The College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Int J Mol Sci. 2023 Jun 16;24(12):10217. doi: 10.3390/ijms241210217.
Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat.
作物遗传多样性是农业适应和生产力的基础。先前的研究表明，小麦商业品种的等位基因多样性较差是其进一步改良的主要障碍。同一品种内的同源物，包括多倍体中的旁系同源物和直系同源物，占一个物种总基因的很大一部分。同源物多样性、品种内多样性（IVD）及其功能尚未阐明。普通小麦是一种重要的粮食作物，是一种六倍体物种，具有三个亚基因组。本研究基于两个代表性品种的高质量参考基因组，分析了普通小麦同源基因的序列、表达和功能多样性，这两个品种分别是现代商业品种爱康 58（AK58）和地方品种春小麦（CS）。共鉴定出 85908 个同源基因，占所有小麦基因的 71.9%，包括旁系同源物（IPs）、直系同源物（OPs）和单拷贝直系同源物（SORs），表明同源物是小麦基因组的重要组成部分。OPs 和 SORs 的序列、表达和功能变异水平高于 IPS，这表明多倍体比二倍体具有更多的同源多样性。扩张基因是 OPs 的一种特殊类型，对作物进化和适应做出了巨大贡献，并赋予作物特殊的特征。几乎所有农艺重要基因都来自 OPs 和 SORs，这表明它们对多倍体进化、驯化和改良具有重要功能。我们的研究结果表明，IVD 分析是评估基因组内变异的一种新方法，利用 IVD 可能为植物育种，特别是多倍体作物如小麦的育种开辟新的道路。
