Development of genomic resources in water yam (Dioscorea alata L.) for accelerated breeding and improvement

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.

薯蓣（Yams，属名Dioscorea）是非洲、亚洲、太平洋地区及拉丁美洲数百万小农的重要粮食与收入来源。薯蓣富含碳水化合物，同时含有蛋白质与维生素C，且可全年供应，相较于季节性作物更具优势。薯蓣在西非的重要性体现在其在传统文化、仪式与宗教中的核心地位；然而受病虫害威胁，薯蓣的产量正持续下滑。因此，在全球人口激增的背景下，亟需改良薯蓣育种技术。

大薯（Water yam，亦称greater yam，学名Dioscorea alata）是全球分布最广的栽培薯蓣品种，其优势在于营养丰富、块茎耐储性强，且可在贫瘠土壤中正常结薯。本项目将依托前沿DNA测序与计算分析技术，为全球薯蓣研究群体提供高质量的基因组组装（genome assembly）与遗传图谱（genetic map），助力育种者借助现代遗传手段更高效地开展作物育种工作。本项目同时将对全球种质资源库中的自然遗传变异进行表征分析，阐明其在作物改良中的应用潜力，并助力解析大薯DNA序列与小农关注的重要农艺性状之间的关联机制。推动大薯进入现代基因组学时代，将有助于加快改良品种的选育进程，并将其快速推广至有需求的农户手中。

大薯（Dioscorea alata）相较于多数栽培薯蓣品种更具优势：可在低至中等肥力的土壤中结薯、繁殖简便、苗期长势旺盛可抑制杂草，且采后损耗率低。然而，大薯也面临诸多威胁：其中炭疽病可造成最高达90%的产量损失；且由于其为同源多倍体且具有高度杂合性、生长周期长、开花不稳定等特性，靶向改良目标性状的育种工作难度极大。

本项目将通过以下三项任务加速大薯的遗传改良：（1）通过基因注释与比较分析，构建D. alata的高质量染色体级基因组组装（chromosome-scale genome assembly）；（2）通过分析与农户关注性状相关的分离作图群体，构建D. alata的框架遗传图谱；（3）对全球D. alata栽培品种种质资源库进行遗传变异表征。本项目将采用多项先进技术，包括PacBio从头测序（de novo sequencing）、全基因组重测序（whole-genome resequencing）、测序分型（genotyping-by-sequencing, GBS）、用于倍性分析（ploidy analysis）的流式细胞术（flow cytometry），以及公开可用与自主开发的生物信息学工具。

该染色体级基因组组装结果与遗传图谱将为大薯的高效育种手段（如基因组选择育种）奠定基础。对炭疽病抗性与块茎品质相关的分离作图群体进行数量性状位点（quantitative trait locus, QTL）分析，有望鉴定出与这些性状关联的特异性序列变异，从而解析其分子调控机制。对全球种质资源库中的大薯遗传多样性进行研究，将阐明其育种历史、揭示遗传瓶颈，并为拓宽其基因库提供可行策略。所有测序相关资源将通过美国国家生物技术信息中心（NCBI，National Center for Biotechnology Information）与Phytozome植物基因组数据库向公众开放。