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

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). Lablab is a legume native to Africa and cultivated throughout the tropics for food and forage; however, as an orphan crop, limited genomic resources hampers its genetic improvement. Here, an African-led South-North plant genome collaboration produces an improved genome assembly and population genomic resource to accelerate its breeding.

Automated summary

Under-utilised orphan crops, such as Lablab purpureus, are important for creating diversified and climate-resilient food systems. In this study, an African-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome, providing valuable resources for lablab improvement. The collaborative approach used in this research can be explored by other researchers sequencing indigenous crops, especially from low and middle-income countries (LMIC).