玉米NF-YA家族基因的生物信息学分析与克隆

doi:10.3969/j.issn.1004-1524.20241020

浙江农业学报 ›› 2025, Vol. 37 ›› Issue (8): 1605-1614.DOI: 10.3969/j.issn.1004-1524.20241020

玉米NF-YA家族基因的生物信息学分析与克隆

关秀生¹(), 刘铁山², 王娟², 张茂林², 刘春晓², 董瑞², 关海英², 刘强², 徐扬¹, 何春梅²^,^*()

1.扬州大学农学院,江苏扬州 225009
2.山东省农业科学院小麦玉米国家工程实验室,农业农村部黄淮海北部玉米生物学与遗传育种重点实验室,山东济南 250100

收稿日期:2024-11-25 出版日期:2025-08-25 发布日期:2025-09-03
作者简介:关秀生(2000—),女,安徽霍邱人,硕士研究生,研究方向为作物遗传育种。E-mail:mx120220781@stu.yzu.edu.cn
通讯作者: *何春梅,E-mail: chunmeihe11@163.com
基金资助:
山东省重点研发计划(2022LZGCQY004-2)

Bioinformatics analysis and cloning of NF-YA family genes in maize(Zea mays)

GUAN Xiusheng¹(), LIU Tieshan², WANG Juan², ZHANG Maolin², LIU Chunxiao², DONG Rui², GUAN Haiying², LIU Qiang², XU Yang¹, HE Chunmei²^,^*()

1. Agricultural College, Yangzhou University, Yangzhou 225009, Jiangsu, China
2. National Engineering Laboratory of Wheat and Maize, Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Jinan 250100, China

Received:2024-11-25 Online:2025-08-25 Published:2025-09-03
Contact: HE Chunmei

摘要/Abstract

摘要：

核因子Y(nuclear factor Y, NF-Y)由NF-YA、NF-YB和NF-YC亚基组成,能特异性识别靶基因启动子的CCAAT-box,是重要的转录因子。为探索玉米(Zea mays)NF-YA家族成员的功能,利用玉米基因数据库对玉米NF-YA家族16个成员进行生物信息学分析,成功克隆了13个成员,并测定了各成员的组织表达模式与盐胁迫下的表达规律。结果显示,除ZmNF-YA16外,玉米其他NF-YA家族成员均含有高度保守的CBFB_NF-YA结构域。系统进化分析表明,玉米NF-YA家族成员可分为3类。亚细胞定位预测显示,除ZmNF-YA14定位于细胞核和线粒体外,其他成员均定位于细胞核。启动子顺式作用原件分析表明,玉米NF-YA家族成员基因含有多种顺式作用元件。组织表达分析表明,5个玉米NF-YA家族成员表现出组织特异性,ZmNF-YA2、ZmNF-YA4在检测的所有组织中都有表达。盐胁迫条件下,ZmNF-YA5和ZmNF-YA10表现出正响应模式,而ZmNF-YA13则负调控玉米对盐胁迫的响应。本研究初步分析了玉米NF-YA家族成员的基因结构和盐胁迫响应规律,为进一步研究该家族成员的功能提供基础。

关键词: 玉米, 核因子Y(NF-Y), NF-YA亚基, 盐胁迫

Abstract:

The nuclear factor (NF-Y), composed of NF-YA, NF-YB, and NF-YC subunits, specifically recognizes the CCAAT-box in the promoters of target genes and is a critically important transcription factor. To explore the functions of the NF-YA family members in maize (Zea mays), 16 maize NF-YA family members were identified by bioinformatics methods using the maize gene database, and 13 of these members were cloned, and their tissue-specific expression patterns as well as expression profiles under salt stress were determined. The results showed that except for ZmNF-YA16, the other maize NF-YA family members contain a highly conserved CBFB_NF-YA domain. Maize NF-YA family members were classified into three types according to phylogenetic analysis. Subcellular localization prediction indicated that except for ZmNF-YA14, which was localized to both the nucleus and mitochondrion, the other maize NF-YA family members were localized in the nucleus. Promoter cis-element analysis revealed that the genes of maize NF-YA family members contained various cis-acting elements. Tissue expression analysis showed that five NF-YA family members exhibited tissue specificity, while ZmNF-YA2 and ZmNF-YA4 were expressed in all tissues examined. Under salt stress, ZmNF-YA5 and ZmNF-YA10 showed positive responses, while ZmNF-YA13 negatively regulated the maize response to salt stress. This study provided a preliminary analysis of the gene structures and salt stress response patterns of maize NF-YA family members, laying a foundation for further research into the functions of this family.

Key words: maize, nuclear factor Y(NF-Y), NF-YA subunit, salt stress

中图分类号:

S513

关秀生, 刘铁山, 王娟, 张茂林, 刘春晓, 董瑞, 关海英, 刘强, 徐扬, 何春梅. 玉米NF-YA家族基因的生物信息学分析与克隆[J]. 浙江农业学报, 2025, 37(8): 1605-1614.

GUAN Xiusheng, LIU Tieshan, WANG Juan, ZHANG Maolin, LIU Chunxiao, DONG Rui, GUAN Haiying, LIU Qiang, XU Yang, HE Chunmei. Bioinformatics analysis and cloning of NF-YA family genes in maize(Zea mays)[J]. Acta Agriculturae Zhejiangensis, 2025, 37(8): 1605-1614.

图/表 9

参考文献 29

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基因名称	基因ID	正向引物序列	反向引物序列
Gene name	Gene ID	Forward primer sequence(5'-3')	Reverse primer sequence(5'-3')
ZmNF-YA1	Zm00001d027874	ATCCATGCTCCCTCCTCATCTCAC	CCCGGCTCACCGCCCCCTCTCG
ZmNF-YA2	Zm00001d031063	ATCCATGACATCTGTTGTTCACAG	CGACTGCCTGCCCTGAT
ZmNF-YA3	Zm00001d031092	ATGATGAGCTTCAGGAGCA	GAATCAAGACCACCCAAGCT
ZmNF-YA4	Zm00001d033215	GCTGCTGGATTCTTTGGTGT	CAGAGAATCCATACCGAGAC
ZmNF-YA5	Zm00001d029489	ATGCTTCTGCGAGAAAT	TGGAGATTGAGTGATGCGAT
ZmNF-YA6	Zm00001d033602	ATCCATGAGCAGCATGGAGTCGC	AGCCTCGTTCTGTCGTAG
ZmNF-YA7	Zm00001d006835	ATCCATGCCTGTGATTTTACGGG	TGGTGGAAACACGCTGCT
ZmNF-YA8	Zm00001d007882	ATCCATGGATCCTCCCGCGTCCT	CAGAAAAAACAGAGGGGT
ZmNF-YA9	Zm00001d041491	ATCCATGCAGGTCACCAGCGAT	TTCACGACTAGGCGCCTG
ZmNF-YA10	Zm00001d013676	ATGATGAGCTTCAAGGGAC	CGCCCTGAGGAGCTCGCAG
ZmNF-YA11	Zm00001d033773	ATGATGAGCTTCAAGGGAC	CGCCCTGAGGAGCTCGC
ZmNF-YA12	Zm00001d018255	ATCCATGTACGCGTCCCTGGATT	TCTCATAACTGGAACCCT
ZmNF-YA13	Zm00001d022109	ATGTGCCTTTTACGGGAAAG	TGGTGGAAACACGCTGCTG
ZmNF-YA14	Zm00001d026305	ATGCCTGTGATTTTACGGGT	AAGCCAATGGATGGTAAAG
ZmNF-YA15	Zm00001d013501	ATGTTGTCGCGGCCGGG	TCAAGCCTCGTTGTGTCG
ZmNF-YA16	Zm00001d013856	ATGAACGGAGCGCATGAGT	TTAAAGCCAATGGATGGT

基因名称	基因ID	正向引物序列	反向引物序列
Gene name	Gene ID	Forward primer sequence(5'-3')	Reverse primer sequence(5'-3')
ZmNF-YA1	Zm00001d027874	ATCCATGCTCCCTCCTCATCTCAC	CCCGGCTCACCGCCCCCTCTCG
ZmNF-YA2	Zm00001d031063	ATCCATGACATCTGTTGTTCACAG	CGACTGCCTGCCCTGAT
ZmNF-YA3	Zm00001d031092	ATGATGAGCTTCAGGAGCA	GAATCAAGACCACCCAAGCT
ZmNF-YA4	Zm00001d033215	GCTGCTGGATTCTTTGGTGT	CAGAGAATCCATACCGAGAC
ZmNF-YA5	Zm00001d029489	ATGCTTCTGCGAGAAAT	TGGAGATTGAGTGATGCGAT
ZmNF-YA6	Zm00001d033602	ATCCATGAGCAGCATGGAGTCGC	AGCCTCGTTCTGTCGTAG
ZmNF-YA7	Zm00001d006835	ATCCATGCCTGTGATTTTACGGG	TGGTGGAAACACGCTGCT
ZmNF-YA8	Zm00001d007882	ATCCATGGATCCTCCCGCGTCCT	CAGAAAAAACAGAGGGGT
ZmNF-YA9	Zm00001d041491	ATCCATGCAGGTCACCAGCGAT	TTCACGACTAGGCGCCTG
ZmNF-YA10	Zm00001d013676	ATGATGAGCTTCAAGGGAC	CGCCCTGAGGAGCTCGCAG
ZmNF-YA11	Zm00001d033773	ATGATGAGCTTCAAGGGAC	CGCCCTGAGGAGCTCGC
ZmNF-YA12	Zm00001d018255	ATCCATGTACGCGTCCCTGGATT	TCTCATAACTGGAACCCT
ZmNF-YA13	Zm00001d022109	ATGTGCCTTTTACGGGAAAG	TGGTGGAAACACGCTGCTG
ZmNF-YA14	Zm00001d026305	ATGCCTGTGATTTTACGGGT	AAGCCAATGGATGGTAAAG
ZmNF-YA15	Zm00001d013501	ATGTTGTCGCGGCCGGG	TCAAGCCTCGTTGTGTCG
ZmNF-YA16	Zm00001d013856	ATGAACGGAGCGCATGAGT	TTAAAGCCAATGGATGGT

基因名称 Gene name	基因号 Gene ID	正向引物序列 Forward primer sequence(5'-3')	反向引物序列 Reverse primer sequence(5'-3')
NF-YA1	Zm00001d027874	GGCATGGTTCCGTCCTCTCG	TCCGCCTCTAGCTTTGCACG
NF-YA2	Zm00001d031063	ATGCATCCGGCTGGCTTACC	CAGCTCCCCTGGCCCTTTTC
NF-YA3	Zm00001d031092	AGCCTGTCGGGTTCAGAGGT	TCAGGAGGTCGCAGCAGACT
NF-YA4	Zm00001d033215	GCTCGCCAAAGGCAGAAAGC	GACACGTCGGAGCCAGACAG
NF-YA5	Zm00001d029489	ACCATTGCCAGTTGGGCCTG	CTGGTCCACGGACTCGCTTC
NF-YA6	Zm00001d033602	GAACGAACCTGGTGGAGCCC	CTCGCTGCTCTCGTCACTCG
NF-YA7	Zm00001d006835	GTGCGGTTGGGGTCTTGACA	AGCACGTGTTTGCCTCCTCC
NF-YA9	Zm00001d041491	CGGCGGCTTATGGTGGACAT	GGCCCTTGACAAGCTTCCGT
NF-YA10	Zm00001d013676	TCAGCGACGGCAGCAACCC	GCGGCAGCGGGGTGAAGAA
NF-YA12	Zm00001d018255	TGCCACTGTGTTCCGTTCCC	CGGAACCTCGTGCCCTCTTC
NF-YA13	Zm00001d022109	CAGCAGTACCAGGCGTCGAG	ACTGAAGTTGGCTGTGGGGC
NF-YA14	Zm00001d026305	GCACGTGTTTGCCTCCTCCT	TGCCATTGTCCATCCCCAGC
NF-YA15	Zm00001d013501	GGGCGGGACGACGAACCTG	CCGCGGTACTGCTTGGCGT

基因名称 Gene name	基因号 Gene ID	正向引物序列 Forward primer sequence(5'-3')	反向引物序列 Reverse primer sequence(5'-3')
NF-YA1	Zm00001d027874	GGCATGGTTCCGTCCTCTCG	TCCGCCTCTAGCTTTGCACG
NF-YA2	Zm00001d031063	ATGCATCCGGCTGGCTTACC	CAGCTCCCCTGGCCCTTTTC
NF-YA3	Zm00001d031092	AGCCTGTCGGGTTCAGAGGT	TCAGGAGGTCGCAGCAGACT
NF-YA4	Zm00001d033215	GCTCGCCAAAGGCAGAAAGC	GACACGTCGGAGCCAGACAG
NF-YA5	Zm00001d029489	ACCATTGCCAGTTGGGCCTG	CTGGTCCACGGACTCGCTTC
NF-YA6	Zm00001d033602	GAACGAACCTGGTGGAGCCC	CTCGCTGCTCTCGTCACTCG
NF-YA7	Zm00001d006835	GTGCGGTTGGGGTCTTGACA	AGCACGTGTTTGCCTCCTCC
NF-YA9	Zm00001d041491	CGGCGGCTTATGGTGGACAT	GGCCCTTGACAAGCTTCCGT
NF-YA10	Zm00001d013676	TCAGCGACGGCAGCAACCC	GCGGCAGCGGGGTGAAGAA
NF-YA12	Zm00001d018255	TGCCACTGTGTTCCGTTCCC	CGGAACCTCGTGCCCTCTTC
NF-YA13	Zm00001d022109	CAGCAGTACCAGGCGTCGAG	ACTGAAGTTGGCTGTGGGGC
NF-YA14	Zm00001d026305	GCACGTGTTTGCCTCCTCCT	TGCCATTGTCCATCCCCAGC
NF-YA15	Zm00001d013501	GGGCGGGACGACGAACCTG	CCGCGGTACTGCTTGGCGT

基因名称	染色体	起始位点	终止位点	编码区	氨基酸数量	分子量	等电点
Gene name	Chr	Start/bp	End/bp	CDS/bp	Amino acid number	Molecular mass/u	pI
NF-YA1	1	15805373	15808637	750	214	27 207.16	8.96
NF-YA2	1	175263789	175269072	2 229	742	85 041.59	9.42
NF-YA3	1	174875434	174876987	993	330	35 231.81	8.93
NF-YA4	1	250376435	250383733	897	322	34 122.58	9.61
NF-YA5	1	71587764	71597309	273	90	10 062.62	11.87
NF-YA6	1	263505895	263513358	795	264	26 775.89	9.52
NF-YA7	2	211453451	211457855	898	300	32 759.35	9.02
NF-YA8	2	235102149	235107745	881	294	31 336.04	9.78
NF-YA9	3	123429802	123439843	1 020	215	31 009.56	9.39
NF-YA10	5	16478975	16486358	1 040	341	35 736.46	9.40
NF-YA11	1	268502777	268507502	570	262	29 076.26	9.80
NF-YA12	5	211713589	211721532	882	265	31 907.09	10.31
NF-YA13	7	165029459	165036770	901	301	29 607.50	6.63
NF-YA14	10	141890017	141899048	876	291	48 253.63	6.16
NF-YA15	5	12556164	12560070	562	111	14 415.92	10.90
NF-YA16	5	23241181	23243549	397	156	16 876.48	9.64

玉米NF-YA家族基因的生物信息学分析与克隆

Bioinformatics analysis and cloning of NF-YA family genes in maize(Zea mays)

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