玉米NRL基因家族鉴定与逆境表达分析

doi:10.7668/hbnxb.20192757

华北农学报 ›› 2022, Vol. 37 ›› Issue (4): 1-10. doi: 10.7668/hbnxb.20192757

所属专题： 玉米；盐碱胁迫；生物技术；热点文章；

• 作物遗传育种·种质资源·生物技术 • 下一篇

玉米NRL基因家族鉴定与逆境表达分析

赵长江¹^,²^,³^,⁴, 都梦翔¹^,²^,³^,⁴, 宋巨奇¹^,²^,³^,⁴, 徐尚缘¹^,²^,³^,⁴, 贺琳¹^,²^,⁴, 徐晶宇¹^,²^,⁴, 杨克军¹^,²^,³^,⁴, 李佐同¹^,²^,³^,⁴^,

¹ 黑龙江八一农垦大学农学院,黑龙江大庆 163319
² 农业农村部东北平原农业绿色低碳重点实验室,黑龙江大庆 163319
³ 黑龙江省秸秆资源化利用工程技术研究中心,黑龙江大庆 163319
⁴ 黑龙江省现代农业栽培技术与作物种质改良重点实验室,黑龙江大庆 163319

收稿日期:2022-02-22 出版日期:2022-08-28
通讯作者: 李佐同
作者简介:
赵长江(1979-),男,黑龙江海伦人,副教授,博士,主要从事作物逆境生理分子生物学及秸秆生物炭还田利用研究。
基金资助:
国家自然科学基金项目(31701328); 黑龙江省自然基金重点项目(ZD2020C007)

Genome-wide Identification and Expression Response to Stresses Analysis of NRL Gene Family in Zea mays

ZHAO Changjiang¹^,²^,³^,⁴, DU Mengxiang¹^,²^,³^,⁴, SONG Juqi¹^,²^,³^,⁴, XU Shangyuan¹^,²^,³^,⁴, HE Lin¹^,²^,⁴, XU Jingyu¹^,²^,⁴, YANG Kejun¹^,²^,³^,⁴, LI Zuotong¹^,²^,³^,⁴^,

¹ College of Agriculture,Heilongjiang Bayi Agricultural University,Daqing 163319,China
² Key Laboratory of Low-carbon Green Agriculture in Northeastern China,Ministry of Agriculture and Rural Affairs,Daqing 163319,China
³ Engineering Research Center of Crop Straw Utilization, Heilongjiang Province,Daqing 163319,China
⁴ Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement,Daqing 163319,China

Received:2022-02-22 Published:2022-08-28
Contact: LI Zuotong

摘要/Abstract

摘要：

NRL(NPH3/RPT2-Like)是植物所特有的一类光响应蛋白,在向光素信号途径中发挥重要作用。利用生物信息学手段结合qRT-PCR技术,在玉米基因组水平对该家族基因进行鉴定并对其编码蛋白的性质、结构、进化、生育期组织表达和逆境表达进行分析。结果鉴定了31个ZmNRL基因,不均匀地分布于玉米9条染色体上,编码的氨基酸序列长度在464~749个,预测具有叶绿体、细胞核和细胞质等亚细胞定位。依据蛋白保守性将ZmNRL家族划分为四大类,基因结构也具有一定的保守性,多数基因含有4个外显子。基因启动子存在大量脱落酸、茉莉酸、光响应和抗氧化等顺式元件分析,其中G-box和Sp1等两类光相关元件数量较多。ZmNRL家族基因在生育期组织部位表达具有一定的时空特异性,总体表达量不高,仅有ZmNRL2、ZmNRL4、ZmNRL24和ZmNRL29相对高表达。通过生育期组织表达数据共表达及其模块GO富集分析发现,6个ZmNRL基因可通过叶绿体等生物发生及组装生物过程,参与对叶片生长发育的调控。qRT-PCR结果表明,高温处理玉米幼苗ZmNRL12上调表达显著,干旱、盐和病原物接种处理ZmNRL5、ZmNRL7和ZmNRL19基因下调表达。综上,在玉米基因组鉴定出31个ZmNRL基因,该家族基因不仅具有明显的组织表达特异性,而且可参与玉米幼苗对生物和非生物逆境应答。

关键词: 玉米, NRL, 基因家族, 逆境胁迫, 表达分析

Abstract:

NRL(NPH3/RPT2-Like)is a type of light-responsive protein unique to plants and plays a vital role in the phototropic signal pathway. To reveal the NRL gene maize genome's characteristics and expression,we analyzed them using bioinformatics methods combined with qRT-PCR technology. The property,structure,evolution of their encoded proteins,and growth period tissue expression and stress expression were analyzed. 31 ZmNRL genes identified were located in nine maize chromosomes,encoding protein amino acids 464-749 aa,which predicted to have chloroplast,nuclear and cytoplasmic locations. According to protein conservation,ZmNRL family was divided into four categories. Their gene structure also presented certain conservation,the most contained four exons. Analysis of the cis-elements of gene promoters revealed a large number of abscisic acids,jasmonic acid,light response,and anti-oxidation elements,among which G-box and Sp1 were two types of light-related elements. The expression of ZmNRL family genes in tissues during the growth period showed a temporal and spatial specificity,and the majority expression level was not high. Only ZmNRL2,ZmNRL4,ZmNRL24,and ZmNRL29 highly expressed. Furthermore,the characteristic modules were produced based on the data of the tissue co-expression genes. And the GO enrichment analysis of a particular leaf growth module containing six ZmNRL genes,mainly associated with the plastid organization biological processes and rRNA binding molecular functions. The expression of ZmNRL5,ZmNRL7,ZmNRL12,and ZmNRL19 genes were analyzed by qRT-PCR under salt,drought,high temperature,and Rhizoctonia solani inoculation treatments. The results showed that ZmNRL12 was significantly up-regulated in maize seedlings treated with high temperature,while ZmNRL5,ZmNRL7 and ZmNRL19 genes were down-regulated in drought,salt and pathogen treatments. In summary,31 ZmNRL genes were identified in the maize genome. They not only had apparent specific tissue expression but also participated in biotic and abiotic stress responses.

Key words: Maize, NRL, Gene family, Stresses, Expression analysis

赵长江, 都梦翔, 宋巨奇, 徐尚缘, 贺琳, 徐晶宇, 杨克军, 李佐同. 玉米NRL基因家族鉴定与逆境表达分析[J]. 华北农学报, 2022, 37(4): 1-10. doi: 10.7668/hbnxb.20192757.

ZHAO Changjiang, DU Mengxiang, SONG Juqi, XU Shangyuan, HE Lin, XU Jingyu, YANG Kejun, LI Zuotong. Genome-wide Identification and Expression Response to Stresses Analysis of NRL Gene Family in Zea mays[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(4): 1-10. doi: 10.7668/hbnxb.20192757.

http://www.hbnxb.net/CN/Y2022/V37/I4/1

图/表 10

表1 qRT-PCR引物序列信息

Tab.1 Primers for qRT-PCR

引物名称 Primer name	上游引物(5'-3') Forward primer(5'-3')	下游引物(5'-3') Reverse primer(5'-3')	退火温度/℃ Tm
ZmNRL5	ATCAAGTGTGTTCCGCACCT	TACCGTTCTCAGACGGGAGT	60
ZmNRL7	CGCGCTCTTCTCCAAGATCA	ATGTCGTCGAACCACCACTC	60
ZmNRL12	AGATGGCTGCCAGACTCCTA	TTCTTCCTTCACGTGCTCCC	60
ZmNRL19	CCTGGTGGACCTTCAGCATT	GAGTCCTTCCAGGTGCGAAA	60
β-Actin	CACCTTCTAVAACGAGCTCC	CAGTCAGGATCTTCATGAGG	60

表2 ZmNRL编码蛋白序列理化性质分析

Tab.2 Physiochemical property of ZmNRLs gene and their coding protein

基因名称 Gene name	基因号 Gene ID	染色体 Chromosome	CDS长度/bp CDS length	氨基酸数量/个 Amino acids	分子质量/ku Molecular weight	等电点 pI	亚细胞定位预测 Predicted subcellular localization
ZmNRL1	Zm00001d028056	1	1 794	597	66.26	5.82	叶绿体
ZmNRL2	Zm00001d028075	1	1 842	613	67.00	8.22	细胞质
ZmNRL3	Zm00001d030864	1	1 926	641	68.43	5.84	细胞质
ZmNRL4	Zm00001d033240	1	1 890	629	69.69	6.40	细胞核
ZmNRL5	Zm00001d033344	1	1 908	635	69.15	5.49	内质网
ZmNRL6	Zm00001d033941	1	1 896	631	68.72	6.19	叶绿体
ZmNRL7	Zm00001d001858	2	1 680	559	60.37	9.01	叶绿体
ZmNRL8	Zm00001d002146	2	1 863	620	66.98	4.97	叶绿体
ZmNRL9	Zm00001d003297	2	1 851	616	65.82	9.15	叶绿体
ZmNRL10	Zm00001d004440	2	1 917	638	69.84	7.60	叶绿体
ZmNRL11	Zm00001d005051	2	1 734	577	60.60	9.11	叶绿体
ZmNRL12	Zm00001d005769	2	1 878	625	69.48	8.27	细胞核
ZmNRL13	Zm00001d006553	2	1 416	471	50.61	8.89	细胞质-细胞核
ZmNRL14	Zm00001d039639	3	1 395	464	48.64	9.59	叶绿体
ZmNRL15	Zm00001d040369	3	1 473	490	52.92	10.04	叶绿体
ZmNRL16	Zm00001d043271	3	1 944	647	69.67	5.23	细胞质
ZmNRL17	Zm00001d050959	4	1 884	627	67.34	8.25	叶绿体
ZmNRL18	Zm00001d013182	5	2 064	687	74.45	5.64	叶绿体
ZmNRL19	Zm00001d013741	5	1 932	643	69.91	5.58	叶绿体
ZmNRL20	Zm00001d016898	5	2 250	749	80.02	7.23	细胞核
ZmNRL21	Zm00001d017079	5	1 875	624	66.94	8.07	叶绿体
ZmNRL22	Zm00001d035208	6	1 992	663	72.72	6.36	细胞核
ZmNRL23	Zm00001d019944	7	1 746	581	63.91	6.97	细胞质
ZmNRL24	Zm00001d020512	7	1 860	619	68.73	8.12	细胞核
ZmNRL25	Zm00001d021714	7	1 692	563	60.33	8.81	叶绿体
ZmNRL26	Zm00001d021949	7	2 061	686	75.09	7.84	内质网
ZmNRL27	Zm00001d045098	9	1 914	637	69.46	7.12	细胞核
ZmNRL28	Zm00001d047483	9	1 932	643	69.47	9.17	叶绿体
ZmNRL29	Zm00001d048138	9	1 875	624	67.71	8.54	细胞质
ZmNRL30	Zm00001d023313	10	1 977	658	71.31	6.87	叶绿体
ZmNRL31	Zm00001d023314	10	1 917	638	67.25	9.19	叶绿体

表2 ZmNRL编码蛋白序列理化性质分析

Tab.2 Physiochemical property of ZmNRLs gene and their coding protein

基因名称 Gene name	基因号 Gene ID	染色体 Chromosome	CDS长度/bp CDS length	氨基酸数量/个 Amino acids	分子质量/ku Molecular weight	等电点 pI	亚细胞定位预测 Predicted subcellular localization
ZmNRL1	Zm00001d028056	1	1 794	597	66.26	5.82	叶绿体
ZmNRL2	Zm00001d028075	1	1 842	613	67.00	8.22	细胞质
ZmNRL3	Zm00001d030864	1	1 926	641	68.43	5.84	细胞质
ZmNRL4	Zm00001d033240	1	1 890	629	69.69	6.40	细胞核
ZmNRL5	Zm00001d033344	1	1 908	635	69.15	5.49	内质网
ZmNRL6	Zm00001d033941	1	1 896	631	68.72	6.19	叶绿体
ZmNRL7	Zm00001d001858	2	1 680	559	60.37	9.01	叶绿体
ZmNRL8	Zm00001d002146	2	1 863	620	66.98	4.97	叶绿体
ZmNRL9	Zm00001d003297	2	1 851	616	65.82	9.15	叶绿体
ZmNRL10	Zm00001d004440	2	1 917	638	69.84	7.60	叶绿体
ZmNRL11	Zm00001d005051	2	1 734	577	60.60	9.11	叶绿体
ZmNRL12	Zm00001d005769	2	1 878	625	69.48	8.27	细胞核
ZmNRL13	Zm00001d006553	2	1 416	471	50.61	8.89	细胞质-细胞核
ZmNRL14	Zm00001d039639	3	1 395	464	48.64	9.59	叶绿体
ZmNRL15	Zm00001d040369	3	1 473	490	52.92	10.04	叶绿体
ZmNRL16	Zm00001d043271	3	1 944	647	69.67	5.23	细胞质
ZmNRL17	Zm00001d050959	4	1 884	627	67.34	8.25	叶绿体
ZmNRL18	Zm00001d013182	5	2 064	687	74.45	5.64	叶绿体
ZmNRL19	Zm00001d013741	5	1 932	643	69.91	5.58	叶绿体
ZmNRL20	Zm00001d016898	5	2 250	749	80.02	7.23	细胞核
ZmNRL21	Zm00001d017079	5	1 875	624	66.94	8.07	叶绿体
ZmNRL22	Zm00001d035208	6	1 992	663	72.72	6.36	细胞核
ZmNRL23	Zm00001d019944	7	1 746	581	63.91	6.97	细胞质
ZmNRL24	Zm00001d020512	7	1 860	619	68.73	8.12	细胞核
ZmNRL25	Zm00001d021714	7	1 692	563	60.33	8.81	叶绿体
ZmNRL26	Zm00001d021949	7	2 061	686	75.09	7.84	内质网
ZmNRL27	Zm00001d045098	9	1 914	637	69.46	7.12	细胞核
ZmNRL28	Zm00001d047483	9	1 932	643	69.47	9.17	叶绿体
ZmNRL29	Zm00001d048138	9	1 875	624	67.71	8.54	细胞质
ZmNRL30	Zm00001d023313	10	1 977	658	71.31	6.87	叶绿体
ZmNRL31	Zm00001d023314	10	1 917	638	67.25	9.19	叶绿体

图1 NRL家族系统进化关系 Ⅰ~Ⅳ代表基因所属亚族;玉米、高粱和水稻分别用圆形、菱形和正方形来表示;拟南芥和番茄分别用倒三角形和三角形表示。

Fig.1 The phylogenetic relationship of NRL gene family Ⅰ-Ⅳ represents the gene subgroup;Zea mays,Sorghum bicolor,and Oryza sativa are represented by circles,diamonds, and squares;Arabidopsis thaliana and Lycopersicon esculentum are represented by inverted triangles and triangles.

图2 玉米、拟南芥和高粱NRL基因染色体定位及共线性图中Chr和chr以及数字1~5分别表示玉米、高粱和拟南芥的染色体;红色线条为玉米物种内的片段重复基因对;灰色线条为玉米和高粱的片段重复基因对;蓝色线条为玉米和拟南芥物种间的片段重复基因对;绿色线条为拟南芥和高粱物种间的片段重复基因对;玉米物种内的串联重复基因用红色菱形来标识。

Fig.2 Localization and collinearity of NRL gene in Zea mays,Arabidopsis thaliana and Sorghum bicolor Chr,chr and the number 1-5 in the figure represent the chromosomes of Zea mays, Arabidopsis thaliana and Sorghum bicolor,respectively;Segmental duplication gene pairs in Zea mays were represented by red lines;it between Zea mays and Sorghum bicolor were represented by gray lines;it between Zea mays and Arabidopsis thaliana were represented by blue lines;it between Arabidopsis thaliana and Sorghum bicolor were represented by green lines;the tandem duplication gene pairs in the Zea mays species were marked with red diamonds.

图3 ZmNRL家族基因结构(A)和保守基序(B、C)分析 A中数字代表内含子的数量,下方比例尺表示基因碱基数;B下方比例尺表示蛋白长度,CDS为编码区,UTR为非编码区。

Fig.3 The gene structure(A)and conserved motifs(B,C)analysis of ZmNRL family The number in A represents intron number,and the lower scale represents gene bases the number;the lower scale of B represents the length of the protein,CDS is the coding region,and UTR is the non-coding region.

图4 ZmNRL家族基因全生育期表达热图图例表示标准化的FPKM值,红色表示高表达水平,蓝色表示低表达水平。

Fig.4 Expression heat map of ZmNRL family gene during whole growth period The legend shows the standardized FPKM value, the red shows the high expression level, and the blue shows the low expression level.

图5 WGCNA聚类树状图

Fig.5 WGCNA clustering dendrogram

图6 WGCNA模块-特征关系图

Fig.6 WGCNA module-feature relationship diagram

图7 MEbrown模块GO富集分析

Fig.7 GO enrichment analysis of the MEbrown module

图8 ZmNRL家族基因的启动子顺式作用元件与逆境表达分析 A为顺式作用元件分布图;B为4种胁迫(高温、NaCl、PEG干旱、AG1-IA立枯丝核菌)下基因表达谱。图中小写字母表示基因在0.05水平差异显著。

Fig.8 Analysis of cis-acting elements located in promoter and gene expression response to stress of ZmNRL family A is the distribution map of cis-acting elements;B is the gene expression profile under 4 stresses(high temperature, NaCl,PEG drought, Rhizoctonia solani AG1-IA).Lowercase letters present the significant difference at 0.05 level.

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玉米NRL基因家族鉴定与逆境表达分析

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