Nomura Yasuyuki, Okada Moeko, Tameshige Toshiaki, Takenaka Shotaro, Shimizu Kentaro K, Nasuda Shuhei, Nagano Atsushi J
Research Institute for Food and Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194 Japan.
Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan.
Plant Cell Physiol. 2025 Mar 31;66(3):347-357. doi: 10.1093/pcp/pcaf011.
Common wheat is an allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3' RNA-seq, is technology efficient at obtaining homoeolog-distinguished transcriptomes. Here, we applied Lasy-Seq to obtain transcriptome data from the seedlings, second leaves, and root tips of 25 common wheat lines mainly from East Asia. Roots and seedlings were similar to each other in transcriptome profiles, but they were different from the leaves. We then asked how three homoeologous genes from different subgenomes (i.e. triads) show different levels of expression. Specifically, we examined the effects of subgenomes, lines, and their interaction on the expression levels of each homoeolog triad, separately in each tissue. Of the 19 805 homoeolog triads, 51-55% showed significant effect of subgenome, suggesting cis-regulation, whereas 24-30% showed significant effect line, suggesting trans-regulation. We also found that 7.7-9.0% triads showed significant effects of the interaction. Hierarchical clustering and co-trans regulation network analysis of homoeolog triads revealed that the patterns of expression polymorphisms among the lines were shared in different genes. Our results also implied that expression variation between lines is caused by changes in a smaller number of common trans-factors. We performed gene ontology (GO)-term enrichment analysis using newly annotated and substantially improved GO annotations, which revealed that GO terms related to each tissue-type function were enriched in genes expressed in the leaves and roots. Our information provides fundamental knowledge for the future breeding of plants possessing complex gene regulatory networks such as common wheat.
普通小麦是一种异源六倍体，很难获得区分同源基因的转录组数据。Lasy-Seq是一种3' RNA测序技术，在获取区分同源基因的转录组方面效率很高。在这里，我们应用Lasy-Seq从主要来自东亚的25个普通小麦品系的幼苗、第二片叶子和根尖获取转录组数据。根和幼苗的转录组图谱彼此相似，但与叶子不同。然后，我们研究了来自不同亚基因组的三个同源基因（即三联体）如何表现出不同水平的表达。具体来说，我们分别在每个组织中研究了亚基因组、品系及其相互作用对每个同源三联体表达水平的影响。在19805个同源三联体中，51-55%表现出亚基因组的显著影响，表明存在顺式调控，而24-30%表现出品系的显著影响，表明存在反式调控。我们还发现7.7-9.0%的三联体表现出相互作用的显著影响。同源三联体的层次聚类和共反式调控网络分析表明，品系间表达多态性模式在不同基因中是共享的。我们的结果还暗示，品系间的表达变异是由较少数量的常见反式因子的变化引起的。我们使用新注释且大幅改进的基因本体（GO）术语注释进行了GO术语富集分析，结果显示与每种组织类型功能相关的GO术语在叶和根中表达的基因中富集。我们的信息为未来培育具有复杂基因调控网络的植物（如普通小麦）提供了基础知识。
