Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet
The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (<i>xm<...
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2025-04-01
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| author | Ruimiao Li Cuiyun Lei Qiang Zhang Xiaomeng Guo Xiting Cui Xingchun Wang Xukai Li Jianhua Gao |
| author_facet | Ruimiao Li Cuiyun Lei Qiang Zhang Xiaomeng Guo Xiting Cui Xingchun Wang Xukai Li Jianhua Gao |
| author_sort | Ruimiao Li |
| collection | DOAJ |
| description | The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (<i>xm</i> and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature (<i>Accession_SiSRSN[.n]_xDy or xTy</i>) was proposed to unify gene family nomenclature, enabling the direct visualization of member number variation across germplasms and the identification of core/variable members while highlighting chromosomal translocations. Focusing on the two high-quality genomes, both harboring six core SRS members, we performed whole-genome collinearity analysis with Arabidopsis, rice, maize, soybean, and green foxtail. Ka/Ks analysis of collinear gene pairs revealed purifying selection acting on <i>SiSRS</i> genes. Promoter analysis identified abundant stress-responsive <i>cis</i>-elements. Among core members, the <i>xm_SiSRS5</i> gene exhibited the highest expression during vegetative growth but showed significant downregulation under drought and salt stress, suggesting its role as a key negative regulator in abiotic stress responses. This study demonstrates the utility of pan-genomics in resolving gene family dynamics and establishes <i>SiSRS5</i> as a critical target for stress tolerance engineering in foxtail millet. |
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| institution | OA Journals |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-04-01 |
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| series | Plants |
| spelling | doaj-art-fbac532cee83476b926d5a74e5c24b7c2025-08-20T02:28:19ZengMDPI AGPlants2223-77472025-04-01148125710.3390/plants14081257Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail MilletRuimiao Li0Cuiyun Lei1Qiang Zhang2Xiaomeng Guo3Xiting Cui4Xingchun Wang5Xukai Li6Jianhua Gao7Shanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaShanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, ChinaThe Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (<i>xm</i> and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature (<i>Accession_SiSRSN[.n]_xDy or xTy</i>) was proposed to unify gene family nomenclature, enabling the direct visualization of member number variation across germplasms and the identification of core/variable members while highlighting chromosomal translocations. Focusing on the two high-quality genomes, both harboring six core SRS members, we performed whole-genome collinearity analysis with Arabidopsis, rice, maize, soybean, and green foxtail. Ka/Ks analysis of collinear gene pairs revealed purifying selection acting on <i>SiSRS</i> genes. Promoter analysis identified abundant stress-responsive <i>cis</i>-elements. Among core members, the <i>xm_SiSRS5</i> gene exhibited the highest expression during vegetative growth but showed significant downregulation under drought and salt stress, suggesting its role as a key negative regulator in abiotic stress responses. This study demonstrates the utility of pan-genomics in resolving gene family dynamics and establishes <i>SiSRS5</i> as a critical target for stress tolerance engineering in foxtail millet.https://www.mdpi.com/2223-7747/14/8/1257foxtail milletpan-genomeSRS transcription factors |
| spellingShingle | Ruimiao Li Cuiyun Lei Qiang Zhang Xiaomeng Guo Xiting Cui Xingchun Wang Xukai Li Jianhua Gao Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet Plants foxtail millet pan-genome SRS transcription factors |
| title | Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet |
| title_full | Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet |
| title_fullStr | Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet |
| title_full_unstemmed | Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet |
| title_short | Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet |
| title_sort | pan genome based characterization of the srs transcription factor family in foxtail millet |
| topic | foxtail millet pan-genome SRS transcription factors |
| url | https://www.mdpi.com/2223-7747/14/8/1257 |
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