甘薯IbNRT2基因家族全基因组鉴定和表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-1277

生物技术通报 ›› 2025, Vol. 41 ›› Issue (7): 193-204.doi: 10.13560/j.cnki.biotech.bull.1985.2024-1277

甘薯IbNRT2基因家族全基因组鉴定和表达分析

王芳¹^,²(), 乔帅¹^,², 宋伟¹^,², 崔鹏娟³, 廖安忠¹^,², 谭文芳¹^,²(), 杨松涛¹^,²()

^1.四川省农业科学院作物研究所（四川省种质资源中心），成都 610066
^2.粮油作物绿色种质创新与遗传改良四川省重点实验室，成都 610066
^3.河南省种业发展中心，郑州 450000

收稿日期:2024-12-30 出版日期:2025-07-26 发布日期:2025-07-22
通讯作者: 谭文芳，女，研究员，研究方向：甘薯遗传育种；E-mail: zwstwf414@163.com
杨松涛，男，博士，研究方向：甘薯遗传育种；E-mail: yost60@126.com
作者简介:王芳，女，博士，助理研究员，研究方向：作物养分高效生理基础及分子机制；E-mail: wangfangsaas@126.com
基金资助:
四川省青年基金(2024NSFSC1329);国家甘薯现代农业产业技术体系(CARS-10);宜宾市对外科技合作项目(2024NYHZZ002);四川省育种攻关(2021YFYZ0019);四川省育种攻关(2021YFYZ0020);优质高效薯豆关键技术研究与应用(51000024Y000010717763)

Genome-wide Identification of the IbNRT2 Gene Family and Its Expression in Sweet Potato

WANG Fang¹^,²(), QIAO Shuai¹^,², SONG Wei¹^,², CUI Peng-juan³, LIAO An-zhong¹^,², TAN Wen-fang¹^,²(), YANG Song-tao¹^,²()

^1.Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066
^2.Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066
^3.Henan Seed Industry Development Center, Zhengzhou 450000

Received:2024-12-30 Published:2025-07-26 Online:2025-07-22

摘要/Abstract

摘要：

目的鉴定甘薯高亲和硝酸盐转运体NRT2家族成员，分析其理化性质、基因结构和不同胁迫下表达分析，为甘薯NRT2家族成员功能鉴定提供理论支持。方法利用NCBI和甘薯基因组数据库，采用生物信息学、转录组分析和低氮表型筛选等方法，系统鉴定IbNRT2基因成员，并对其基因结构、保守基序和表达特性等进行分析。结果在甘薯全基因组中鉴定到7个IbNRT2高亲和硝酸盐转运体基因。理化性质分析结果显示，IbNRT2家族成员编码氨基酸残基数为462-536，理论等电点均大于7，且所有编码蛋白为疏水蛋白。7个甘薯IbNRT2和9个近缘野生二倍体甘薯（Ipomoea trifida）ItfNRT2基因均分布在5条染色体上。系统进化树分析显示，7个IbNRT2家族成员分成3个亚组，甘薯与野生二倍体的亲缘关系最近。顺式作用元件分析表明，IbNRT2基因启动子区域存在大量环境及激素类响应元件，其中光信号响应元件最多。甘薯种内共线性关系显示，7个IbNRT2基因存在2对共线性关系；种间共线性关系结果显示，甘薯与野生二倍体ItfNRT2基因之间形成7对共线性关系，与拟南芥AtNRT2形成4对共线性关系。不同部位组织和盐胁迫表达分析结果揭示IbNRT2.7具有较为广泛的表达，在种子和叶片中表达最高且受盐胁迫诱导表达上调；IbNRT2.1、IbNRT2.2主要在根部表达且受盐胁迫诱导表达下调。在不同氮处理甘薯品种中进行RT-qPCR分析，结果揭示IbNRT2.1和IbNRT2.2受低硝酸盐诱导最明显，且在氮高效甘薯品种中（川薯221、川薯228、西成薯007）的诱导表达倍数高于氮低效甘薯品种（普薯32、绵紫薯9）。结论甘薯中鉴定出7个IbNRT2基因，在不同部位、盐胁迫和低氮胁迫下的表达模式存在差异，为进一步研究IbNRT2在不同部位的功能奠定基础。

关键词: 甘薯, NRT2基因, 组织表达模式, 盐胁迫表达模式, 低氮表型

Abstract:

Objective To identify the high-affinity nitrate transporter NRT2 family members of sweet potato (Ipomoea batatas (L.) Lam.), and to analyze the physicochemical properties, structure and expression analysis under different stresses, thus providing theoretical support for the functional identification of NRT2 family members in sweet potato. Method The IbNRT2 gene members were systematically identified by bioinformatics, transcriptome analysis and low-nitrogen phenotype screening using NCBI and sweet potato genome databases, and the gene structure, conserved motifs and expression characteristics were analyzed. Result Seven IbNRT2 genes were identified in the whole genome of sweet potato. The results of physicochemical property analysis showed that the residual number of amino acids encoded by the members of the IbNRT2 family was 462-536, the theoretical isoelectric points were greater than 7, and all the encoded proteins were hydrophobic proteins. Seven IbNRT2 and nine closely related wild diploid (Ipomoea trifida) ItfNRT2 genes were distributed on 5 chromosomes. Phylogenetic tree analysis showed that the seven IbNRT2 family members were divided into three subgroups, and sweet potato was the most closely related to the wild diploid. The cis-actingelement analysis showed that there were numerous environmental and hormone response elements in the promoter region of IbNRT2 gene, among which the light response element was the most. The intraspecific collinearity relationship of sweet potato showed that there were two pairs of collinearity between the seven IbNRT2 genes. The results of interspecific collinearity showed that 7 pairs of collinearity were formed between sweet potato and wild diploid ItfNRT2 genes, and 4 pairs of collinearity were formed with ArabidopsisAtNRT2s. The results of tissue and salt stress expression analysis showed that IbNRT2.7 was widely expressed, with the highest expression in the seeds and leaves, and the expression was up-regulated by salt stress. IbNRT2.1 and IbNRT2.2 were mainly expressed in the roots and down-regulated by salt stress. RT-qPCR analysis of different nitrogen-treated sweet potato varieties showed that IbNRT2.1 and IbNRT2.2 were most significantly induced by low nitrate, and the induced expression folds of IbNRT2.1 and IbNRT2.2 were more pronounced in nitrogen-efficient sweet potato varieties (Chuanshu 221, Chuanshu 228, Xichengshu 007) than in nitrogen-inefficient sweet potato varieties (Pushu 32, Mianzi 9). Conclusion Seven IbNRT2 genes are identified in sweet potato, and the expression patterns of IbNRT2 vary in different parts, salt stress and low nitrogen stress, which lays a foundation for further study of the function of IbNRT2 in different parts.

Key words: sweet potato, NRT2 gene, tissue-expression pattern, expression pattern under salt stress, phenotype at low nitrogen

王芳, 乔帅, 宋伟, 崔鹏娟, 廖安忠, 谭文芳, 杨松涛. 甘薯IbNRT2基因家族全基因组鉴定和表达分析[J]. 生物技术通报, 2025, 41(7): 193-204.

WANG Fang, QIAO Shuai, SONG Wei, CUI Peng-juan, LIAO An-zhong, TAN Wen-fang, YANG Song-tao. Genome-wide Identification of the IbNRT2 Gene Family and Its Expression in Sweet Potato[J]. Biotechnology Bulletin, 2025, 41(7): 193-204.

图/表 11

表1 RT-qPCR引物序列

Table 1 Primer sequences for RT-qPCR

Gene	Forward sequences （5´-3´）	Reverse sequences （5´-3´）
IbNRT2.1	TCATGTTAACTGCCCCCACC	AAGAGACGAAAGTGGCGAGG
IbNRT2.2	GGGATGGCTTCATGTGGTGA	GTGACCGCGTACCAAAACAC
IbNRT2.3	GGGTTCCCAAACTATTCCC	AAGGTGGAGATGAAGCAGG
IbNRT2.4	TGGCTGGGATGGAAGATTC	TCTGAGTCAACGGGCAATG
IbNRT2.5	GCGGCTAGTTTTGGATTGGC	CACAGGCAGCTTGAACGAAC
IbNRT2.6	GCCTTCCTCAACCTCCTCAC	GTCCAGAAGGAGCAGGACAC
IbNRT2.7	AATCTCCCAACCCAAGCAGG	CAGAACATTCCGCCCCATCT
IbACTIN	GTATTGTGCTGGATTCTGGTGAT	TCAGCAGTAGTGGTGAACATGT

表2 甘薯IbNRT2硝酸盐转运蛋白基本理化性质分析

Table 2 Analysis on the physical and chemical properties of nitrate transporter IbNRT2 in sweet potato

Gene ID	Gene name	Chr	AA Number	Mw	pI	GRAVY	Predicted location
IB12G06570	IbNRT2.1	12	525	56 854.18	9.19	0.387	Cell membrane
IB12G06560	IbNRT2.2	12	524	56 885.85	8.94	0.393	Cell membrane
IB02G04080	IbNRT2.3	2	536	58 419.54	8.90	0.382	Cell membrane
IB06G26510	IbNRT2.4	6	462	50 169.9	7.89	0.64	Cell membrane
IB10G16710	IbNRT2.5	10	502	54 245.02	9.17	0.423	Cell membrane
IB12G06540	IbNRT2.6	12	334	36 679.66	9.41	0.25	Cell membrane
IB07G31450	IbNRT2.7	7	459	50 338.97	8.90	0.053	Cell membrane

图1 甘薯（A）和近缘野生二倍体（B）硝酸盐转运体NRT2在染色体上的分布

Fig. 1 Distribution of nitrate transporter NRT2 on chromosome in sweet potato (A) and closely related wild diploid (B)

图2 甘薯IbNRT2家族成员保守基序、保守结构域和基因结构

Fig. 2 Conserved motif, domain and gene structure of IbNRT2 in sweet potato

图 3 甘薯（Ib），近缘野生二倍体（Itf），拟南芥（At）和水稻（Os）NRT2家族成员系统进化树

Fig. 3 Phylogenetic tree analysis of NRT2 family member in sweet potato (Ib), closely related wild diploid (Itf), Arabidopsis (At), and Oryza sativa (Os)

图4 甘薯 IbNRT2基因启动子顺式作用元件分布（A）和数量统计（B）

Fig. 4 Distribution (A) and numeric statistics (B) of cis-acting elements of IbNRT2 gene promoter in sweet potato

图5 甘薯IbNRT2基因家族种内（A）和种间（B）共线性分析

Fig. 5 Intraspecies (A) and interspecies collinearity (B) analysis of IbNRT2 gene family in sweet potato

图6 IbNRT2家族成员不同组织表达分析A：转录组分析不同组织表达热图，数值代表FPKM值； B-F：RT-qPCR分析不同组织中IbNRT2s的表达，#代表对照， ** P<0.01

Fig. 6 Expression analysis of IbNRT2 family members in different tissuesA: Heat maps of different tissue expression via transcriptome analysis, the value indicates the FPKM value; B-F: RT-qPCR analying the relative expressions of IbNRT2s in different tissues, # indicates control, ** P<0.01

图7 IbNRT2家族成员盐胁迫诱导表达分析A：地上部分盐胁迫诱导表达；B：根部盐胁迫诱导表达；NaCl处理浓度为100 mmol/L

Fig. 7 Expression analysis of IbNRT2 family members under salt stressA: Expression induced by salt stress in the shoot. B: Expression induced by salt stress in the root. The concentration of NaCl in the treatment is 100 mmol/L

图8 不同甘薯材料低氮表型筛选（A）、生物量统计分析（B-D）和生理指标检测（E-G）HN： 5 mmol/L NO3-； LN： 0.1 mmol/L NO3-. Bar： 5 cm， *， P<0.05， ** P<0.01

Fig. 8 Low nitrogen phenotype screening of different sweet potato materials (A), biomass statistical analysis (B-D) and physiological index detection (E-G)

图9 不同甘薯材料IbNRT2家族成员表达量检测热图

Fig. 9 Detection heat map of IbNRT2 family members in different sweet potato varieties

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甘薯IbNRT2基因家族全基因组鉴定和表达分析

Genome-wide Identification of the IbNRT2 Gene Family and Its Expression in Sweet Potato

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