Bioinformatics analysis of SiNF-YA subfamily genes and drought resistance gene mining in Setaria italica

doi:10.3969/j.issn.1000-1565.2025.01.009

Abstract

Abstract: To explore the function of SiNF-YA subfamily genes in Setaria italica. Firstly, the bioinformatics of 10 members of the SiNF-YA subfamily genes in foxtail millet were analyzed by using several online websites. Secondly, Ubuntu system and RStudio software were used for haplotype analysis of SiNF-YA subfamily genes. At last, through analysis of transcriptome data, the expression of SiNF-YA5 in different tissues of drought-sensitive and drought-tolerant varieties was investigated. The results showed that SiNF-YA subfamily genes of foxtail millet were distributed on four chromosomes, mainly located in the nucleus and extracellular secretion. The cis-acting elements related to abiotic stress response were distributed in the promoter region. Meanwhile, the subfamily genes were strongly correlated with drought resistance. In addition, the expression of SiNF-YA5 was detected before and after PEG treatment. There were significant differences between leaf and root expression levels. This study provide - DOI:10.3969/j.issn.1000-1565.2025.01.009谷子SiNF-YA亚家族基因的生物信息学分析与抗旱基因挖掘王春芳¹,张霈涵²,史慎奎¹,杨佳怡²,王玉芳¹,祁东梅¹(1.河北民族师范学院生物与食品科学学院,冀北山区杂粮产业协同创新中心,河北承德 067000;2.河北师范大学生命科学学院,河北石家庄 050024)摘要:为探究谷子(Setaria italica)SiNF-YA亚家族基因的功能,首先,利用多个在线网站对谷子10个SiNF-YA亚家族基因进行了相关的生物信息学分析;其次,利用Ubuntu系统和RStudio软件对谷子SiNF-YA基因进行单倍型分析;最后,通过对转录组数据的分析,探究谷子SiNF-YA5亚家族基因在干旱敏感品种、耐旱品种各组织中的表达量差异.结果表明,谷子SiNF-YA亚家族基因分布在4条染色体上,主要定位于细胞核和胞外分泌中,其启动子区含有与非生物胁迫响应相关的顺式作用元件.同时该基因亚家族成员与抗旱性具有很强的相关性,并且谷子SiNF-YA5亚家族基因在PEG处理前后,叶片和根部的表达量具有显著性差异.本研究为谷子抗旱品种的育种提供理论支持.关键词:谷子;SiNF-YA亚家族基因;抗旱;生物信息学分析;单倍型分析中图分类号:S515 文献标志码:A 文章编号:1000-1565(2025)01-0082-09Bioinformatics analysis of SiNF-YA subfamily genes and drought resistance gene mining in Setaria italicaWANG Chunfang¹, ZHANG Peihan², SHI Shenkui¹, YANG Jiayi², WANG Yufang¹, QI Dongmei¹(1. Collaborative Innovation Center of Minor Cereals Industry in North Hebei, College of Biological and Food Science,Hebei Minzu Normal University, Chengde 067000,China; 2. College of Life Science, Hebei Normal University, Shijiazhuang 050024,China)Abstract: To explore the function of SiNF-YA subfamily genes in Setaria italica. Firstly, the bioinformatics of 10 members of the SiNF-YA subfamily genes in foxtail millet were analyzed by using several online websites. Secondly, Ubuntu system and RStudio software were used for haplotype analysis of SiNF-YA subfamily genes. At last, through analysis of transcriptome data, the expression of SiNF-YA5 in different tissues of drought-sensitive and drought-tolerant varieties was investigated. The results showed that SiNF-YA subfamily genes of foxtail millet were distributed on four chromosomes, mainly located in the nucleus and extracellular secretion. The cis-acting elements related to abiotic stress response were distributed in the promoter region. Meanwhile, the subfamily genes were strongly correlated with drought resistance. In addition, the expression of SiNF-YA5 was detected before and after PEG treatment. There were significant differences between leaf and root expression levels. This study provide - 收稿日期:2024-06-12;修回日期:2024-08-24 基金项目: 承德市基础研究项目(202305B093);河北民族师范学院青年基金项目(QN2019003) 第一作者:王春芳(1983—),女,河北民族师范学院副教授,博士,主要从事谷子分子育种方面的研究.E-mail:wangchunfang18@126.com 通信作者:祁东梅(1990—),女,河北民族师范学院讲师,博士,主要从事谷子功能基因方面的研究.E-mail: dmqikaka@163.com 第1期王春芳等:谷子SiNF-YA亚家族基因的生物信息学分析与抗旱基因挖掘河北大学学报(自然科学版) 第45卷theoretical support for functional verification of subsequent SiNF-YA gene subfamilies and breeding of foxtail millet varieties with drought resistance.

Key words: Setaria italica, SiNF-YA subfamily genes, drought resistance, bioinformatics analysis, haplotype analysis

CLC Number:

S515

WANG Chunfang, ZHANG Peihan, SHI Shenkui, YANG Jiayi, WANG Yufang, QI Dongmei. Bioinformatics analysis of SiNF-YA subfamily genes and drought resistance gene mining in Setaria italica[J]. Journal of Hebei University(Natural Science Edition), 2025, 45(1): 82-90.

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