP density than that reported for lablab recently (one GBS-based SNP markers per ca. 100Kb) [19, 28]. Despite the high number of genome-wide SNP markers identified in the present study, the rate of unique SNPs identified decays with half of the genotyped accessions (Fig 2) which implies possible duplications in our panel.…”

“…Exploring the crop's genetic potential by collecting appropriate germplasm and understanding its diversity status, using genomic tools in combination with phenotyping, is a key approach to fast-track breeding efforts and accelerate the crop's full domestication [19,22,23]. Recently, some agronomic studies have shed light on seed maturity, yield, feed quality traits and intercropping capabilities of lablab [24][25][26][27] but there have been few studies on genetic variability and population dynamics [28][29][30][31]. For fast-tracking improvement plans, integrated approaches such as phenotyping, genotyping and phenotype-genotype association studies should be carried out and developing genomic tools is an integral part of this endeavor [32][33][34].…”

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

“…Profiling of 25,039 DNA markers (9320 DArT SNPs and 15,719 SilicoDart) data on 65 lablab bean germplasm showed low discriminating ability and three subpopulations unrelated to site of origin. High within population variance suggests a greater degree of gene exchange or low genetic differentiation among the populations (Sserumaga et al, 2021). Another data set involving 1,000 SNP and SilicoDArT markers data on 142 lablab accessions unfolded five major groups, each with further subgroups (Muktar et al, 2021).…”

Recent developments in Lablab purpureus genomics: A focus on drought stress tolerance and use of genomic resources to develop stress‐resilient varieties

“…In their steps of advancement, the first group of markers, amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), and random amplification of polymorphic DNA (RAPD), was employed to understand the diversity and genetic characterization. The second group, namely, sequence‐based markers including single nucleotide polymorphism (SNPs), microsatellite or simple sequence repeats (SSRs), and expressed sequence tags (ESTs), was utilized in mapping studies (Dholakia et al, 2019; Kamotho et al, 2016; Keerthi et al, 2018; Kimani et al, 2012; Konduri et al, 2000; Rai et al, 2018a; Sserumaga et al, 2021; Vaijayanthi et al, 2018). Despite their applications in Lablab, there has been little utilization of these markers to improve drought tolerance.…”