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

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

Abstract

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

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.

Figures/Tables 11

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

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

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

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

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

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

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

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

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

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

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

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