Guerra-Garcia Azalea, Haile Teketel, Ogutcen Ezgi, Bett Kirstin E, von Wettberg Eric J
Department of Plant Sciences University of Saskatchewan Saskatoon Saskatchewan Canada.
Conservatoire et Jardin Botaniques de la Ville de Genève Geneva Switzerland.
Evol Appl. 2022 Aug 21;15(8):1313-1325. doi: 10.1111/eva.13467. eCollection 2022 Aug.
The characterization and preservation of genetic variation in crops is critical to meeting the challenges of breeding in the face of changing climates and markets. In recent years, the use of single nucleotide polymorphisms (SNPs) has become routine, allowing us to understand the population structure, find divergent lines for crosses, and illuminate the origin of crops. However, the focus on SNPs overlooks other forms of variation, such as copy number variation (CNVs). Lentil is the third most important cold-season legume and was domesticated in the Fertile Crescent. We genotyped 324 accessions that represent its global diversity, and using both SNPs and CNVs, we dissected the population structure and genetic variation, and identified candidate genes. Eight clusters were detected, most of them located in or near the Fertile Crescent, even though different clusters were present in distinct regions. The cluster from South Asia was particularly differentiated and presented low diversity, contrasting with the clusters from the Mediterranean and the northern temperate. Accessions from North America were mainly assigned to one cluster and were highly diverse, reflecting the efforts of breeding programs to integrate variation. Thirty-three genes were identified as candidates under selection and among their functions were sporopollenin synthesis in pollen, a component of chlorophyll B reductase that partially determines the antenna size, and two genes related to the import system of chloroplasts. Eleven percent of all lentil genes and 21% of lentil disease resistance genes were affected by CNVs. The gene categories overrepresented in these genes were "enzymes," "Cell Wall Organization," and "external stimuli response." All the genes found in the latter were associated with pathogen response. CNVs provided information about population structure and might have played a role in adaptation. The incorporation of CNVs in diversity studies is needed for a broader understanding of how they evolve and contribute to domestication.
作物遗传变异的表征与保存对于应对气候变化和市场变化带来的育种挑战至关重要。近年来，单核苷酸多态性（SNP）的使用已成为常规操作，使我们能够了解种群结构、找到用于杂交的不同品系，并阐明作物的起源。然而，对SNP的关注忽略了其他形式的变异，如拷贝数变异（CNV）。兵豆是第三重要的冷季豆类，在新月沃地被驯化。我们对代表其全球多样性的324份种质进行了基因分型，并利用SNP和CNV剖析了种群结构和遗传变异，还鉴定了候选基因。检测到八个聚类，其中大多数位于新月沃地或其附近，尽管不同区域存在不同的聚类。来自南亚的聚类特别分化且多样性较低，与来自地中海和北温带的聚类形成对比。来自北美的种质主要被归为一个聚类且高度多样，这反映了育种计划整合变异的努力。33个基因被鉴定为受选择的候选基因，其功能包括花粉中孢粉素的合成、部分决定天线大小的叶绿素B还原酶的一个组分，以及与叶绿体导入系统相关的两个基因。所有兵豆基因的11%和兵豆抗病基因的21%受CNV影响。这些基因中过度富集的基因类别是“酶”“细胞壁组织”和“外部刺激反应”。在后者中发现的所有基因都与病原体反应相关。CNV提供了有关种群结构的信息，可能在适应过程中发挥了作用。为了更广泛地了解CNV如何进化以及如何促进驯化，需要将CNV纳入多样性研究中。
