Genomic resources to guide improvement of the shea tree

Show simple item record Hale, Iago Ma, Xiao Melo, Arthur T.O. Padi, Francis Kwame Hendre, Prasad S. Kingan, Sarah B. Sullivan, Shawn T. Chen, Shiyu Boffa, Jean-Marc Muchugi, Alice Danquaah, Agyemang Danquah, Agyemang Barnor, Michael Teye Jamnadass, Ramni Van de Peer, Yves Van Deynze, Allen 2022-03-10T11:41:12Z 2022-03-10T11:41:12Z 2021-09-09
dc.description.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 longread 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. en_ZA
dc.description.department Biochemistry en_ZA
dc.description.department Genetics en_ZA
dc.description.department Microbiology and Plant Pathology en_ZA
dc.description.librarian am2022 en_ZA
dc.description.sponsorship The Basic Research to Enhance Agricultural Development (BREAD) program (award #1543942), jointly funded by the National Science Foundation (NSF) and the Bill & Melinda Gates Foundation (BMGF); the CGIAR Research Program (CRP) on Forests, Trees, and Agroforestry (FTA) ; the CGIAR (ICRAF) Genebank Platform; European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program; Ghent University; the AOCC and the UC Davis Seed Biotechnology Center. en_ZA
dc.description.uri en_ZA
dc.identifier.citation Hale, I., Ma, X., Melo, A.T.O., Padi, F.K., Hendre, P.S., Kingan, S.B., Sullivan, S.T., Chen, S.Y., Boffa, J.M., Muchugi, A., Danquah, A., Barnor, M.T., Jamnadass, R., Van de Peer, Y. & Van Deynze, A. (2021) Genomic Resources to Guide Improvement of the Shea Tree. Frontiers in Plant Science 12:720670. DOI: 10.3389/fpls.2021.720670. en_ZA
dc.identifier.issn 1664-462X (online)
dc.identifier.other 10.3389/fpls.2021.720670
dc.language.iso en en_ZA
dc.publisher Frontiers Research Foundation en_ZA
dc.rights © 2021 Hale, Ma, Melo, Padi, Hendre, Kingan, Sullivan, Chen, Boffa, Muchugi, Danquah, Barnor, Jamnadass, Van de Peer and Van Deynze. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). en_ZA
dc.subject Shea tree en_ZA
dc.subject Vitellaria paradoxa en_ZA
dc.subject Reference genome en_ZA
dc.subject Fatty acid en_ZA
dc.subject Plant breeding en_ZA
dc.subject Sahelo-Sudanian Africa (SSA) en_ZA
dc.subject Whole genome duplication (WGD) en_ZA
dc.subject Single nucleotide polymorphism (SNP) en_ZA
dc.title Genomic resources to guide improvement of the shea tree en_ZA
dc.type Article en_ZA

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