論文 - 詳細
| RRC ID | 85509 |
|---|---|
| 著者 | Nomura Y, Okada M, Tameshige T, Takenaka S, Shimizu KK, Nasuda S, Nagano AJ. |
| タイトル | Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans-regulation architectures. |
| ジャーナル | Plant Cell Physiol |
| Abstract |
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. |
| 巻・号 | 66(3) |
| ページ | 347-357 |
| 公開日 | 2025-3-31 |
| DOI | 10.1093/pcp/pcaf011 |
| PII | 7962036 |
| PMID | 39829360 |
| MeSH | Gene Expression Profiling Gene Expression Regulation, Plant / genetics Genome, Plant* / genetics Models, Statistical Plant Leaves / genetics Plant Roots / genetics Seedlings / genetics Transcriptome* / genetics Triticum* / genetics |
| IF | 4.062 |
| オルトメトリクス指標 |
オルトメトリクス指標項目
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| 最多言及媒体 | X(Twitter) |
| 各媒体での言及数の合計 | 25 |
| 過去6か月間でのオルトメトリクス指標の変動値 | 0.0 |
| リソース情報 | |
| コムギ | LPGKU2306 LPGKU2307 LPGKU2308 LPGKU2309 LPGKU2310 LPGKU2311 LPGKU2312 LPGKU2313 LPGKU2314 LPGKU2315 LPGKU2316 LPGKU2317 LPGKU2318 LPGKU2319 LPGKU2320 |