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).

We conducted a survey to assess the occurrence and severity of rice blast and brown spot disease on popular cultivars in paddies in the Busia, Kirinyaga, and Kisumu counties of Kenya during 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae, in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.

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).

Purpose Arbuscular mycorrhizal fungi (AMF) play a key role in medicinal plant species, besides their ecological role in shaping plant communities. Knowledge about the diversity and structure of AMF communities associated with the endangered Prunus africana is valuable in the conservation and domestication of the species for its medicinal products. Methods We investigated the diversity and structure of AMF species communities in the rhizosphere soils of P. africana trees occurring in four fragmented Afromontane forests found in Cameroon (Mount Cameroon and Mount Manengouba) and Kenya (Chuka and Malava) using Illumina Miseq sequencing of 18S rRNA gene amplicons. Results A total of 64 virtual taxa (VT) belonging to eight genera were detected, namely Glomus (43 VT), Claroideoglomus (6 VT), Paraglomus (5 VT), Acaulospora (4 VT), Diversispora (3 VT), and Archaeospora, Pacispora, and Scutellospora with 1 VT each. Scutellospora heterogama VTX00286 was the most abundant and common species in all four sites (49.62%). Glomeraceae and Gigasporaceae were the most abundant families found across the sites, while Acaulosporaceae, Pacisporaceae, and Archaeosporaceae were rare, represented by < 1% of all the detected taxa. Conclusion Our data shows a high diversity of AMF species associated with P. africana and variable community structure partially shaped by local edaphic factors.

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).

Purpose Arbuscular mycorrhizal fungi (AMF) play a key role in the phytochemical modulation of medicinal plant species, besides their ecological role in shaping plant communities. Knowledge about the diversity and structure of AMF species associated with the endangered Prunus africana is valuable in the conservation and domestication of the species for its medicinal products. Methods Thus, we investigated the diversity and structure of AMF species communities in the rhizosphere soils of P. africana trees occurring in four fragmented Afromontane forests found in Cameroon; (Mount Cameroon and Mount Manengouba) and Kenya (Chuka and Malava) using Illumina Miseq of 18S rRNA gene amplicons. Results The forward and the reverse reads were A total of 64 virtual taxa (VT) belonging to eight genera were detected, namely Glomus (43 VT), Claroideoglomus (6 VT), Paraglomus (5 VT), Acaulospora (4 VT), Diversispora (3 VT), and Archaeospora, Pacispora, and Scutellospora with 1 VT each. Scutellospora heterogama VTX00286 was the most abundant and common species in all four sites (49.62%). Glomeraceae and Gigasporaceae were the most abundant families found across the sites, while Acaulosporaceae, Pacisporaceae, and Archaeosporaceae were rare, represented by <1% of all the detected taxa. Conclusion Our data show a high diversity of AMF species associated with P. africana, and variable community structure partially shaped by local edaphic factors. This study provides preliminary information on the possibility of using indigenous AMF inoculum, for the cultivation and domestication of P. africana for the sustainable management of this important medicinal plant.