时空转录组学揭示小麦谷物产量和品质的关键基因调控

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Xiaohui Li, Yiman Wan, Dongzhi Wang, Xingguo Li, Jiajie Wu, Jun Xiao, Kunming Chen, Xue Han, Yuan Chen
{"title":"时空转录组学揭示小麦谷物产量和品质的关键基因调控","authors":"Xiaohui Li, Yiman Wan, Dongzhi Wang, Xingguo Li, Jiajie Wu, Jun Xiao, Kunming Chen, Xue Han, Yuan Chen","doi":"10.1186/s13059-025-03569-8","DOIUrl":null,"url":null,"abstract":"Cereal grain size and quality are critical agronomic traits in crop production. Wheat grain development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene expression to establish functional compartments in different cell types. Here, we perform a spatial transcriptomics study covering the early stages of wheat grain development, from 4 to 12 days after pollination. We classify the grain into 10 distinct cell types and identify 192 marker genes associated with them. WGCNA analysis reveals that highly expressed genes in different cell types exhibit distinct enrichment patterns, significantly influencing grain development and filling. Through co-expression and motif analyses, we identify a specific group of genes that may regulate wheat grain development, including TaABI3-B1, a transcription factor specifically expressed in the embryo and surrounding endosperm, which negatively affects embryo and grain size. This study presents a comprehensive spatiotemporal transcriptional dataset for understanding wheat grain development. Additionally, it identifies key genetic resources with potential applications for improving wheat yield.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"74 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat\",\"authors\":\"Xiaohui Li, Yiman Wan, Dongzhi Wang, Xingguo Li, Jiajie Wu, Jun Xiao, Kunming Chen, Xue Han, Yuan Chen\",\"doi\":\"10.1186/s13059-025-03569-8\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Cereal grain size and quality are critical agronomic traits in crop production. Wheat grain development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene expression to establish functional compartments in different cell types. Here, we perform a spatial transcriptomics study covering the early stages of wheat grain development, from 4 to 12 days after pollination. We classify the grain into 10 distinct cell types and identify 192 marker genes associated with them. WGCNA analysis reveals that highly expressed genes in different cell types exhibit distinct enrichment patterns, significantly influencing grain development and filling. Through co-expression and motif analyses, we identify a specific group of genes that may regulate wheat grain development, including TaABI3-B1, a transcription factor specifically expressed in the embryo and surrounding endosperm, which negatively affects embryo and grain size. This study presents a comprehensive spatiotemporal transcriptional dataset for understanding wheat grain development. Additionally, it identifies key genetic resources with potential applications for improving wheat yield.\",\"PeriodicalId\":12611,\"journal\":{\"name\":\"Genome Biology\",\"volume\":\"74 1\",\"pages\":\"\"},\"PeriodicalIF\":10.1000,\"publicationDate\":\"2025-04-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13059-025-03569-8\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-025-03569-8","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

谷物粒度和品质是作物生产中至关重要的农艺性状。小麦籽粒发育受复杂的调控网络控制,需要精确的基因表达时空协调才能在不同细胞类型中建立功能区室。在这里,我们进行了一项空间转录组学研究,涵盖了小麦籽粒发育的早期阶段,从授粉后的4到12天。我们将谷物分为10种不同的细胞类型,并鉴定出192个与之相关的标记基因。WGCNA分析显示,高表达基因在不同细胞类型中表现出不同的富集模式,显著影响籽粒发育和灌浆。通过共表达和基序分析,我们确定了一组可能调控小麦籽粒发育的特定基因,其中包括TaABI3-B1,这是一种在胚胎和周围胚乳中特异性表达的转录因子,对胚胎和籽粒大小有负面影响。本研究为了解小麦籽粒发育提供了一个全面的时空转录数据集。此外,它还确定了在提高小麦产量方面具有潜在应用价值的关键遗传资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat
Cereal grain size and quality are critical agronomic traits in crop production. Wheat grain development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene expression to establish functional compartments in different cell types. Here, we perform a spatial transcriptomics study covering the early stages of wheat grain development, from 4 to 12 days after pollination. We classify the grain into 10 distinct cell types and identify 192 marker genes associated with them. WGCNA analysis reveals that highly expressed genes in different cell types exhibit distinct enrichment patterns, significantly influencing grain development and filling. Through co-expression and motif analyses, we identify a specific group of genes that may regulate wheat grain development, including TaABI3-B1, a transcription factor specifically expressed in the embryo and surrounding endosperm, which negatively affects embryo and grain size. This study presents a comprehensive spatiotemporal transcriptional dataset for understanding wheat grain development. Additionally, it identifies key genetic resources with potential applications for improving wheat yield.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信