Multi-omics reveals the genetic regulation and functions of long non-coding RNAs in tomato
文献类型： 外文期刊
作者： Wu, Yaoyao 1 ; Ye, Keyi 1 ; Yin, Jian 3 ; Du, Ran 1 ; Cao, Xue 1 ; Lyu, Hongjun 1 ; Wang, Yanling 1 ; Lyu, Yaqing 1 ; Hu, Yong 1 ; Jia, Yuxin 1 ; Xu, Yuanchao 1 ; Huang, Sanwen 1 ; Zhang, Jinzhe 3 ;
作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen,Minist Agr & Rural Affairs, Natl Key Lab Trop Crop Breeding,Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Genome Anal Lab, Shenzhen 518120, Guangdong, Peoples R China
2.Nanjing Agr Univ, Coll Hort, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Peoples R China
3.Chinese Acad Agr Sci, Inst Vegetables & Flowers, State Key Lab Vegetable Biobreeding, Beijing 100081, Peoples R China
4.Yunnan Acad Agr Sci, Food Crops Res Inst, Natl Wheat Improvement Ctr, Yunnan Branch, Kunming 650205, Yunnan, Peoples R China
5.China Acad Chinese Med Sci, Inst Chinese Mat Med, State Key Lab Qual Ensurance & Sustainable Use Dao, Beijing 100700, Peoples R China
6.Shandong Acad Agr Sci, Inst Vegetables, Shandong Prov Key Lab Biol Greenhouse Vegetables, Shandong Branch,Natl Improvement Ctr Vegetables, Jinan 250100, Peoples R China
7.Hebei Agr Univ, Coll Hort, Baoding 071000, Peoples R China
8.Yunnan Normal Univ, AGISCAAS YNNU Joint Acad Potato Sci, Kunming 650500, Yunnan, Peoples R China
9.Chinese Acad Trop Agr Sci, State Key Lab Trop Crop Breeding, Haikou 571101, Hainan, Peoples R China
期刊名称：PLANT PHYSIOLOGY （ 影响因子：6.9； 五年影响因子：7.7 ）
ISSN： 0032-0889
年卷期： 2025 年 198 卷 4 期
页码：
收录情况： SCI
摘要： Long non-coding RNAs (lncRNAs) play vital roles in signal transduction and plant development. However, how lncRNA expression might have been globally altered during Solanum lycopersicum (tomato) breeding and what potential roles they play in regulating metabolite accumulation in fruit remain unclear. Here, we identified 15,548 lncRNAs using RNA-sequencing data from 404 tomato accessions. Among these lncRNAs, 2,115 were identified as high-confidence panel-expressed lncRNAs, which were expressed in more than 100 accessions with high confidence, as validated by strand-specific RNA-seq data. By exploring the variation of expression level and nucleotide diversity of lncRNAs during tomato domestication and improvement, we identified 776 differentially expressed lncRNAs during selective breeding. Furthermore, we determined that 695 lncRNAs were regulated by 1,383 lncRNA expression quantitative trait loci (eQTLs). Among these lncRNAs, 450 were associated with metabolite contents in tomato fruits. Transgenic experiments confirmed that the lncRNA MSTRG.24434.1 co-mapped with 2-phenylethanol at chromosome 8 (lncRNA-PEL8) positively regulates the content of the tomato fruit flavor volatile 2-phenylethanol. The expression levels of all panel-expressed lncRNAs could be used to predict metabolite contents with high accuracy, suggesting that lncRNAs play key roles in global metabolite processes. This study thus presents a multi-omics view of the breeding history of lncRNAs and provides valuable insights into their possible roles in regulating tomato flavor, highlighting their potential application in tomato breeding. Tomato breeding alters lncRNAs that regulate fruit flavor metabolites, offering valuable breeding insights for improving tomato flavor.
- 相关文献
作者其他论文 更多>>
-
Leveraging a phased pangenome for haplotype design of hybrid potato
作者：Cheng, Lin;Wang, Nan;Bao, Zhigui;Yang, Yuting;Wang, Pei;Zhang, Zhiyang;Tang, Die;Zhang, Pingxian;Wu, Yaoyao;Zhou, Yao;Zheng, Yi;Hu, Yong;Lian, Qun;Ma, Zhaoxu;Zhang, Chunzhi;Zhou, Yongfeng;Huang, Sanwen;Cheng, Lin;Lassois, Ludivine;Wang, Nan;Zhou, Yongfeng;Huang, Sanwen;Bao, Zhigui;Zhou, Qian;Guarracino, Andrea;Garrison, Erik;Tang, Die;Wu, Yaoyao;Zhou, Yao;Lucas, William J.;Stein, Nils;Stein, Nils;Staedler, Thomas;Staedler, Thomas
关键词：
-
Developmental innovation of inferior ovaries and flower sex orchestrated by KNOX1 in cucurbits
作者：Dong, Zhaonian;Liu, Xiaolin;Liu, Xun;Wang, Bowen;Tian, Caihuan;Zheng, Yingying;Yu, Qiong;Sun, Jinjing;Xin, Tongxu;Yang, Xueyong;Dong, Zhaonian;Wang, Bowen;Huang, Sanwen;Guo, Xing;Shao, Wenwen;Zhong, Liyuan;Shao, Wenwen;Zhong, Liyuan;Li, Shengkang;Zhang, Bohan;Xu, Xun;Liu, Huan;Shao, Wenwen;Tian, Caihuan;Yang, Tao;Lu, Haorong;Rose, Jocelyn K. C.;Lucas, William J.;Huang, Sanwen
关键词：
-
The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems
作者：Peng, Yanling;Wang, Yiwen;Liu, Yuting;Fang, Xinyue;Cheng, Lin;Long, Qiming;Su, Dalu;Zhang, Tianhao;Shi, Xiaoya;Xu, Xiaodong;Xu, Qi;Wang, Nan;Zhang, Fan;Liu, Zhongjie;Xiao, Hua;Huang, Sanwen;Zhou, Yongfeng;Yao, Jin;Tian, Ling;Hu, Wei;Chen, Songbi;Huang, Sanwen;Zhou, Yongfeng;Wang, Haibo;Gaut, Brandon S.
关键词：grapevine; clonal propagation; structural variation; integrative genomics; heterozygosity
-
Glutathione triggers leaf-to-leaf, calcium-based plant defense signaling
作者：Li, Rui;Yang, Yongfang;Lou, Hao;Wang, Weicheng;Du, Xiaoxi;Hu, Shuai;Shan, Xiaoyi;Xie, Daoxin;Li, Rui;Yang, Yongfang;Lou, Hao;Wang, Weicheng;Du, Xiaoxi;Hu, Shuai;Wang, Guo-Liang;Shan, Xiaoyi;Xie, Daoxin;Li, Rui;Du, Ran;Chen, Haidong;Yan, Jianbin;Yang, Yongfang;Du, Xiaoxi;Hu, Shuai;Du, Xiaoxi;Hu, Shuai;Wang, Guo-Liang;Xie, Daoxin
关键词：
-
Rational Redomestication for Future Agriculture
作者：Wang, Nan;Li, Hongbo;Huang, Sanwen;Wang, Nan;Huang, Sanwen;Li, Hongbo
关键词：breeding; agriculture; redomestication; de novo domestication; breeding systems
-
Molecular breeding of tomato: Advances and challenges
作者：Du, Minmin;Du, Minmin;Sun, Chuanlong;Deng, Lei;Li, Chang-Bao;Li, Chuanyou;Du, Minmin;Sun, Chuanlong;Li, Chuanyou;Deng, Lei;Li, Chang-Bao;Li, Chuanyou;Zhou, Ming;Li, Chang-Bao;Li, Junming;Du, Yongchen;Ye, Zhibiao;Huang, Sanwen;Huang, Sanwen;Li, Tianlai;Yu, Jingquan
关键词：genome editing; genome sequencing; germplasm; molecular breeding; tomato
-
Transgenerational epigenetic inheritance of cold adaptation in rice: Evidence for neo-Lamarckian concepts
作者：Zhang, Pingxian;Huang, Sanwen;Huang, Sanwen
关键词：
