谷子AP基因家族鉴定及其对非生物胁迫的响应分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-0588

生物技术通报 ›› 2023, Vol. 39 ›› Issue (11): 238-251.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0588

谷子AP基因家族鉴定及其对非生物胁迫的响应分析

邢媛¹^,²(), 宋健³, 李俊怡¹, 郑婷婷¹^,², 刘思辰¹^,²(), 乔治军¹^,²()

1.山西农业大学农学院，太谷 030801
2.山西农业大学农业基因资源研究中心农业农村部黄土高原作物基因资源与种质创制重点实验室，太原 030031
3.山西农业大学农业经济作物研究所，吕梁 032200

收稿日期:2023-06-20 出版日期:2023-11-26 发布日期:2023-12-20
通讯作者: 刘思辰，女，副研究员，研究方向：谷子种质资源评价利用；E-mail: lsch@163.com；
乔治军，男，研究员，研究方向：旱作栽培与逆境生理；E-mail: nkypzs@126.com
作者简介:邢媛，女，硕士，研究方向：作物遗传育种；E-mail: xy15315514037@163.com
基金资助:
山西省重点研发计划项目(201903D221087);现代农业产业技术体系建设专项(CARS-06-14.5-A16);中央引导地方科技发展资金项目(YDZJSX20231A040);山西农业大学校科技创新提升工程(CXGC2023094);山西省吕梁市科技局农业攻关(2022NYGG012)

Identification of AP Gene Family and Its Response Analysis to Abiotic Stress in Setaria italica

XING Yuan¹^,²(), SONG Jian³, LI Jun-yi¹, ZHENG Ting-ting¹^,², LIU Si-chen¹^,²(), QIAO Zhi-jun¹^,²()

1. Center for Agricultural Genetic Resources Research, College of Agronomy, Shanxi Agricultural University, Taigu 030801
2. Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture and Rural Affairs, Taiyuan 030031
3. Agricultural Cash Crop Research Institute of Shanxi Agricultural University, Lvliang 032200

Received:2023-06-20 Published:2023-11-26 Online:2023-12-20

摘要/Abstract

摘要：

天冬氨酸蛋白酶（AP）是一类重要的水解酶，在植物生长发育及抵御生物和非生物胁迫方面发挥着重要作用。谷子（Setaria italica）作为禾本科C₄植物抗逆研究的模式作物，目前关于天冬氨酸蛋白酶家族基因功能的研究较少。为深入探究AP基因家族在谷子中的功能作用，本研究基于AP保守Pfam序列全基因组筛选鉴定谷子AP基因家族的成员，并通过生物信息学方法对其理化性质、亚细胞定位、基因结构、保守结构域、系统进化发育、启动子顺式作用元件及共线性等分析，同时利用荧光定量PCR技术对其在非生物胁迫下的表达模式进行了研究。结果表明，谷子基因组中共有AP基因家族成员58个；系统进化树显示该基因家族可分为5个亚家族，其中Group B编码非典型天冬氨酸蛋白酶，其他亚家族编码类nucellin天冬氨酸蛋白酶；基因结构和保守基序分析表明，谷子AP家族同一亚家族成员具有较高的保守性；共线性分析结果显示，谷子AP基因家族与水稻（Oryza sativa）和玉米（Zea mays）AP基因家族成员之间存在大量的同源基因对；启动子顺式作用元件分析表明，SiAPs基因家族中大部分成员含有与非生物胁迫和生物激素响应相关的顺式元件，如响应干旱和低温胁迫的顺式作用元件、水杨酸有关的应答元件等。进一步RT-qPCR结果发现，SiAPs基因家族成员在谷子根、茎、叶、穗中差异表达；在低温胁迫下，SiAP3、SiAP9、SiAP48基因表达量显著升高；在干旱胁迫和水杨酸处理下，部分基因表达的变化趋势基本一致。SiAPs对谷子响应非生物胁迫起重要的调控作用，本研究结果可为SiAPs的抗逆功能分析提供参考。

关键词: 谷子, 天冬氨酸蛋白酶, 水杨酸响应, 干旱响应, 低温胁迫, 生物信息学

Abstract:

Aspartic protease（AP）is a pivotal hydrolase enzyme that assumes a critical role in plant growth, development, resilience against both biological and abiotic stressors. Foxtail millet（Setaria itlica）is the model crop for stress resistance study of C₄ gramineous plants, but there are few studies on the gene function of AP（SiAPs）in foxtail millet. In order to further explore the functional role of the APs in foxtail millet, the members of the SiAPs were indentified based on whole-genome screening of SiAPs conserved Pfam sequences, and bioinformatics method was used to analyze their physical and chemical properties, subcellular localization, gene structure, conserved domain, phylogenetic development, promoter cis-acting elements and collinearity by bs. Meanwhile, fluorescence quantitative PCR technique was used to study its expression mode under abiotic stress. The results showed that there were 58 AP gene family members in foxtail millet genome. Phylogenetic tree analysis demonstrated that the gene family could be divided into 5 subfamilies, among which Group B encoded atypical AP, while other subfamilies encoded nucellin-like AP. The analysis of gene structure and conserved motifs revealed that members of the same subfamily of APs in foxtail millet were highly conserved. Collinearity analysis showed that there were a large number of homologous gene pairs between SiAPs and rice（Oryza sativa）and maize（Zea mays）AP genes. The study of promoter cis-acting elements indicated that most members of SiAPs contained cis-acting elements related to abiotic stress and biohormone response, such as cis-acting elements in response to drought and low-temperature stress, and salicylic acid response elements. Further quantitative PCR results uncovered that SiAPs were differentially expressed in the root, stem, leaf and panicle of foxtail millet. The expressions of SiAP3, SiAP9 and SiAP48 genes significantly increased under low temperature stress. Under drought stress and SA treatments, the change trend of some gene expression was basically the same. SiAPs play an important role in regulating foxtail millet response to abiotic stress. The results of this study may provide reference for stress resistance analysis of SiAPs.

Key words: foxtail millet（Setaria itlica）, aspartate protease, salicylic acid response, drought response, low-temperature stress, bioinformatics

邢媛, 宋健, 李俊怡, 郑婷婷, 刘思辰, 乔治军. 谷子AP基因家族鉴定及其对非生物胁迫的响应分析[J]. 生物技术通报, 2023, 39(11): 238-251.

XING Yuan, SONG Jian, LI Jun-yi, ZHENG Ting-ting, LIU Si-chen, QIAO Zhi-jun. Identification of AP Gene Family and Its Response Analysis to Abiotic Stress in Setaria italica[J]. Biotechnology Bulletin, 2023, 39(11): 238-251.

图/表 12

表1 引物序列表

Table 1 Sequences of primers

基因名称Gene name	序列Sequence（5'-3'）
25S-F	AGGCAACAGAAACTCCATACG
25S-R	ATGGCATAGCATTCATCACG
SiAP2-F	AACATACCCACCTCGGTCTTC
SiAP2-R	CGCCTTGTACTTCTTCATCCC
SiAP3-F	GATACCTGCTACGACTTCACCG
SiAP3-R	GCCGACATCATAGAGCACCTC
SiAP4-F	ATGTCAGAGGGCGGCTACG
SiAP4-R	TGGTGAGGCAGTACGAGAAGG
SiAP9-F	TCCAGTCCACGCCGCTTATC
SiAP9-R	CGAAGATGATGCCGCCACTC
SiAP32-F	GGTGGTGGGCGGCAACTC
SiAP32-R	CCAGCAGGCGGTTCTCCATC
SiAP36-F	GCTGTCGTCGGCGTTCAAG
SiAP36-R	GTCGGTATCGTGATGCTTCTCTG
SiAP48-F	CATCAGCCAGAGGTGCCAGAG
SiAP48-R	CGTGTTGGTGTAGTCGTCGTATTG

图1 SiAPs基因家族成员基因结构和其编码蛋白的保守基序分析 A：谷子AP基因家族成员聚类分析；B：谷子AP基因家族成员的保守结构域；C：谷子AP基因家族成员基因结构；D：谷子AP基因家族保守基序的序列Logo

Fig. 1 Gene structure and conservative motif analysis of members of SiAPs in Setaria italic A: Cluster analysis of AP gene family members in foxtail millet（Seitaria italic）. B: Conservative domain of AP gene family members in foxtail millet. C: Gene structure map of SiAPs members in foxtail millet. D: Logo of conserved motif of SiAPs in foxtail millet

图2 谷子（Si）、水稻（Os）、拟南芥（At）AP基因家族系统进化树

Fig. 2 Unrooted phylogenetic tree of AP gene family in Seitaria italic（Si）, Oryza sativa（Os）and Arabi-dopsis thaliana（At）

图3 AP基因家族成员在谷子染色体上的分布 1-9 代表谷子第1-9染色体；染色体内部以基因密度填充，颜色由蓝到红代表基因密度由小到大

Fig. 3 Distribution of AP gene family members on chromosomes in S. italic 1-9 represents chromosome 1-9 in S. italic, respectively. The interior of the chromosome is filled with gene density, with colors ranging from blue to red indicating a gradual increase in gene density

图4 谷子种内AP基因家族共线性分析 1-9代表谷子1-9号染色体；热图代表基因密度，由蓝到红基因密度越来越大

Fig. 4 Collinearity analysis of AP gene family in S. italic 1-9 represents chromosome 1-9 of S. itlica. The heat map represents gene density, with increasing gene density from blue to red

图5 谷子与拟南芥、水稻和玉米AP基因家族成员的共线性分析 A：谷子与玉米 AP 基因共线性分析；B：谷子与水稻 AP 基因共线性分析；C：谷子与拟南芥 AP 基因共线性分析

Fig. 5 Collinearity analysis of SiAPs gene family members and AP genes in A. thaliana, O. sativa and Z. mays A: The synteny analysis of AP genes in S. italica and Z. mays; B: the synteny analysis of AP genes in S. italica and O. sativa; C: the synteny analysis of AP genes in S. italica and A. thaliana

图6 谷子AP基因家族启动子顺式作用元件统计

Fig. 6 Statistics of cis-acting elements of AP gene family in S. italic

图7 谷子AP基因家族启动子顺式作用元件分析

Fig. 7 Cis-acting elements analysis in the promotors of AP gene family in S. italica

图8 谷子AP家族基因在不同组织部位中的表达分析

Fig. 8 Expression analysis of AP gene family members in the different tissues of S. italica

图9 谷子AP家族基因在0.25 mmol/L水杨酸诱导下的表达分析误差线为标准误，图中不同字母表示差异显著（P < 0.05），下同

Fig. 9 Expression analysis of AP gene family members in S. italica induced by 0.25 mmol/L salicylic acid Error bars are standard errors. The different letters in the figure indicate significant differences（P < 0.05）. The same below

图10 谷子AP家族基因响应干旱胁迫的表达分析

Fig. 10 Expression analysis of AP gene family members in response to drought stress

图11 谷子AP家族基因响应低温胁迫的表达分析

Fig. 11 Expression analysis of AP gene family members in response to low temperature stress

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谷子AP基因家族鉴定及其对非生物胁迫的响应分析

Identification of AP Gene Family and Its Response Analysis to Abiotic Stress in Setaria italica

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