Institute of Life Sciences, Scuola Superiore Sant'Anna, P.zza Martiri della Libertà 33, Pisa, 56127, Italy.
Institute of Applied Genomics, Via J. Linussio, 51 ZIU, Udine, 33100, Italy.
Plant J. 2018 May;94(4):670-684. doi: 10.1111/tpj.13888. Epub 2018 Apr 18.
Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next-generation sequencing was used to generate 1.3 million genome-wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the A subgenome of modern wheat. A set of 75 511 high-quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the A subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome-wide association approach, identifying several marker-environment associations (MEAs). Fifty-seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding.
现代植物育种可以利用在不同生境条件下进化的作物野生近缘种自然群体中存在的等位基因变异。本研究利用下一代测序技术，在小麦 A 基因组的野生供体二粒小麦（Triticum urartu L.）的离体收集物上生成了 130 万个全基因组单核苷酸多态性（SNP）。保留了一组 75511 个高质量的 SNP 来描述在新月沃地收集的 298 份二粒小麦材料。二粒小麦表现出复杂的遗传多样性模式，有两个主要的遗传群从西向东依次分布。将采样点的地理信息纳入后，表明遗传多样性与分离自约旦和黎巴嫩、叙利亚和土耳其南部以及土耳其东部、伊朗和伊拉克的样本之间的地理距离（R=0.19）相关。利用野生一粒小麦基因组，将 SNP 的物理位置映射到 A 亚基因组的 7 条染色体上，这使我们能够描述收集物中连锁不平衡的相对缓慢衰减。根据二粒小麦材料的地理分布描述了局域适应性的位点，在 4A 染色体上鉴定到一个定向选择的热点。从网格数据推导出生物气候的变化，并使用全基因组关联方法将其与等位基因变异相关联，鉴定出几个标记-环境关联（MEA）。57 个 MEA 与海拔和温度测量值相关，而 358 个与降雨量测量值相关。利用最显著的 MEA 和局域适应性的位点，鉴定出具有潜在适应性的基因组位点（其中一些已在小麦中报道），包括休眠和抗冻位点。我们提倡将基因组学和景观基因组学应用于作物野生近缘种的离体收集，以有效地鉴定出有前途的等位基因和遗传材料，用于现代作物育种。
