Genomic Resources to Guide Improvement of the Shea Tree.

Autor:	Hale I; Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States., Ma X; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; Center for Plant Systems Biology, VIB, Ghent, Belgium., Melo ATO; Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States., Padi FK; Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana., Hendre PS; AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya., Kingan SB; Pacific Biosciences, Menlo Park, CA, United States., Sullivan ST; Phase Genomics, Seattle, WA, United States., Chen S; Seed Biotechnology Center, University of California, Davis, Davis, CA, United States., Boffa JM; AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya., Muchugi A; AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya.; The Forage Genebank, Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa, Ethiopia., Danquah A; West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana., Barnor MT; Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana., Jamnadass R; AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya., Van de Peer Y; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; Center for Plant Systems Biology, VIB, Ghent, Belgium.; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.; Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa., Van Deynze A; AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya.; Seed Biotechnology Center, University of California, Davis, Davis, CA, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in plant science [Front Plant Sci] 2021 Sep 09; Vol. 12, pp. 720670. Date of Electronic Publication: 2021 Sep 09 (Print Publication: 2021).
DOI:	10.3389/fpls.2021.720670
Abstrakt:	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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2021 Hale, Ma, Melo, Padi, Hendre, Kingan, Sullivan, Chen, Boffa, Muchugi, Danquah, Barnor, Jamnadass, Van de Peer and Van Deynze.)
Databáze:	MEDLINE
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