糜子SBP基因家族的全基因组鉴定及表达分析

doi:10.11983/CBB23065

植物学报 ›› 2024, Vol. 59 ›› Issue (2): 0-0.DOI: 10.11983/CBB23065

• 研究报告 •

糜子SBP基因家族的全基因组鉴定及表达分析

段政勇[1], 丁敏¹, 王宇卓¹, 丁艺冰², 陈凌³, 王瑞云^{1, 3*}, 乔治军^3*

¹山西农业大学农学院, 太谷 030801; ²山西农业大学玉米研究所, 忻州 034000; ³山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室, 太原 030031

收稿日期:2023-05-21 修回日期:2023-12-18 出版日期:2024-03-01 发布日期:2024-01-12
通讯作者: 王瑞云, 乔治军
基金资助:
国家现代农业产业技术体系建设专项(No.CARS-06-14.5-A16)、山西省现代农业产业技术体系建设(杂粮)项目(No.2023CYJSTX03-12)、山西省重点研发项目(No.2022ZDYF110)和国家自然科学基金(No.31271791)

Genome-wide identification and Expression Analysis of SBP Gene Family in Proso Millet

Zhengyong Duan¹, Min Ding¹, Yuzhuo Wang¹, Yibing Ding², Ling Chen³, Ruiyun Wang^{1, 3*}, Zhijun Qiao^3*

¹College of Agronomy, Shanxi Agricultural University, Taigu 030801, China; ²Corn Research Institute, Shanxi Agricultural University, Xinzhou 034000, China; ³Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs/Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops/Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China

Received:2023-05-21 Revised:2023-12-18 Online:2024-03-01 Published:2024-01-12
Contact: Ruiyun Wang, Zhijun Qiao

摘要/Abstract

摘要： SBP (squamosa promoter binding protein)家族广泛参与植物生长发育、信号转导及多种生理生化过程。为探究糜子(Panicum miliaceum)中SBP转录因子基因家族的组成与功能, 以双粒糜子和单粒糜子为材料, 基于糜子全基因组Pm_0390_v2, 利用生物信息学方法从中筛选并鉴定到25个SBP基因(PmSBP1–PmSBP25), 并对其理化性质、染色体分布、基因结构特征、系统进化关系、组织特异性以及不同时期基因表达模式进行系统分析。结果表明, 25个PmSBPs基因不均匀分布在13条染色体上, 其编码蛋白的氨基酸残基介于105– 1 109 aa之间, 等电点为5.60–11.92, 分子量介于9.0320–1 215.1362 kDa之间。基因结构和系统发育分析表明, PmSBP家族成员可分为6个亚家族。共线性分析表明, PmSBP与拟南芥(Arabidopsis thaliana) AtSBP和水稻(Oryza sativa) OsSBP分别形成7对和31对直系同源基因。顺式作用元件分析表明, PmSBP启动子区富含逆境胁迫、光反应及激素信号响应相关元件。基因表达模式分析表明, PmSBP基因具有明显的组织表达特异性, 双粒糜子和单粒糜子中PmSBP表达模式不同, 抽穗期和开花期的表达趋势存在差异。研究结果为揭示SBP基因在糜子生长发育中的生物学功能奠定了基础, 也为其它作物SBP基因研究和遗传转化提供借鉴参考。

关键词: 糜子, PmSBP基因, 全基因组鉴定, 基因表达分析

Abstract: Squamosa promoter binding protein (SBP) gene family is widely involved in plant growth and development, signal transduction, and many physiological and biochemical processes. However, the genes of the proso millet (Panicum miliaceum) SBP gene family have not been systematically studied. A total of 25 SBP genes were identified and systematically named in the proso millet genome, and the SBP genes were divided into 6 subfamilies through phylogenetic analysis. The members of the same subfamily had similar gene structure and conserved motifs. The collinearity analysis showed that 7 pairs of direct homologous genes were formed with Arabidopsis thaliana AtSBP and 31 pairs with Oryza sativa OsSBP. The analysis of cis-acting elements showed that the promoter region of SBP gene in proso millet was rich in elements related to stress, plant light response and plant hormone signal response. The analysis of gene expression patterns showed that the SBP gene in proso millet had obvious tissue specificity, and the SBP gene expression pattern was also specific in different varieties, and the expression trend was different in different periods, suggesting that SBP gene should play an important role in the growth and development of proso millet. The results laid a foundation for revealing the biological function of SBP gene family in the growth and development of proso millet, and also provided a reference for the research and application of other crops.

Key words: proso millet, SBP gene, complete genome identification, analysis of gene expression

段政勇, 丁敏, 王宇卓, 丁艺冰, 陈凌, 王瑞云, 乔治军. 糜子SBP基因家族的全基因组鉴定及表达分析. 植物学报, 2024, 59(2): 0-0.

Zhengyong Duan, Min Ding, Yuzhuo Wang, Yibing Ding, Ling Chen, Ruiyun Wang, Zhijun Qiao. Genome-wide identification and Expression Analysis of SBP Gene Family in Proso Millet. Chinese Bulletin of Botany, 2024, 59(2): 0-0.

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参考文献

王菲菲, 周振祥, 洪益, 谷洋洋, 吕超, 郭宝健, 朱娟, 许如根 (2019). 大麦NF-YC基因鉴定及在盐胁迫下的表达分析. 植物学报 58, 140-149.
张雅文, 梁山, 徐国云, 郭无瑕, 邓书林 (2021). 烟草CONSTANS-like基因家族的鉴定与分析. 植物学报56, 33-43.
宋敏, 张瑶, 王丽莹, 彭向永 (2019). 甘蓝型油菜ZF-HD基因家族的鉴定与系统进化分析. 植物学报 54, 699-710.
李明, 李长生, 赵传志, 李爱芹, 王兴军 (2013). 植物SPL转录因子研究进展. 植物学报 48, 107–116
王瑞云 (2021). 糜子遗传多样性及进化研究进展. 北京: 中国农业出版社. pp. 8–9.
石甜甜, 何杰丽, 高志军, 陈凌, 王海岗, 乔治军, 王瑞云 (2019). 利用EST-SSR评估糜子资源遗传差异. 中国农业科学 52, 4100–4109.
何杰丽, 石甜甜, 陈凌, 王海岗, 高志军, 杨美红, 王瑞云, 乔治军 (2019). 糜子EST-SSR分子标记的开发及种质资源遗传多样性分析. 植物学报 54, 723–732.
张磊 (2019). SPL转录因子研究进展. 农业与技术 42, 25–27.
杨柳 (2018). 拟南芥SPL8同源基因的克隆和功能分析. 硕士论文. 太原: 山西大学. pp. 102–119.
邵正伟, 曾志鹏, 陈彦竹, 何敏红, 张毅, 陈善兰, 朱宏波 (2018). 甘薯全基因组SBP基因家族鉴定及表达分析. 分子植物种 10, 1–20.
位欣欣, 兰海燕 (2022). 植物MYB转录因子调控次生代谢及逆境响应的研究进展. 生物技术通报 38, 12–23
路保顺, 朱永静, 张舒婷, 吕煜梦, 李晓斐, 宋雨洋, 赖钟雄, 林玉玲 (2020). 龙眼SPL基因家族全基因组鉴定及表达分析. 中国农业科学 53, 4259–4270.
陈小红, 林元香, 王倩, 丁敏, 王海岗, 陈凌, 高志军, 王瑞云, 乔治军 (2022). 基于高基元SSR构建黍稷种质资源的分子身份证. 作物学报 48, 908–919.
刘敏轩, 许月, 陆平 (2020). 中国野生黍稷资源收集保存与遗传多样性研究进展. 植物遗传资源学报 21, 1435–1445.
Devi P B, Vijayabharathi R, Sathyabama S, Malleshi N G. Priyadarisini V B (2014). Health benefits of finger millet (Eleusine coracana L.) polyphenols and dietary fiber: a review. J Food sci 51, 1021–1040.
Gupta S, Shrivastava S K, Shrivastava M (2014). Proximste composition of seeds of hybrid varieties of minor millets. Int J Res Eng Technol 3, 687–693.
Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S (2004). A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J Mol Biol 337, 49–63.
Chen X, Zhang Z, Liu D, Zhang K, Li A, Mao L (2010). SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development. J Integr Plant Biol 52, 946–951.
Chuck G, Whipple C, Jackson D, Hake S (2010). The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Deve lopment 137, 1243–1250.
Yao T, Park B S, Mao H Z (2019). Regulation of flowering time by SPL10 /MED25 module in Arabidopsis. New Phytol 224, 493－504.
Wang S, Li S, Liu Q, Wu K, Zhang J Q, Wang S S, Wang Y, Chen X B, Zhang Y, Gao CA X, Wang F, Huang H X, Fu X D (2015). The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature Genetics 47, 949–954.
Cardon G H, H?hmann S, Nettesheim K, Saedler H, Huijser P (1997). Functional analysis of the Arabidopsis thaliana SBP gene SPL3: a novel gene involved in the floral transition. Plant J 12, 367–377.
Manning K, T?r M, Poole M, Hong Y, Thompson A J, King G J, Giovannoni J J (2006). Seymour GBA naturally occurring epigenetic mutation in a gene encoding an SBP transcription factor inhibits tomato fruit ripening. Nat Genet 38, 948–952.
Tripathi R K, Bregitzer P, Singh J (2018). Genome-wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley. Sci Rep 8, 70–85.
Shao Y L, Zhou H Z, Wu Y R, Zhang H, Lin J, Jiang X Y, He Q J, Zhu J S, Li Y, Yu H, Mao C Z (2019). OsSPL3 an SBP－Domain Protein Regulates Crown Root Development in Rice. The Plant Cell 31, 1257–1275.
Liu H, Yang X, Liao X, Zuo T, Qin C, Cao S, Dong L, Zhou H, Zhang Y, Liu S, Shen Y, Lin H, Lübberstedt T, Zhang Z, Pan G (2015). Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development. Genomics 106, 52–60.
Ma J Q, Jian H J, Yang B, Lu K, Zhang A X, Liu P, Li J N (2017). Genome-wide analysis and expression profiling of the GRF gene family in oilseed rape (Brassica napus L.). Gene 620, 36–45.
Arshad M, Feyissa B A, Amyot L, Aung B, Hannoufa A (2017). MicroＲNA156 improves drought stress tolerance in alfalfa ( Medicago sativa) by silencing SPL13. Plant Sci 258, 122–136.
Zhang D, Han Z, Li J (2020). Genome-wide analysis of the SBP gene family transcription factors and their responses to abiotic stresses in tea (Camellia sinensis). Genomics 112, 2194–2202.
Hou H M, Jia H, Yan Q, Wang X P (2018). Overexpression of a SBP Gene (VpSBP16) from Chinese Wild Vitis Species in Arabidopsis Improves Salinity and Drought Stress Tolerance. Int J of Mol Sci 9, 940-945.
Zhang Y, Schwarz S, Saedler H, Huijser P (2007). SPL8 a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol Biol 63, 429–439.
Gao R, Wang Y, Gruber M Y, Hannoufa A (2017). miR156 /SPL10 Modulates Lateral Root Development Branching and Leaf Morphology in Ara- bidopsis by Silencing AGAMOUS-LIKE 79. Front Plant Sci 8, 2226.
Yu Z X, Wang L J, Zhao B, Shan C M, Zhang Y H, Chen D F, Chen X Y (2015). Progressive regulation of sesquiterpene biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156- targeted SPL transcription factors. Mol Plant 8, 98–110.
Yu N, Cai W J, Wang S C, Shan C M, Wang L J, Chen X Y (2010). Temporal control of trichome distribution by microRNA156-targeted SPL Genes in Arabidopsis thaliana. The Plant Cell 22, 2322–2335.
Jung J H, Ju Y, Seo P J, Lee J H, Park C M (2012). The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis. Plant J 69, 577–588.
Gou J Q, Tang C R, Chen N C, Wang H, Debnath S, Sun L, Flanagan A, Tang Y H, Jiang Q Z, Allen R D, Wang Z Y (2019). SPL7 and SPL8 represent a novel flowering regulation mechanism in switchgrass. New Phytol 222, 1610–1623.
Martin R C, Asahina M, Liu P P, Kristof J R, Coppersmith J L, Pluskota W E, Bassel G W, Goloviznina N A, Nguyen T T, Pupel P, Nonogaki H (2010). The microRNA156 and microRNA172 gene regulation cascades at post-germinative stages in Arabidopsis. Seed Sci Res 20, 79–87.
Lu H Y, Zhang J P, Liu K B, Wu N Q, Li Y M, Zhou K S, Ye M L, Zhang T Y, Zhang H J, Yang X Y, Shen L C, Xu D K, Li Q (2009). Earliest domestication of common millet (Panicum miliaceum L.) in East Asia extended to 10,000 years ago. Proc natl Acad Sci USA 106, 7367–7372.
Nielsen D C, Vigil M F (2017). Water use and environmental parameters influence proso millet yield. Field Crops Res 212, 34–44.

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糜子SBP基因家族的全基因组鉴定及表达分析

Genome-wide identification and Expression Analysis of SBP Gene Family in Proso Millet

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