Ma Jian, Zheng Zhi, Stiller Jiri, Lan Xiu-Jin, Liu Yaxi, Deng Mei, Wang Penghao, Pu Zhien, Chen Guangdeng, Jiang Qian-Tao, Wei Yuming, Zheng You-Liang
a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
b CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia.
Genome. 2017 Mar;60(3):208-215. doi: 10.1139/gen-2016-0076. Epub 2016 Nov 1.
Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the 'Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat. Unexpectedly, no bias in expression breadth or in the distribution patterns of GO (gene ontology) terms for these genes was detected among the high-confidence genes. Further, network and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses indicated that most of these genes were not functionally related to each other. Interestingly, 30.7% of these SSG genes were most highly expressed in root, showing biased distribution given the distribution of the whole high-confidence genes. Collectively, these results facilitate our understanding of the loss of the genes that were retained in a SSG during the formation of hexaploid wheat.
六倍体面包小麦形成过程中的基因丢失已被多次报道。然而，我们对面包小麦单个亚基因组（SSG）上存在的基因进行全基因组分析的了解仍然有限。在本研究中，通过分析“中国春”染色体臂鸟枪法序列以及高可信度基因模型，我们在一个SSG上检测到了433个基因。与B亚基因组相比，在A和D亚基因组中观察到了更多的基因丢失。这些SSG基因中超过79%的直系同源基因在六倍体小麦的二倍体和四倍体亲属中被检测到。出乎意料的是，在高可信度基因中未检测到这些基因在表达广度或基因本体（GO）术语分布模式上的偏差。此外，网络和京都基因与基因组百科全书（KEGG）通路分析表明，这些基因中的大多数在功能上彼此不相关。有趣的是，这些SSG基因中有30.7%在根中表达最高，鉴于整个高可信度基因的分布，显示出偏向性分布。总的来说，这些结果有助于我们理解六倍体小麦形成过程中保留在一个SSG中的基因的丢失情况。
