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, Danquah Agyemang, Barnor Michael Teye, Jamnadass Ramni, Van de Peer Yves, Van Deynze Allen
Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Front Plant Sci. 2021 Sep 9;12:720670. doi: 10.3389/fpls.2021.720670. eCollection 2021.
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree () 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 (, , , , , and ), 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.
乳木是萨赫勒 - 苏丹非洲地区（SSA）农林复合公园地的一个决定性组成部分，对于维持当地生计和农村社区的农业环境至关重要。然而，尽管它具有经济和文化价值，更不用说它作为主要公园地物种所发挥的生态作用，但乳木仍处于半驯化状态，几乎没有系统遗传改良的历史。事实上，乳木较长的幼年期使得传统育种方法难以实施；但如果有基础资源，基因组辅助育种的机会巨大。在此，我们报告此类资源的开发及公开发布情况。利用FALCON-Phase工作流程，将162.6 Gb的长读长PacBio序列数据组装成一个658.7 Mbp的染色体规模参考基因组，该基因组注释有38,505个编码基因。基于此基因空间的全基因组复制（WGD）分析揭示了乳木进化历史中两次古老WGD事件的明显特征，一次发生在菊超目 - 蔷薇分支分化之前（1.16 - 1.26亿年前），另一次发生在杜鹃花目根部（6500 - 9000万年前）。在首次对可能控制硬脂含量（乳木果脂质量的主要决定因素）的脂肪酸（FA）生物合成基因进行全基因组研究时，发现了六种关键酶（、、、、和）的相对高拷贝数，其中一些可能源于乳木较近期的WGD事件。为了帮助将这些发现转化为用于特征鉴定、选择和全基因组关联研究（GWAS）的实用工具，利用来自乳木多样性样本的重测序数据开发了一个包含超过350万个功能注释、物理定位的单核苷酸多态性（SNP）的数据库。还展示了两个更小、更精选的推荐SNP集，一个用于GWAS（104,211个SNP），另一个针对FA生物合成基因（90个SNP）。有了这些资源，希望能支持乳木带沿线各国的项目，对乳木进行战略性的、基于基因组的保护，并实现其长期改良，以造福SSA地区。
