College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China.
Int J Mol Sci. 2020 Apr 24;21(8):3015. doi: 10.3390/ijms21083015.
Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) revealed a total of 88,733 high-confidence homologous genes of four major types (1:1:1, 1:1:0, 0:1:1 and 1:0:1) among the A, B and D subgenomes of wheat. This data was used to compare homologous gene densities among chromosomes, clarify their distribution and correspondence relationship, and compare their functional enrichment. The average density of 1:1:1 homologous genes was about 10 times more than the density of the other three types of homologous genes, although the homologous gene densities of the various chromosomes were similar within each homologous type. Three regions of exceptional density were detected in 1:1:1 homologous genes, the isolate peak on the tail of chromosome 4A, and the desert regions at the start of chromosome 7A and 7D. The correspondence between homologous genes of the wheat subgenomes demonstrated translocation between the tail segments of chromosome 4A and 5A, and the inversion of the segment of original 5A and 7B into the tail of 4A. The homologous genes on the inserting segments of 5A and 7B to 4A were highly enriched in nitrogen, primary metabolite and small molecular metabolism processes, compared with genes on other regions of the original 4A chromosome. This study provides a refined genome-scale reference of homologous genes for wheat molecular research and breeding, which will help to broaden the application of the wheat genome and can be used as a template for research on other polyploid plants.
确定小麦中基因组规模同源基因的分布和对应关系是揭示作物进化和驯化过程中发生的染色体重排的有效方法，这有助于改进作物育种。国际小麦基因组测序联盟（IWGSC）对小麦基因组进行的高分辨率和全面分析揭示了小麦 A、B 和 D 亚基因组中总共 88733 个高可信度的四种主要类型（1:1:1、1:1:0、0:1:1 和 1:0:1）同源基因。该数据用于比较染色体间同源基因密度，阐明其分布和对应关系，并比较其功能富集情况。1:1:1 同源基因的平均密度约为其他三种类型同源基因密度的 10 倍，尽管每种同源类型中各染色体的同源基因密度相似。在 1:1:1 同源基因中检测到三个异常密度区域，即 4A 染色体尾部的孤立峰以及 7A 和 7D 染色体起始处的沙漠区域。小麦亚基因组同源基因的对应关系表明，4A 和 5A 染色体尾部之间发生了易位，原始 5A 和 7B 染色体片段发生了倒位到 4A 尾部。与原始 4A 染色体其他区域的基因相比，5A 和 7B 插入到 4A 上的同源基因在氮、初级代谢物和小分子代谢过程中高度富集。这项研究为小麦分子研究和育种提供了精细化的基因组规模同源基因参考，有助于拓宽小麦基因组的应用，并可作为其他多倍体植物研究的模板。
