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

牛油果树是维持撒哈拉以南非洲广大萨赫勒地区数千个农村社区生计的核心。牛油果树独特地适应了这一严酷的半干旱地区，生产出富含油脂的坚果，估计有1840万妇女采集这些坚果，并手工加工成营养丰富的黄油，用作食用油、肥皂和家庭药品。乳木果还为21个国家的这些自给家庭提供了一种罕见的收入来源，因为化妆品和巧克力行业都重视这种黄油。乳木果被称为“妇女的黄金”，是该地区农村家庭中女性成员从收获到商业化控制的少数资源之一。尽管其文化，经济和粮食安全的重要性，然而，牛油果树受到威胁。生长缓慢的乳木果树传统上不种植;相反，坚果是从成熟的，基本上是野生树木在最低限度管理的地区发现的，称为公园。由于土地使用压力的增加，这些帕克兰的牛油果树的数量正在下降。该项目与区域组织建立了广泛的伙伴关系，力求通过现代育种提高牛油果的价值，从而扭转这一趋势。通过将这种半野生、产量不稳定的物种转变为更积极管理和有意种植的树木作物，该项目的长期影响将不亚于改善生计（增强营养，增加收入，和更强有力的风险缓解），为数百万农村妇女及其家庭提供服务。撒哈拉非洲目前依赖于高度重视但受到威胁的帕克兰种群。（Vitellaria paradoxa）使传统的育种方法站不住脚，有效地改善物种需要现代育种工具，包括公开的基础基因组学资源和高度特征化的作图群体。该项目将开发这些资源，从而使长期基因组使能改善这一目前未驯化的物种。高度杂合（37%）0.8Gb二倍体基因组的组装将使用cv的长读段（PacBio; HGAP）测序来完成。AK 01是迄今为止西非牛油果育种工作中的一个关键亲本。一旦使用来自复制的多组织文库（Illumina Hi-seq; MAKER-P）的RNA-seq数据进行注释，将通过重新测序（Ion Proton）从物种的自然分布中收集的100个不同的V. paradoxa登记来开发映射和功能分类的SNP的综合集合。通过开发一个嵌套的关联映射群体，一个复制的关联映射面板，以及一个所有基因型和表型数据的开源存储库，该项目旨在将区域育种和帕克兰计划范围内的改良牛油果种群的基因组选择。通过培训一名博士生和举办区域研讨会，该项目还投资于必要的能力建设，以充分发挥这些基因组、信息和植物遗传资源的潜力。通过与国家项目、国际农业研究磋商组织系统、非洲孤生作物联盟（AOCC）和全球乳木果联盟（GSA）的广泛合作，所有项目成果都将立即转化为乳木果改良部门。

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.