BREAD: Advancing the Cowpea Genome for Food Security

面包：推进豇豆基因组的发展以保障粮食安全

• 批准号: 1543963
• 负责人: Timothy Close
• 金额: $ 158.58万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2021-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1543963&HistoricalAwards=false
• 关键词: BREAD; Advancing; Cowpea; Genome; Food

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.

豇豆，在美国也被称为黑眼豌豆，是一种富含蛋白质的谷物生产植物，原产于非洲。当豇豆与玉米、高粱或大米等淀粉质谷物结合时，其结果是能量和生长的主要营养素的完整来源。它还提供富含蛋白质的叶子，并用于动物饲料。 豇豆是撒哈拉以南非洲（SSA）人民的主要蛋白质来源，目前主要由拥有小块土地的农民在2000多万英亩的土地上生产。它的受欢迎程度也是由于它对低降雨量和热量的适应能力，同时也丰富了土壤。尽管豇豆与非洲和其他地区的粮食安全有关，但对豇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”豇豆的遗传物质，并破译最终提供作物改良的指令（基因和遗传变异）。 为豇豆生产优化的参考基因组序列是该项目的主要目标之一，这一壮举已经在人类、小鼠、奶牛和经济上重要的作物植物如玉米、大豆、水稻、菜豆和白杨上完成。一个更广泛的目的是提供遗传资源，以提高非洲豇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进行杂交并选择具有双亲有利性状的后代来培育新品种。该项目将为后代选择提供新的材料，除了知识，将促进新的豇豆品种的发展，以增加粮食产量。豇豆（Vigna unguiculata）属于豆科、菜豆族（Phaseoleae），其包括其它暖季豆科植物如大豆、菜豆和木豆，以及豇豆属物种红小豆和绿豆。豇豆是二倍体，2n=22条染色体，基因组大小为620 Mb。与其他豆类不同，豇豆缺乏已发表的参考基因组。自2011年以来，之前的工作（harvest-blast.org; harvest-web.org）已提供了高度片段化的基因组序列组装草图，该草图源自60 x短读段结合BAC末端和基因调查桑格序列。该项目将通过以下方式将豇豆的序列提升到最先进水平：（1）添加长读段序列和光学图谱;（2）将重叠群锚定到最近开发的包含37，372个SNP的遗传图谱上;（3）改善更广泛的豆类社区的浏览器访问。这将使豇豆种质资源的基因发现和标记开发的更深层次的利用，同时提供了一个更强大的基础，豇豆遗传和育种界。将进行遗传杂交，以产生新的育种前品系，这些品系理论上将携带精英品系内存在的性状的最佳组合，使用最近开发的基于八个亲本品系的多亲本高级世代杂交（MAGIC）群体。将在基因组序列和单倍型的背景下传播标记-性状信息，以广泛采用标记知情育种。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通过美援署“未来粮食”和国际农业研究磋商组织热带豆类项目开展的主要育种方案密切相关。

项目成果

OMGS: Optical Map-based Genome Scaffolding

OMGS：基于光学图谱的基因组支架

• DOI: 10.1007/978-3-030-17083-7_12
• 发表时间: 2019
• 期刊: RECOMB 2019 - ACM Annual Conference on Research in Computational Molecular Biology
• 作者: W. Pan, T. Jiang

Accurate detection of chimeric contigs via Bionano optical maps

• DOI: 10.1093/bioinformatics/bty850
• 发表时间: 2019-05-15
• 期刊: BIOINFORMATICS
• 影响因子: 5.8
• 作者: Pan, Weihua;Lonardi, Stefano
• 通讯作者: Lonardi, Stefano