Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

Abstract

Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).

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

“…uncinatus, uncharacteristically clustered with 4-seeded accessions which is not in line with what has been reported previously [19,72] and hence needs further investigation further. However, phylogenetic analysis based on agro-morphological data clustered all 2-seeded accessions into cluster I (Fig 1) with only two 4-seeded accessions (24783 and 21048) included as predicted previously by Njaci et al [19]. Interestingly 24783, is a 4-seeded lablab accession which clustered with the 2-seeded accessions in both SNP and morphological data based phylogenetic trees (Fig 1) while 21048 was not successfully genotyped.…”

“…In this study, two QTL, on chromosomes Lp1 and Lp9, were significantly associated with NoDF (Fig 4). However, Njaci et al [19] reported QTL on a different chromosome for the same trait suggesting that different regions of the genome may be impacting on this trait.…”

“…This work started [21] and a lablab reference genome (0.5 Gb, 11 chromosomes designated Lp (Lablab purpureus)) was published very recently [19]. 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].…”

“…Lablab was identified, a decade ago, by the African Orphan Crops Consortium (AOCC) as one of the 101 under-researched but highly nutritious African food/feed crops, important for supporting the dietary requirements of consumers and incomes of small-holder farmers in Africa, to have its genome sequenced. This work started [21] and a lablab reference genome (0.5 Gb, 11 chromosomes designated Lp ( Lablab purpureus )) was published very recently [19]. 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].…”

Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis

“…In order to achieve high-quality chromosome-level de-novo assembly, the most commonly-used approach integrates low-error second-generation sequencing (SGS), long-read TGS, and Hi-C sequencing 26,27,28,29 . Firstly, long TGS reads are assembled into contigs.…”