Genome-wide identification of the maize calcium-dependent protein kinase and drought expression analysis of the CDPK gene family in maize

doi:10.6048/j.issn.1001-4330.2023.04.009

Abstract

Abstract:

【Objective】Genome-wide identification of the maize calcium-dependent protein kinase and drought expression analysis of the CDPK gene family in maize.【Methods】NCBI Blast, DNAMAN and MotifScan were used to analyze the protein domains and phylogeny of CDPK in maize by genome-wide analysis. Real-time RT-PCR was performed to analyze the expression of CDPK gene in maize seedlings under drought stress, and to evaluate the effect of CDPK gene on maize response to drought stress.【Results】Through bioinformatics analysis of the whole genome of maize, 39 CDPK genes were identified in maize. According to phylogenetic analysis of CDPKs in maize, rice and Arabidopsis thaliana, these CDPK genes were divided into four groups. The members of each group share a common protein motif and exon and intron structure, suggesting that they may have a common evolutionary origin. The 39 maize CDPK genes are grouped according to their phylogenetic relationships and are anchored to specific maize chromosomes. It was found that the expression levels of most CDPK genes changed in maize under drought stress, indicating the response of these CDPK genes to drought stress.【Conclusion】39 CDPK genes were identified from maize genome database. Most of the CDPK genes in maize showed different expression levels in different tissues and different development stages, indicating that CDPK genes play different roles in maize development. At the same time, the expression levels of most CDPK genes changed under drought stress, which laid a foundation for further screening and studying the function of CDPK gene family under drought stress.

Key words: calcium-dependent protein kinase; genome-wide identification; drought stress; expression analysis; maize

摘要：

【目的】分析研究玉米钙依赖蛋白激酶全基因组鉴定及抗旱表达。【方法】使用NCBI Blast、DNAMAN和MotifScan等程序分析玉米钙依赖蛋白激酶CDPK的蛋白结构域和系统发育。采用Real-time RT-PCR方法分析CDPK基因在干旱胁迫处理玉米幼苗中的表达,评价CDPK基因对玉米干旱胁迫反应能力。【结果】鉴定出了在玉米中含有39个CDPK基因。将CDPK基因分为4个组。每个群体中的成员有共同的蛋白质基序和外显子及内含子结构,共同的进化起源。39个玉米CDPK基因根据它们的系统发育关系分组,并锚定在特定的玉米染色体上。多数CDPK基因在玉米干旱胁迫中的表达水平发生改变,CDPK基因参与对干旱胁迫的响应。【结论】从玉米基因组数据库中鉴定出了39个CDPK基因,大多数玉米CDPK基因在不同组织和不同发育阶段表现出不同的表达水平,CDPK基因在玉米发育中发挥不同的作用。多数CDPK基因在干旱胁迫下的表达量均发生变化。

关键词: 钙依赖蛋白激酶, 全基因组鉴定, 干旱胁迫, 表达分析, 玉米

CLC Number:

S188

Chen Guo, Hao Xiaoyan, Gao Shengqi, Hu Wenran, Zhao Zhun, Huang Quansheng. Genome-wide identification of the maize calcium-dependent protein kinase and drought expression analysis of the CDPK gene family in maize[J]. Xinjiang Agricultural Sciences, 2023, 60(4): 857-864.

陈果, 郝晓燕, 高升旗, 胡文冉, 赵准, 黄全生. 玉米钙依赖蛋白激酶全基因组鉴定及抗旱表达分析[J]. 新疆农业科学, 2023, 60(4): 857-864.

Figures/Tables 4

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名称 Name	序列号 ID	CDs	氨基酸 Amino acid	分子量 MW (kDa)	EF手型数量 No. of EF Hands	N端序列 N-terminal	N端豆蔻酰化基元 N-Myristoylation
ZmCDPK1	GRMZM2G028926_T01	1 827	608	66.4	4	MGNTCVGP	No
ZmCDPK2	GRMZM2G320506_T01	1 863	620	67.7	4	MGNTCVGP	No
ZmCDPK3	GRMZM2G025387_T01	1 593	530	59.9	4	MGNRASRH	Yes
ZmCDPK4	GRMZM2G035843_T01	1 527	508	56.5	4	MQPDPSGN	No
ZmCDPK5	GRMZM2G314396_T01	1 644	547	60.4	4	MGNACSGA	Yes
ZmCDPK6	GRMZM2G321239_T01	1 671	556	61.2	4	MGNACGGA	Yes
ZmCDPK7	GRMZM2G104125_T01	1 608	535	60.3	4	MGNCCATP	Yes
ZmCDPK8	AC210013.4_FGP014	1 617	538	60.4	4	MGNCCAAP	Yes
ZmCDPK9	GRMZM2G154489_T01	1 596	531	59.4	4	MGQCCSRA	Yes
ZmCDPK10	GRMZM2G030673_T01	1 626	541	60.5	4	MGNCCRSP	No
ZmCDPK11	GRMZM2G463464_T01	1 548	515	56.8	4	MQPDPQGP	No
ZmCDPK12	GRMZM2G047486_T01	1 533	510	60.2	4	MQPDPSGN	No
ZmCDPK13	GRMZM2G311220_T01	1 611	536	60.2	4	MGNCCRSP	No
ZmCDPK14	GRMZM2G028086_T01	1 620	539	60.8	4	MGNCCVTP	Yes
ZmCDPK15	GRMZM2G058305_T01	1 620	539	60.7	4	MGGRASRH	Yes
ZmCDPK16	GRMZM2G015703_T01	1 779	592	65.4	1	MGLCHGKP	Yes
ZmCDPK17	GRMZM2G167276_T01	1 533	510	56.2	4	MGNCCPGS	Yes
ZmCDPK18	GRMZM2G157068_T02	1 569	522	58.5	4	MGACFSSA	Yes
ZmCDPK19	GRMZM2G347047_T01	1 467	488	53.9	4	MGGHQLHL	No
ZmCDPK20	GRMZM2G121228_T01	1 743	580	63.7	4	MGNTCVGP	No
ZmCDPK21	GRMZM2G027351_T01	1 755	584	64.1	4	MGNTCVGP	No
ZmCDPK22	GRMZM2G347226_T01	1 548	515	56.8	4	MQPDPQGS	No
ZmCDPK23	GRMZM2G040743_T01	1 623	540	60.9	4	MGNQCQNG	No
ZmCDPK24	GRMZM2G080871_T02	1 536	511	57.0	3	MGGCHSAI	No
ZmCDPK25	GRMZM2G353957_T01	1 941	646	71.7	4	MGNVCVGP	No
ZmCDPK26	GRMZM2G081310_T01	1 689	562	61.9	4	MGNTCGVT	No
ZmCDPK27	GRMZM2G032852_T02	1 635	544	61.7	4	MGNQCPNG	No
ZmCDPK28	GRMZM2G365035_T01	1 539	512	57.5	4	MGLCSSST	Yes
ZmCDPK29	GRMZM2G112057_T01	1 620	539	61.0	4	MGNCFTRK	Yes
ZmCDPK30	GRMZM2G088361_T01	1 623	540	60.2	4	MGNCCRSP	No
ZmCDPK31	GRMZM5G856738_T03	1 575	524	59.5	4	MGNRASRH	Yes
ZmCDPK32	GRMZM2G099425_T01	1 620	539	60.8	4	MGNCCVTP	Yes
ZmCDPK33	GRMZM2G168706_T01	1 596	531	59.4	4	MGQCCSRA	Yes
ZmCDPK34	GRMZM2G340224_T01	1 842	613	67.5	4	MRPSVSMI	Yes
ZmCDPK35	GRMZM2G365815_T01	1 659	552	60.0	4	MGQCCSKG	Yes
ZmCDPK36	GRMZM2G472311_T01	1 746	581	63.4	4	MGQCCSKG	Yes
ZmCDPK37	AC203294.3_FGP001	1 395	464	50.9	4	MGNCCPGS	No
ZmCDPK38	GRMZM2G332660_T01	1 707	568	62.8	4	MGGCYSAF	Yes
ZmCDPK39	GRMZM2G097533_T01	1 317	438	48.5	1	MGNCCVSR	Yes

名称 Name	序列号 ID	CDs	氨基酸 Amino acid	分子量 MW (kDa)	EF手型数量 No. of EF Hands	N端序列 N-terminal	N端豆蔻酰化基元 N-Myristoylation
ZmCDPK1	GRMZM2G028926_T01	1 827	608	66.4	4	MGNTCVGP	No
ZmCDPK2	GRMZM2G320506_T01	1 863	620	67.7	4	MGNTCVGP	No
ZmCDPK3	GRMZM2G025387_T01	1 593	530	59.9	4	MGNRASRH	Yes
ZmCDPK4	GRMZM2G035843_T01	1 527	508	56.5	4	MQPDPSGN	No
ZmCDPK5	GRMZM2G314396_T01	1 644	547	60.4	4	MGNACSGA	Yes
ZmCDPK6	GRMZM2G321239_T01	1 671	556	61.2	4	MGNACGGA	Yes
ZmCDPK7	GRMZM2G104125_T01	1 608	535	60.3	4	MGNCCATP	Yes
ZmCDPK8	AC210013.4_FGP014	1 617	538	60.4	4	MGNCCAAP	Yes
ZmCDPK9	GRMZM2G154489_T01	1 596	531	59.4	4	MGQCCSRA	Yes
ZmCDPK10	GRMZM2G030673_T01	1 626	541	60.5	4	MGNCCRSP	No
ZmCDPK11	GRMZM2G463464_T01	1 548	515	56.8	4	MQPDPQGP	No
ZmCDPK12	GRMZM2G047486_T01	1 533	510	60.2	4	MQPDPSGN	No
ZmCDPK13	GRMZM2G311220_T01	1 611	536	60.2	4	MGNCCRSP	No
ZmCDPK14	GRMZM2G028086_T01	1 620	539	60.8	4	MGNCCVTP	Yes
ZmCDPK15	GRMZM2G058305_T01	1 620	539	60.7	4	MGGRASRH	Yes
ZmCDPK16	GRMZM2G015703_T01	1 779	592	65.4	1	MGLCHGKP	Yes
ZmCDPK17	GRMZM2G167276_T01	1 533	510	56.2	4	MGNCCPGS	Yes
ZmCDPK18	GRMZM2G157068_T02	1 569	522	58.5	4	MGACFSSA	Yes
ZmCDPK19	GRMZM2G347047_T01	1 467	488	53.9	4	MGGHQLHL	No
ZmCDPK20	GRMZM2G121228_T01	1 743	580	63.7	4	MGNTCVGP	No
ZmCDPK21	GRMZM2G027351_T01	1 755	584	64.1	4	MGNTCVGP	No
ZmCDPK22	GRMZM2G347226_T01	1 548	515	56.8	4	MQPDPQGS	No
ZmCDPK23	GRMZM2G040743_T01	1 623	540	60.9	4	MGNQCQNG	No
ZmCDPK24	GRMZM2G080871_T02	1 536	511	57.0	3	MGGCHSAI	No
ZmCDPK25	GRMZM2G353957_T01	1 941	646	71.7	4	MGNVCVGP	No
ZmCDPK26	GRMZM2G081310_T01	1 689	562	61.9	4	MGNTCGVT	No
ZmCDPK27	GRMZM2G032852_T02	1 635	544	61.7	4	MGNQCPNG	No
ZmCDPK28	GRMZM2G365035_T01	1 539	512	57.5	4	MGLCSSST	Yes
ZmCDPK29	GRMZM2G112057_T01	1 620	539	61.0	4	MGNCFTRK	Yes
ZmCDPK30	GRMZM2G088361_T01	1 623	540	60.2	4	MGNCCRSP	No
ZmCDPK31	GRMZM5G856738_T03	1 575	524	59.5	4	MGNRASRH	Yes
ZmCDPK32	GRMZM2G099425_T01	1 620	539	60.8	4	MGNCCVTP	Yes
ZmCDPK33	GRMZM2G168706_T01	1 596	531	59.4	4	MGQCCSRA	Yes
ZmCDPK34	GRMZM2G340224_T01	1 842	613	67.5	4	MRPSVSMI	Yes
ZmCDPK35	GRMZM2G365815_T01	1 659	552	60.0	4	MGQCCSKG	Yes
ZmCDPK36	GRMZM2G472311_T01	1 746	581	63.4	4	MGQCCSKG	Yes
ZmCDPK37	AC203294.3_FGP001	1 395	464	50.9	4	MGNCCPGS	No
ZmCDPK38	GRMZM2G332660_T01	1 707	568	62.8	4	MGGCYSAF	Yes
ZmCDPK39	GRMZM2G097533_T01	1 317	438	48.5	1	MGNCCVSR	Yes