Abstract
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea’s extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea’s evolutionary past, one prior to the Astrid-Rosid divergence (116–126 Mya) and the other at the root of the order Ericales (65–90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea’s more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.
Highlights
Shea tree (Vitellaria paradoxa) is a unique agroforestry tree species central to sustaining local livelihoods and the farming environments of rural communities across Africa’s SudanoSahelian agroclimactic belt
The FALCON-Unzip pipeline resulted in a 784.3 Mb assembly consisting of 1,215 putative primary contigs with a contig length N50 of 2.03 Mbp (Table 1)
The primary contigs from the final assembly were placed into chromosome-level scaffolds on the basis of three-dimensional proximity information obtained via chromosome conformation capture (Hi-C) analysis (Burton et al, 2013; Bickhart et al, 2017)
Summary
Shea tree (Vitellaria paradoxa) is a unique agroforestry tree species central to sustaining local livelihoods and the farming environments of rural communities across Africa’s SudanoSahelian agroclimactic belt. Rural families in hundreds of thousands of villages across the so-called “shea belt,” a 500–750 km wide semi-arid area stretching 6,000 km and spanning 21 countries from Senegal to South Sudan, use shea in their daily lives as an edible butter/oil, soap, cosmetic, and medicine. Shea agroforestry parklands, comprised of annual crops and scattered shea trees that can reach densities of 20–50 trees/ha in areas of strong shea culture, result from self-sown propagation and systematic management (selection and protection, as opposed to planting) by farmers through successive fallow and cultivation cycles. Farmer selection of preferred individuals and removal of inferior trees for charcoal production or building materials serve to increase the levels of locally valued traits, resulting in what has been called a semi-domestication of the species (Lovett and Haq, 2000; Maranz and Wiesman, 2003)
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