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).

Fig. 1. Genome assembly of lablab.

a Lablab purpureus plant showing flowers, leaves and pods. b Gene and repeat landscape of the lablab genome. The tracks from the outer to the inner track show 1) gene density, 2) repeat density, 3) LTR-RT density, 4) tandem repeat density. c BUSCO scores of the lablab genome and gene annotation using the embryophyta and fabales reference lineages. d LAI index of the 11 lablab chromosomes. Source data are provided as a Source Data file.

Fig. 2. Gene families in lablab.

a Venn diagram of the number of gene families common among and unique to lablab, Phaseolus vulgaris, Vigna angularis, Medicago truncatula, and Cajanus cajan. b Cladogram of the analysed species showing the number of expanded and contracted gene families in each. Figure constructed with iTol. c Gene ontology terms enriched in the set of expanded gene families in Lablab purpureus. Source data are provided as a Source Data file.

Fig. 3. Trypsin inhibitor gene family in lablab.

a Phylogeny of the trypsin inhibitor encoding genes in five different legume species including lablab; branch thickness corresponds to bootstrap values and increases with higher bootstrap; tree is rooted with the most divergent sequence from Arabidopsis; outer blue connections: tandemly duplicated genes, outer red connection: syntenic collinear genes. b Copy number of trypsin inhibitor genes in different plant species. c Organisation of the trypsin inhibitor gene clusters in the lablab genome. d Expression of the trypsin inhibitor genes in four different tissues. Genes in clusters are grouped in the heatmap. The variance stabilising transformed (vst) TPM levels correlate with the intensity of yellow to red colouring. Source data are provided as a Source Data file.

Fig. 4. Phylogenetics of lablab.

Left, Neighbor Joining phylogenetic relationships among lablab samples (2-seeded and 4-seeded purpureus (domesticated) and uncinatus (wild) subspecies) rooted on Dipogon lignosus. All nodes received full (100%) bootstrap support. Asterisks indicate the two domestication events. Right, STRUCTURE analysis of the same samples. The optimum number of clusters (K) was determined to be three (upper right), which are indicated as white, grey and black bars. Source data are provided as a Source Data file.

Fig. 5. Population genetic analysis of lablab.

a Bar plots based on the admixture model in STRUCTURE for multiple K (Membership of individual accessions to each subgroup is given in Supplementary Table 6). b Clusters detected by hierarchical clustering. c Clusters detected by PCA. The colours in (b) and (c) are according to the STRUCTURE K = 7 in (a). Accessions in admixture groups shown by light grey colour in (b) and (c). Source data are provided as a Source Data file.

Fig. 6. GWAS in lablab.

Circos plots showing the distribution of significant marker-trait associations (MTA) identified in the lablab genome. Only significant markers with adjusted p-value > 0.05 (after correcting for multiple comparison using False Discovery Rate approach) from at least two out of five association models tested are shown (Supplementary Table 11). Vertical axis represents −log(raw p value). The size of the bubble represents the number of models where the MTA was significant. The colour of the bubble represents the MTA trait. Source data are provided as a Source Data file.