BREAD ABRDC: Integrated Resource Development for the Genome-enabled Improvement of Shea Tree for sub-Saharan Africa

University Of New Hampshire, Durham NH

Investigators

Abstract

Shea trees are central to sustaining the livelihoods of thousands of rural communities across the vast Sahel region of sub-Saharan Africa. Uniquely adapted to this harsh semi-arid zone, shea trees produce oil-rich nuts, which an estimated 18.4 million women gather and manually process into a nutrient-rich butter used as cooking oil, soap, and medicine for their families. Shea also provides a rare source of income to these subsistence households across 21 countries, as the butter is valued by both the cosmetics and chocolate industries. Referred to as "women's gold," shea is one of the few resources that female members of rural households in the region control, from harvesting to commercialization. Despite its cultural, economic, and food security importance, however, the shea tree is under threat. Slow-growing shea trees traditionally are not planted; rather, nuts are gathered from mature, essentially wild trees found in minimally-managed areas called parklands. Due to increasing land-use pressures, the number of these parkland shea trees is declining. In a broad partnership with regional organizations, this project seeks to reverse this trend by improving the value of shea through modern breeding. By turning this semi-wild, variably-yielding species into a more actively managed and deliberately planted tree crop, the long-term impact of this project will be no less than improved livelihoods (enhanced nutrition, increased income, and more robust risk mitigation) for the millions of rural women and their families across sub-Saharan Africa currently dependent on the highly valued but threatened parkland populations of shea tree. With the long juvenile period of shea tree (Vitellaria paradoxa) making traditional breeding approaches untenable, efficient improvement of the species requires modern breeding tools, including publicly-available foundational genomics resources and highly characterized mapping populations. This project will develop such resources, thereby enabling the long-term genome-enabled improvement of this currently undomesticated species. An assembly of the highly heterozygous (>37%) 0.8 Gb diploid genome will be accomplished using long-read (PacBio; HGAP) sequencing of cv. 'AK01,' a key parent in West African shea breeding efforts to date. Once annotated using RNA-seq data from replicated, multiple-tissue libraries (Illumina Hi-seq; MAKER-P), a comprehensive collection of mapped and functionally-classified SNPs will be developed by resequencing (Ion Proton)100 diverse V. paradoxa accessions gathered from across the species' natural distribution. By also developing a nested association mapping population, a replicated association mapping panel, and an open-source repository for all genotypic and phenotypic data, this project aims to put genomic selection of improved shea populations within the reach of regional breeding and parkland regeneration programs. By training a PhD student and holding a regional workshop, the project also invests in the capacity building necessary to bring the full potential of these genomic, informatic, and plant genetic resources to fruition. Through a broad partnership with national programs, the CGIAR system, the African Orphan Crops Consortium (AOCC), and the Global Shea Alliance (GSA), all project outcomes are poised for immediate translation to the shea improvement sector.