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Liu X, Hou J, Chen L, Li Q, Fang X, Wang J, Hao Y, Yang P, Wang W, Zhang D, Liu D, Guo K, Teng Z, Liu D, Zhang Z. Natural variation of GhSI7 increases seed index in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3661-3672. [PMID: 36085525 DOI: 10.1007/s00122-022-04209-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
qSI07.1, a major QTL for seed index in cotton, was fine-mapped to a 17.45-kb region, and the candidate gene GhSI7 was verified in transgenic plants. Improving production to meet human needs is a vital objective in cotton breeding. The yield-related trait seed index is a complex quantitative trait, but few candidate genes for seed index have been characterized. Here, a major QTL for seed index qSI07.1 was fine-mapped to a 17.45-kb region by linkage analysis and substitutional mapping. Only GhSI7, encoding the transcriptional regulator STERILE APETALA, was contained in the candidate region. Association test and genetic analysis indicated that an 845-bp-deletion in its intron was responsible for the seed index variation. Origin analysis revealed that this variation was unique in Gossypium hirsutum and originated from race accessions. Overexpression of GhSI7 (haplotype 2) significantly increased the seed index and organ size in cotton plants. Our findings provided a diagnostic marker for breeding and selecting cotton varieties with high seed index, and laid a foundation for further studies to understand the molecular mechanism of cotton seed morphogenesis.
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Affiliation(s)
- Xueying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Juan Hou
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Li Chen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Qingqing Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Xiaomei Fang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Jinxia Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Yongshui Hao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Peng Yang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Wenwen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Dishen Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Dexin Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Kai Guo
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhonghua Teng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Dajun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China.
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Liu N, Xu Y, Li Q, Cao Y, Yang D, Liu S, Wang X, Mi Y, Liu Y, Ding C, Liu Y, Li Y, Yuan YW, Gao G, Chen J, Qian W, Zhang X. A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. Cell Host Microbe 2022; 30:1124-1138.e8. [DOI: 10.1016/j.chom.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/07/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022]
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Quadrana L. The contribution of transposable elements to transcriptional novelty in plants: the FLC affair. Transcription 2020; 11:192-198. [PMID: 32783496 PMCID: PMC7714446 DOI: 10.1080/21541264.2020.1803031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences with the ability to replicate across genomes and generate mutations with major transcriptional effects. Epigenetic silencing mechanisms that target TEs to limit their activity, including DNA methylation, add to the range of gene expression variants generated by TEs. Here, using the iconic gene flowering locus C (FLC) as a case study I discuss the multiple ways by which TEs can affect the expression of genes and contribute to the adaptation of plants to changing environments
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Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University , Paris, France
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Le NT, Harukawa Y, Miura S, Boer D, Kawabe A, Saze H. Epigenetic regulation of spurious transcription initiation in Arabidopsis. Nat Commun 2020; 11:3224. [PMID: 32591528 PMCID: PMC7319988 DOI: 10.1038/s41467-020-16951-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/01/2020] [Indexed: 01/01/2023] Open
Abstract
In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs. Epigenetic regulation can silence transposons and maintain gene expression. Here the authors survey Arabidopsis mutants defective in epigenetic regulation and show ectopic activation of thousands of cryptic TSSs and altered expression of nearby genes demonstrating the importance of suppressing spurious transcription.
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Affiliation(s)
- Ngoc Tu Le
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Yoshiko Harukawa
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Saori Miura
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Damian Boer
- Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, Netherlands
| | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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