Chromosome-scale assembly of the lablab genome - A model for inclusive orphan crop genomics

Abstract

Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-representation of researchers in Africa in the genome sequencing efforts of their indigenous orphan crops. Here we report a radically inclusive approach to orphan crop genomics using the case of Lablab purpureus (L.) Sweet (syn. Dolichos lablab, or hyacinth bean) – a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led South-North plant genome collaboration produced a high-quality chromosome-scale assembly of the lablab genome – the first chromosome-scale plant genome assembly locally produced in Africa. We also re-sequenced cultivated and wild accessions of lablab from Africa confirming two domestication events and examined the genetic diversity in lablab germplasm conserved in Africa. Our approach provides a valuable resource for lablab improvement and also presents a model that could be explored by other researchers sequencing indigenous crops particularly from Low and middle income countries (LMIC).

Beyond the Genome: Genetically Modified Crops in Africa and the Implications for Genome Editing

“…The pipeline of genome‐edited crop technologies in Africa should be transformed into a model of technology co‐development (Hoffmann et al., 2007), where the breeding priorities and programmes are driven by both African scientists and the smallholder farmers who are the intended beneficiaries. One promising example for how to reconfigure such partnerships comes from a recent ‘Africa‐led North–South plant genome collaboration’ that developed the ‘first chromosome‐scale plant genome assembly locally produced in Africa’ (Njaci et al., 2022: 1). The project was initiated and coordinated by African scientists, who sought out international partners as needed and prioritized in‐country, long‐term training and information sharing to ensure that the priorities of African farmers and scientists remained front and centre (ibid.).…”

A Genome-Wide Association Study of Biomass Yield and Feed Quality in Buffel Grass (Cenchrus ciliaris L.)

“…Similarly, high-throughput genomewide markers have also been developed for tropical forages elsewhere [11][12][13]. Reference genomes have also been developed for a few of the key tropical forage crops [14][15][16][17][18][19][20]. These genomic resources have been used for the analysis of genetic diversity, subsetting, genome-wide association and population genetic studies, and will continue to be useful tools and resources for tropical forage research and development.…”