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

doi:10.11983/CBB23065

Abstract

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

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[J]. Chinese Bulletin of Botany, 2024, 59(2): 0-0.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.chinbullbotany.com/EN/10.11983/CBB23065

https://www.chinbullbotany.com/EN/Y2024/V59/I2/0

References

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.