BREAD ABRDC: Development of Genomic Resources in Water Yam (Dioscorea alata L.) for Accelerated Breeding and Improvement

面包 ABRDC：开发水山药 (Dioscorea alata L.) 基因组资源以加速育种和改良

• 批准号: 1543967
• 负责人: Daniel Rokhsar
• 金额: $ 145.86万
• 依托单位: University of California-Berkeley
• 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: 2016-05-15 至 2022-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1543967&HistoricalAwards=false
• 关键词: BREAD; ABRDC; Development; Genomic; Resources

Yams (genus Dioscorea) are an important source of food and income for millions of smallholder farmers in the tropical and sub-tropical regions of Africa, Asia, the Pacific, and Latin America. Rich in carbohydrates, and containing protein and vitamin C, the year-round availability of yams makes them preferable to seasonal crops. The importance of yams in West Africa is exemplified by their vital role in traditional culture, rituals and religion; yam production is declining, however, due to threats from pests and diseases. Thus, in the context of surging global population growth, improved yam breeding techniques are urgently needed. Water yam, also called greater yam (Dioscorea alata) is the most widely distributed cultivated yam species in the world, and its advantages include high nutritional content, long storability of tubers, and ability to yield in poor quality soil. This project will leverage cutting-edge DNA sequencing and computational analysis to provide a high quality water yam genome assembly and genetic map to the yam community, which will allow breeders to use modern genetic methods to breed the crop more efficiently. The project will also characterize the natural genetic variability present in global collections, yielding insight into how they may be used to improve the crop, and contributing to an understanding of the relationship between water yam DNA sequence and traits important to smallholder farmers. Bringing water yam into the modern genomics era will facilitate the accelerated release of improved varieties to the farmers that need them.The water yam Dioscorea alata is superior to most cultivated yam species due to its potential to yield under low to average soil fertility, ease of propagation, early vigor for weed suppression, and low post-harvest losses. Threats, however, include anthracnose disease, which can cause losses of up to 90% of production, and breeding for desired traits in water yam is arduous due to its autopolyploid and heterozygous nature, long growth cycle, and erratic flowering. This project will accelerate the improvement of water yam by (1) constructing a high quality chromosome-scale genome assembly for D. alata, interpreted through annotation and comparative analysis, (2) producing a framework genetic map for D. alata via analysis of mapcrosses segregating for traits important for farmers, and (3) characterizing the global collection of D. alata cultivars. Advanced technologies such as PacBio de novo sequencing, whole-genome resequencing, genotyping-by-sequencing, flow cytometry for ploidy analysis, and publicly available and custom bioinformatics tools, will be leveraged. The chromosome-scale genome assembly and genetic map will lay the groundwork for more efficient breeding approaches such as genomic selection in water yam. Quantitative trait locus analysis of mapping populations segregating for anthracnose resistance and tuber quality is expected to yield specific sequence variants linked to, and thus mechanistic insight into, those traits. Study of water yam diversity across global collections will elucidate its breeding history, reveal bottlenecks, and suggest strategies for broadening the gene pool. All sequencing resources will be publicly available through the NCBI and the phytozome plant genomics resource.

山药是非洲、亚洲、太平洋和拉丁美洲热带和亚热带地区数百万小农的重要食物和收入来源。山药富含碳水化合物，含有蛋白质和维生素C，全年可用，使它们比季节性作物更受欢迎。山药在西非的重要性体现在其在传统文化、仪式和宗教中的重要作用;然而，由于病虫害的威胁，山药产量正在下降。因此，在全球人口激增的背景下，迫切需要改进山药育种技术。山药（学名：Greater Yam，学名：Aurea阿拉塔）是世界上分布最广的山药栽培品种，具有营养价值高、耐贮性好、能在贫瘠的土壤中生长等优点。该项目将利用尖端的DNA测序和计算分析，为山药社区提供高质量的山药基因组组装和遗传图谱，这将使育种者能够使用现代遗传方法更有效地培育作物。该项目还将描述全球收藏品中存在的自然遗传变异性，深入了解它们如何用于改善作物，并有助于了解山药DNA序列与小农重要性状之间的关系。将山药带入现代基因组学时代将有助于加速向有需要的农民提供改良品种。由于其在低至平均土壤肥力下的产量潜力、易于繁殖、早期抑制杂草的活力以及收获后损失低，因此山药翅荚山药上级大多数栽培山药品种。然而，威胁包括炭疽病，其可导致高达90%的产量损失，并且由于其同源多倍体和杂合性质、长生长周期和不稳定的开花，在水山药中育种所需性状是艰巨的。本项目将通过（1）构建高质量的山药染色体级基因组组装体;阿拉塔（Alata）的遗传图谱，并对图谱进行了注释和比较分析。阿拉塔的遗传多样性分析;（3）对D.阿拉塔品种。先进的技术，如PacBio从头测序，全基因组重测序，基因分型测序，流式细胞术倍性分析，以及公开和定制的生物信息学工具，将被利用。染色体规模的基因组组装和遗传图谱将为更有效的育种方法奠定基础，如山药的基因组选择。对炭疽病抗性和块茎质量分离的作图群体进行数量性状基因座分析，预计将产生与这些性状相关的特定序列变异，从而对这些性状进行机理分析。在全球范围内对水山药多样性的研究将阐明其育种历史，揭示瓶颈，并提出扩大基因库的策略。所有测序资源将通过NCBI和植物群植物基因组学资源公开提供。