Project 1

Full-genome sequencing and annotation of the African yam bean (Sphenostylis stenocarpa)

Project objective

To publish and annotate the first full-genome sequence of African yam bean and to study the genetic factors underpinning economically important traits including internal resource partitioning between tuber and pods in African Yam Bean.

Project leader

BecA-ILRI Hub

Dr Jean-Baka Domelevo Entfellner

BecA-ILRI Hub

Co-leader

John Innes Centre

Dr Oluwaseyi Shorinola

John Innes Centre

Researchers

University of Ibadan

Henry Osaiyuwu Osamede

University of Ibadan
KALRO Food Crops Research Institute

Bernice Ngina Waweru

KALRO Food Crops Research Institute
Jomo Kenyatta University

Isaac Njaci

Jomo Kenyatta University
Jomo Kenyatta University of Agriculture and Technology

Mary Maranga

Jomo Kenyatta University of Agriculture and Technology
Egerton University

Edwin Murungi

Egerton University
Artificial Intelligence Research Group – Makerere University

Pius K.B. Mugagga

Artificial Intelligence Research Group – Makerere University
University of Nyala

Hassan Zackaria Ali Ishag

University of Nyala
Nelson Mandela African Institution of Science and Technology

Beatus Lyimo

Nelson Mandela African Institution of Science and Technology
Université Evangélique en Afrique

Bwihangane Birindwa Ahadi

Université Evangélique en Afrique
Jomo Kenyatta University

Mukani Moyo Okoba

Jomo Kenyatta University

Project overview 

The African yam bean (S stenocarpa (Hochst. ex A. Rich.) Harms) is an African orphan legume crop. It is consumed by populations in various countries in Africa, with a centre of diversity in western and central Africa (mainly Nigeria) and reported use also in eastern Africa (Ethiopia, Tanzania). Unlike many legumes which produce only pods, the African yam bean (AYB) is peculiar in that it produces both edible tubers and pods. It has a high protein content (up to 19% in the tubers – about 2.5 times the content found in sweet potatoes, yam and cassava – and ≥30% in the seed grain), while its tubers are also starch-rich. The plant also has high nitrogen-fixing ability and remarkably low susceptibility levels to common field and storage pests affecting legumes. These properties had AYB play a significant role in the survival of population stranded in isolated areas during the Nigerian civil war (Biafran war, 1967–70). In addition, it plays an important role in the cultures of Central and West Africans and it is believed to have traditional medicinal values.

There is however no full-genome sequence available yet for AYB, and the genetic resources overall are very limited. This lack of genomics resource has limited efforts to study the genetic architecture of economic important trait in AYB. For instance, a recent Genotyping-by-Sequencing analysis done at the BecA-ILRI Hub using the closest relative (believed to be cowpea) as a reference, failed to map diagnostic markers for the traits studied. With the Bioinformatics CoP, we are embarking on the full-genome sequencing of AYB using a hybrid approach: we will combine short high-accuracy reads (Illumina technology) and long but lower-accuracy reads (Oxford Nanopore) to assemble the first full-genome sequence for this species. We also plan additional RNA sequencing to guide genome annotation, after which we will study the genetic determinants of the internal partitioning of resources (photosynthesis, nutrient availability) between pods and tubers. This work will pave the way for further studies in order to (1) better understand the genetic diversity of the available germplasm and (2) assist breeding efforts to increase the commercial value of African yambean and target its shortcomings (long maturity period, periodic photosensitivity, hard seed coat leading to long cooking times). We expect this work will lead to several publications, the overarching one to be submitted to a high-level journal like Nature or Nature Genetics.

Project outputs

  1. Accurate estimation of the size of the AYB genome using flow cytometry.
  2. Full genome sequence of AYB using Illumina short reads combined with Oxford Nanopore reads for accurate scaffolding.
  3. Comparative genomics study with the closest species with full genome available (cowpea).
  4. Annotation of the genome (from gene model predictions and RNA sequencing experiments).
  5. Comparative expression analysis (different tissues and different time points throughout the plant growth cycle) to get insights in the dynamics of internal resource partitioning.

Project activities

  1. Two-step DNA extraction for high molecular weight products (after nuclei isolation)
  2. Flow cytometry experiment to determine genome size
  3. Full genome sequencing (multiple runs) on the Illumina MiSeq and Oxford Nanopore to get an approximate coverage of 30x for each technology. Genome assembly using workflows for hybrid approaches.
  4. Plant growth in the greenhouse, RNA extraction in different tissues at different growth stages and RNA sequencing on the Illumina MiSeq.
  5. Genome annotation.
  6. In-silico study of the differentially expressed genes under the different conditions in (4), and full bioinformatics analysis (pathway enrichment, gene regulatory networks, etc).