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

山药（薯蓣属）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，一年四季都有，比季节性作物更受欢迎。山药在西非的重要性体现在它们在传统文化、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，在全球人口急剧增长的背景下，迫切需要改良的山药育种技术。山药，又称大山药（Dioscorea alata），是世界上分布最广泛的栽培山药品种，其优点是营养成分高，块茎储存期长，在劣质土壤中也能高产。该项目将利用尖端的DNA测序和计算分析，为山药群落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集的自然遗传变异性，从而深入了解如何利用它们来改善作物，并有助于了解水药DNA序列与对小农重要的性状之间的关系。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释放改良品种。水山药薯蓣（Dioscorea alata）由于其在低至平均土壤肥力条件下的产量潜力、易于繁殖、抗杂草的早期活力和低收获后损失而优于大多数栽培山药品种。然而，威胁包括炭疽病，可导致高达90%的产量损失，并且由于其自多倍体和杂合性，长生长周期和开花不稳定，在水山药中培育所需性状是艰巨的。本项目将通过(1)通过注释和比较分析构建高质量的山药染色体尺度基因组组合，(2)通过分析对农民重要性状的mapcross分离，生成山药框架遗传图谱，以及(3)对全球山药品种集合进行表征，加快山药的改良。将利用PacBio de novo测序、全基因组重测序、基因分型测序、用于倍体分析的流式细胞术以及公开可用和定制的生物信息学工具等先进技术。染色体尺度的基因组组装和遗传图谱将为更有效的育种方法（如基因组选择）奠定基础。对炭疽病抗性和块茎质量群体分离的数量性状位点分析有望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。对全球水药品种多样性的研究将有助于阐明其育种历史，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phytozome植物基因组资源公开提供。

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.