高粱ZF-HD基因家族鉴定与盐碱胁迫下的表达分析

doi:10.3969/j.issn.1004-1524.20230861

浙江农业学报 ›› 2024, Vol. 36 ›› Issue (6): 1217-1231.DOI: 10.3969/j.issn.1004-1524.20230861

高粱ZF-HD基因家族鉴定与盐碱胁迫下的表达分析

吴国江(), 周伟, 李艳肖, 侯杰, 杨志强, 周亚星^*()

内蒙古民族大学农学院, 内蒙古通辽 028000

收稿日期:2023-07-13 出版日期:2024-06-25 发布日期:2024-07-02
作者简介:吴国江(1997—),男,内蒙古呼和浩特人,硕士研究生,研究方向为作物遗传改良与种质创新。E-mail:2592406718@qq.com
通讯作者: *周亚星,E-mail:zhouyaxing3@163.com
基金资助:
内蒙古自然科学基金(2023LHMS03018);科尔沁沙地生态农业国家民委重点实验室开放基金项目(MDK2022023);内蒙古自治区科技计划(2020GG0102);内蒙古自治区高等学校青年科技英才(NJYT22052);2022年度自治区直属高校基本科研业务费项目(西辽河平原耐盐碱优质高粱种质鉴定研究)

Identification and expression analysis under saline-alkali stress of ZF-HD gene family in sorghum

WU Guojiang(), ZHOU Wei, LI Yanxiao, HOU Jie, YANG Zhiqiang, ZHOU Yaxing^*()

College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, Inner Mongolia, China

Received:2023-07-13 Online:2024-06-25 Published:2024-07-02

摘要/Abstract

摘要：

ZF-HD(zinc finger-homeodomain)是仅存在于植物中的转录因子家族,在植物的生长发育和逆境应答过程中发挥着重要作用。为分析ZF-HD基因家族成员在高粱基因组中的组成与潜在的生物学功能,利用生物信息学分析方法并结合高粱转录组数据,对高粱ZF-HD基因(SbZF-HD)及其编码氨基酸序列进行分析。结果表明:共有14个SbZF-HD基因不均匀地分布在高粱的8条染色体上,且基因结构各异;它们编码的氨基酸的基序组成较为相似,蛋白质的高级结构均以无规则卷曲为主。ZF-HD蛋白质的进化树分析结果表明,SbZF-HD与玉米的ZF-HD亲缘关系较近,与拟南芥的ZF-HD亲缘关系较远。SbZF-HD启动子区域中包含多个激素调控类元件、胁迫响应类元件和光响应元件。SbZF-HD基因组织表达分析显示,SbZF-HD基因有组织表达特异性,在根、叶和种子中的表达量较高。转录组分析表明,盐碱胁迫条件下,SbZF-HD2、SbZF-HD7、SbZF-HD8和SbZF-HD12这4个基因在2份盐碱耐性不同的酿造高粱材料中表现出相反的表达趋势,可能在高粱耐盐碱机制中发挥着重要作用。综上,SbZF-HD基因家族成员可能是高粱耐盐碱胁迫的关键调控基因,该研究为高粱耐盐碱转基因育种提供了基因资源。

关键词: 高粱, ZF-HD基因, 表达模式, 盐碱胁迫

Abstract:

ZF-HD (zinc finger-homeodomain), a transcription factor family only in plants, plays important role in plant growth and development and stress response. In order to analyze the composition and potential biological functions of ZF-HD family genes in sorghum genome (SbZF-HD), the SbZF-HD genes and their encoded amino acid sequence were analyzed by bioinformatics analysis combined with sorghum transcriptome data. The results showed that a total of 14 SbZF-HD genes were unevenly distributed on 8 chromosomes of sorghum, and the gene structures were different. The motif composition of the deduced amino acids was similar, and the advanced structure of the protein was dominated by random coils. The phylogenetic tree analysis of ZF-HD protein showed that SbZF-HD was closely related to ZF-HD of maize and far from ZF-HD of Arabidopsis thaliana. The SbZF-HD promoter region contains multiple hormone regulatory elements, stress response elements and light response elements. Tissue expression analysis showed that SbZF-HD genes had tissue expression specificity, and the expression level were higher in root, leaf and seed. Transcriptome analysis showed that SbZF-HD2, SbZF-HD7, SbZF-HD8 and SbZF-HD12 genes showed opposite expression trends in two brewing sorghum materials with different saline-alkali tolerance under saline-alkali stress, which might play an important role in the saline-alkali tolerance mechanism of sorghum. In summary, the SbZF-HD family members might be the key genes under the regulation of saline-alkali stress in sorghum. This study provided genetic resources for sorghum saline-alkali tolerance transgenic breeding.

Key words: sorghum, ZF-HD gene, expression pattern, saline-alkali stress

中图分类号:

S514

吴国江, 周伟, 李艳肖, 侯杰, 杨志强, 周亚星. 高粱ZF-HD基因家族鉴定与盐碱胁迫下的表达分析[J]. 浙江农业学报, 2024, 36(6): 1217-1231.

WU Guojiang, ZHOU Wei, LI Yanxiao, HOU Jie, YANG Zhiqiang, ZHOU Yaxing. Identification and expression analysis under saline-alkali stress of ZF-HD gene family in sorghum[J]. Acta Agriculturae Zhejiangensis, 2024, 36(6): 1217-1231.

图/表 10

表1 高粱ZF-HD基因家族成员信息及其编码蛋白质的理化性质和二级结构

Table 1 Information of sorghum ZF-HD gene family members and physicochemical properties and secondary structure of their encoded proteins

基因名称 Gene name	序列ID Sequence ID	氨基酸数量 Amino acid number	分子量 Molecular weight/ ku	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index	亲水性指数 Grand average of hydropathicity	亚细胞定位 Subcellular localization	α-螺旋 α-Helix/ %	延伸链 Extended strand/%	β-折叠 β-Sheet/ %	无规则卷曲 Random coil/%
SbZF-HD1	Sobic. 001G112500.1	234	24.35	8.14	56.01	42.22	-0.585	线粒体 Mitochondria	26.50	5.56	7.26	60.68
SbZF-HD2	Sobic. 002G201100.2	110	12.46	8.81	55.42	54.18	-0.545	细胞核 Nucleus	38.18	20.91	4.55	36.36
SbZF-HD3	Sobic. 002G201400.1	381	39.39	7.75	69.35	55.28	-0.504	细胞核 Nucleus	22.05	11.29	5.25	61.42
SbZF-HD4	Sobic. 002G231100.1	302	31.47	7.38	52.79	50.86	-0.579	细胞核 Nucleus	20.53	8.61	6.62	64.24
SbZF-HD5	Sobic. 003G135101.1	265	29.29	11.69	84.56	54.34	-0.817	细胞核 Nucleus	38.49	9.43	2.64	49.43
SbZF-HD6	Sobic. 004G266800.1	406	43.48	6.55	93.15	54.73	-0.791	细胞核 Nucleus	26.35	9.36	3.45	60.84
SbZF-HD7	Sobic. 005G019800.1	98	10.14	6.49	59.24	33.16	-0.661	细胞核 Nucleus	20.41	13.27	9.18	57.14
SbZF-HD8	Sobic. 005G086700.1	394	40.83	7.76	68.95	57.36	-0.538	细胞核 Nucleus	26.90	10.66	5.58	56.85
SbZF-HD9	Sobic. 007G139000.1	127	13.31	7.92	73.21	49.37	-0.156	叶绿体 Chloroplast	31.50	16.54	7.87	44.09
SbZF-HD10	Sobic. 007G139200.1	390	40.29	6.52	71.13	61.05	-0.373	细胞质 Cytoplasm	30.26	8.46	6.41	54.87
SbZF-HD11	Sobic. 007G160400.1	311	31.80	6.80	46.00	55.02	-0.430	细胞核 Nucleus	19.61	11.90	6.75	61.74
SbZF-HD12	Sobic. 008G020700.1	92	9.75	7.67	58.20	38.48	-0.651	细胞核 Nucleus	26.09	13.04	5.43	55.43
SbZF-HD13	Sobic. 008G073200.1	328	34.72	9.15	70.83	54.27	-0.789	细胞核 Nucleus	16.77	9.76	6.10	67.38
SbZF-HD14	Sobic. 009G244200.2	373	39.71	8.82	91.63	47.77	-0.819	叶绿体 Chloroplast	24.93	8.58	5.90	60.59

表1 高粱ZF-HD基因家族成员信息及其编码蛋白质的理化性质和二级结构

Table 1 Information of sorghum ZF-HD gene family members and physicochemical properties and secondary structure of their encoded proteins

基因名称 Gene name	序列ID Sequence ID	氨基酸数量 Amino acid number	分子量 Molecular weight/ ku	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index	亲水性指数 Grand average of hydropathicity	亚细胞定位 Subcellular localization	α-螺旋 α-Helix/ %	延伸链 Extended strand/%	β-折叠 β-Sheet/ %	无规则卷曲 Random coil/%
SbZF-HD1	Sobic. 001G112500.1	234	24.35	8.14	56.01	42.22	-0.585	线粒体 Mitochondria	26.50	5.56	7.26	60.68
SbZF-HD2	Sobic. 002G201100.2	110	12.46	8.81	55.42	54.18	-0.545	细胞核 Nucleus	38.18	20.91	4.55	36.36
SbZF-HD3	Sobic. 002G201400.1	381	39.39	7.75	69.35	55.28	-0.504	细胞核 Nucleus	22.05	11.29	5.25	61.42
SbZF-HD4	Sobic. 002G231100.1	302	31.47	7.38	52.79	50.86	-0.579	细胞核 Nucleus	20.53	8.61	6.62	64.24
SbZF-HD5	Sobic. 003G135101.1	265	29.29	11.69	84.56	54.34	-0.817	细胞核 Nucleus	38.49	9.43	2.64	49.43
SbZF-HD6	Sobic. 004G266800.1	406	43.48	6.55	93.15	54.73	-0.791	细胞核 Nucleus	26.35	9.36	3.45	60.84
SbZF-HD7	Sobic. 005G019800.1	98	10.14	6.49	59.24	33.16	-0.661	细胞核 Nucleus	20.41	13.27	9.18	57.14
SbZF-HD8	Sobic. 005G086700.1	394	40.83	7.76	68.95	57.36	-0.538	细胞核 Nucleus	26.90	10.66	5.58	56.85
SbZF-HD9	Sobic. 007G139000.1	127	13.31	7.92	73.21	49.37	-0.156	叶绿体 Chloroplast	31.50	16.54	7.87	44.09
SbZF-HD10	Sobic. 007G139200.1	390	40.29	6.52	71.13	61.05	-0.373	细胞质 Cytoplasm	30.26	8.46	6.41	54.87
SbZF-HD11	Sobic. 007G160400.1	311	31.80	6.80	46.00	55.02	-0.430	细胞核 Nucleus	19.61	11.90	6.75	61.74
SbZF-HD12	Sobic. 008G020700.1	92	9.75	7.67	58.20	38.48	-0.651	细胞核 Nucleus	26.09	13.04	5.43	55.43
SbZF-HD13	Sobic. 008G073200.1	328	34.72	9.15	70.83	54.27	-0.789	细胞核 Nucleus	16.77	9.76	6.10	67.38
SbZF-HD14	Sobic. 009G244200.2	373	39.71	8.82	91.63	47.77	-0.819	叶绿体 Chloroplast	24.93	8.58	5.90	60.59

图1 高粱ZF-HD家族蛋白质的三级结构

Fig.1 The tertiary structure of sorghum ZF-HD family proteins

图2 高粱ZF-HD基因家族成员染色体定位

Fig.2 Chromosome location of ZF-HD gene family members in sorghum

图3 高粱ZF-HD家族成员的系统进化树(A)、基因结构(B)、结构域(C)和保守基序(D)

Fig.3 Phylogenetic tree (A), gene structure (B), domain (C) and conserved motif (D) of sorghum ZF-HD family members

图4 高粱、拟南芥、水稻、玉米和谷子ZF-HD蛋白质的系统进化树 Sb,高粱;AT,拟南芥;LOC Os,水稻;GRMZM,玉米;Seita.,谷子。

Fig.4 Phylogenetic tree of ZF-HD protein in sorghum, Arabidopsis, rice, maize and millet Sb, Sorghum; AT, Arabidopsis; LOC Os, Rice; GRMZM, Maize; Seita., Millet.

图5 高粱ZF-HD基因家族物种内的共线性关系

Fig.5 The collinear relationship within species of ZF-HD gene family in sorghum

图6 高粱与拟南芥、玉米、水稻、谷子ZF-HD基因家族的共线性关系

Fig.6 The collinear relationship between sorghum and ZF-HD gene family in Arabidopsis, maize, rice and foxtail millet

图7 高粱ZF-HD基因家族成员的启动子顺式作用元件

Fig.7 Promoter cis-acting elements of Sorghum ZF-HD gene family members

图8 高粱ZF-HD基因家族成员在不同组织的表达水平 1,幼苗根;2,幼嫩根尖;3,根尖部营养组织;4,根底部营养组织;5,茎;6,幼苗叶片;7,芽;8,穗花芽分化;9,花序梗花芽分化;10,种子。

Fig.8 Expression level of ZF-HD gene family members in different tissues of Sorghum 1, Root bottom.juvenile; 2, Root top.juvenile; 3, Root top.vegetative; 4, Root bottom.vegetative; 5, Stem ; 6, Leaf blade.juvenile; 7, Shoot; 8, Panicle.floral initiation; 9, Peduncle.floral initiation; 10, Seed.

图9 高粱ZF-HD基因家族成员在盐碱胁迫下的表达 A,极耐盐碱酿造高粱924的ZF-HD基因家族成员在1/2Hoagland营养液(NYCK)、100 mmol·L-1盐碱(NYA)、200 mmol·L-1盐碱(NYB)胁迫下的表达模式;B,盐碱敏感酿造高粱661的ZF-HD基因家族成员在1/2Hoagland营养液(MYCK)、100 mmol·L-1盐碱(MYA)、200 mmol·L-1盐碱(MYB)胁迫下的表达模式。

Fig.9 Expression of ZF-HD family genes in sorghum under saline-alkali stress A shows the expression patterns of ZF-HD family genes in salt-tolerant brewing sorghum ‘924’ under 1/2 Hoagland nutrient solution (NYCK), 100 mmol·L-1 saline-alkaline (NYA) and 200 mmol·L-1 saline-alkaline (NYB) stress; B shows the expression pattern of ZF-HD family genes in saline-alkali sensitive brewing sorghum ‘661’ under the stress of 1/2Hoagland nutrient solution (MYCK), 100 mmol·L-1 saline-alkali (MYA), 200 mmol·L-1 saline-alkali (MYB).

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高粱ZF-HD基因家族鉴定与盐碱胁迫下的表达分析

Identification and expression analysis under saline-alkali stress of ZF-HD gene family in sorghum

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