BREAD: Advancing the Cowpea Genome for Food Security

豌豆在美国也被称为黑眼豌豆，是一种原产于非洲的富含蛋白质的谷物植物。当豌豆与玉米、高粱或大米等淀粉谷物结合时，结果是能量和生长所需的主要营养物质的完整来源。它还提供富含蛋白质的叶子，并用于动物饲料。豌豆是撒哈拉以南非洲(SSA)人民的主要蛋白质来源，目前在那里种植面积超过2000万英亩，主要由拥有少量土地的农民种植。它的受欢迎程度也是因为它对低降雨量和高温的适应能力，同时也使土壤变得肥沃。尽管与非洲和其他地方的粮食安全有关，但对豌豆的基础研究相对较少。下一代测序技术的进步使人们有可能“阅读”豌豆的遗传物质，并破译最终为作物改良提供的指令(基因和遗传变异)。该项目的主要目标之一是为豌豆生产优化的参考基因组序列，这一壮举已经在人、鼠、牛和重要的经济作物上完成，如玉米、大豆、水稻、豆类和杨树。一个更广泛的目的是提供遗传资源，以提高非洲豌豆育种者现有网络的决策能力。育种者通过在携带有利性状的亲本之间杂交，并选择含有双亲有利性状的后代来开发新品种。该项目将为后代选择提供新的材料，此外还将提供有助于开发新的豌豆品种以增加粮食产量的知识。豌豆(Vigna Unguulata)是豆科菜豆属菜豆属植物，包括其他暖季型豆类如大豆、菜豆、木豆等，也包括小豆、绿豆等。豌豆是二倍体，染色体数为2n=22，基因组大小为620Mb。与其他豆科植物不同，豌豆缺乏已公布的参考基因组。自2011年以来，从以前的工作中已经可以获得高度碎片化的草稿基因组序列组合(GREAST-BLAST.org；VAREST-Web.org)，该组合是从60倍短阅读结合BAC-End和基因调查Sanger序列得出的。该项目将通过：(1)增加长阅读序列和光学图谱；(2)将重叠群锚定到最近开发的包含37,372个SNPs的遗传图谱；以及(3)改善更广泛的豆科植物界的浏览器访问，从而将豌豆序列提升到最先进的水平。这将使豌豆种质资源更深层次地利用于基因发现和标记开发，同时为豌豆遗传育种界提供更坚实的基础。将进行遗传杂交，以产生新的预育系，从理论上讲，这些预育系将利用最近开发的基于8个亲本的多亲本高级世代杂交(魔术)群体，携带优秀品系中存在的性状的最佳组合。将在基因组序列和单倍型的背景下传播标记性状信息，以便广泛采用标记信息育种。这项工作与布基纳法索、加纳、莫桑比克、尼日利亚和塞内加尔的领先育种项目密切相关，这些项目包括美国国际开发署的未来饲料项目和CGIAR的热带豆类项目。

Cowpea, also known as black-eyed pea in the U.S.A., is a protein-rich grain-producing plant native to Africa. When cowpea is combined with starchy grains such as corn, sorghum or rice, the result is a complete source of major nutrients for energy and growth. It also provides protein-rich leaves and is used for animal feed. Cowpea is the primary source of protein for people in sub-Saharan Africa (SSA) where it is presently produced on over 20 million acres mainly by farmers with small land holdings. Its popularity is also due to its resilience to low rainfall and heat while also enriching the soil. Despite its relevance to food security in Africa and elsewhere, there has been relatively little basic research on cowpea. Advances in next generation sequencing technology have made it possible to "read" the genetic material of cowpea and decipher the instructions (genes and genetic variation) that ultimately provide for crop improvement. Producing an optimized reference genome sequence for cowpea is one of the main goals of this project, a feat that has been accomplished for human, mouse, cow and economically important crop plants such as corn, soybean, rice, bean and poplar. A broader purpose is to provide genetic resources to improve decision-making abilities within an existing network of African cowpea breeders. Breeders develop new varieties by making crosses between parents that carry favorable traits and selecting progeny containing favorable characteristics of both parents. This project will provide new materials for progeny selection in addition to knowledge that will facilitate the development of new cowpea varieties for increased food production. Cowpea (Vigna unguiculata) is in the family Fabaceae, tribe Phaseoleae which includes other warm season legumes such as soybean, common bean and pigeon pea, as well as Vigna species adzuki bean and mung bean. Cowpea is diploid with 2n=22 chromosomes and a genome size of 620 Mb. Unlike other legumes, cowpea lacks a published reference genome. A highly fragmented draft genome sequence assembly has been available from previous work since 2011 (harvest-blast.org; harvest-web.org) and is derived from 60x short-reads combined with BAC-end and gene survey Sanger sequences. This project will elevate the sequence of cowpea to state-of-the art by: (1) adding long-read sequences and an optical map; (2) anchoring contigs to a recently developed genetic map containing 37,372 SNPs; and (3) improving browser access for the broader legume community. This will enable deeper utilization of cowpea germplasm for gene discovery and marker development, while providing a stronger foundation for the cowpea genetics and breeding community. Genetic intercrosses will be conducted to produce new pre-breeding lines that will theoretically carry optimal combinations of traits present within elite lines using a recently developed multi-parent advanced generation intercross (MAGIC) population based on eight parental lines. Marker-trait information, in the context of the genome sequence and haplotypes, will be disseminated for broad adoption of marker-informed breeding. This work is tightly linked to leading breeding programs in Burkina Faso, Ghana, Mozambique, Nigeria and Senegal through USAID Feed the Future and CGIAR Tropical Legumes projects.