Identification and Expression Analysis of the NHX Gene Family under Salt Stress in Rye

doi:10.7668/hbnxb.20195534

Abstract

Abstract:

Plant sodium-hydrogen antiporter(NHX,Na⁺/H⁺ antiporter)plays a crucial role in plant sodium and potassium ion balance and cellular pH regulation.In order to investigate the relationship between salt tolerance and ScNHXs,it was conducted to identify and analyze the ScNHXs by bioinformatics process,and to examine the expression pattern of ScNHXs under salt stress by RT-qPCR,which can provide the reference information for the investigation of the potential functions of ScNHXs as well as the mining of salt tolerance genes in rye.A total of 10 rye NHX gene family members(ScNHX1—ScNHX10)were identified,and the phylogenetic tree analysis showed that they could be divided into two subfamilies,Vac and Endo,containing four and six genes,respectively.Physicochemical property analysis of the encoded proteins showed that most of the molecular weight ranged from 27.92 to 59.72 ku,the number of amino acids from 253 to 546 aa,and the isoelectric point between 5.17 and 8.81,with most of proteins being classified as acidic proteins.Signal peptide prediction indicated the absence of signal peptides in the members,and transmembrane structure analysis revealed that all members possessed transmembrane structures.The subcellular localization prediction indicated that ScNHXs were located in the plasma membrane and vesicles.Spatial structure prediction showed that their secondary structures mainly consisted of α-helices and irregular convolutions.Gene structure and motif analyses revealed that the number of exons of the ScNHXs varied from 13 to 24,and all of them possessed a conserved Na⁺/H⁺ exchange structural domain.In addition,cis-acting element analysis revealed that numerous elements related to hormone response and abiotic stresses were found in the promoter region of ScNHXs.Analysis of rye transcriptome data revealed significant differences in the expression patterns of ScNHXs in different tissues of rye.RT-qPCR analysis showed that ScNHXs responded differently to different concentrations of NaCl stress,and were able to persistently respond to salt stress over a long period of time.In summary,ScNHXs may be involved in the biological regulation during salt stress in rye.

Key words: Rye, NHX gene family, Bioinformatics, Salt stress, Gene expression

CLC Number:

WANG Zhaoyi, CUI Yuanyuan, HAN Mengqiao, LIU Zhengwen, DENG Xi, DOU Feifei, REN Yuzhao, LIU Caixia, LIU Fenglou, WANG Zhangjun, SUN Yangyang, REN Min, LI Qingfeng. Identification and Expression Analysis of the NHX Gene Family under Salt Stress in Rye[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(3): 9-18. doi: 10.7668/hbnxb.20195534.

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Figures/Tables 12

References 48

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引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')	退火温度/℃ Annealing temperature
NHX1-F	GAGGAGAACCGCTGGCTC	59.8
NHX1-R	TCGCTGAAGACGAGCACG	60.1
NHX2-F	TTGTGAGCCATCCAGCCC	59.6
NHX2-R	TGACCGTGTTGGACTCGC	60.0
NHX3-F	CGTGGTGTCCATCTGCGT	60.0
NHX3-R	TGATGAGCGCGGTGATGG	60.2
NHX4-F	TGGTCATACTGCCGTGCG	60.1
NHX4-R	TTGAGATGTCGGCTGCGG	60.1
NHX5-F	TCGCTGGAGCTGAGCATG	59.8
NHX5-R	CTGCAGCAGGATCCCCAC	60.1
NHX6-F	TGGTGCTCTCCTTCGTGC	60.0
NHX6-R	CCGATGAGGAGGGATGCG	60.0
NHX7-F	GTTCGTGCTCAGCCACCT	60.0
NHX7-R	GCCCTCCCACGATCAACC	60.1
NHX8-F	TCAGAGGACTCCCAGCGT	59.6
NHX8-R	AGCCGATGTGTGACCAGC	60.0
NHX9-F	CCGCGCTGGACAGAAACT	60.4
NHX9-R	TCCACGTCTTGCAGCTCG	60.0
NHX10-F	ATCGCGGCCAGAACATCG	60.6
NHX10-R	AAGCGCAAAAGCCATGGC	60.0

引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')	退火温度/℃ Annealing temperature
NHX1-F	GAGGAGAACCGCTGGCTC	59.8
NHX1-R	TCGCTGAAGACGAGCACG	60.1
NHX2-F	TTGTGAGCCATCCAGCCC	59.6
NHX2-R	TGACCGTGTTGGACTCGC	60.0
NHX3-F	CGTGGTGTCCATCTGCGT	60.0
NHX3-R	TGATGAGCGCGGTGATGG	60.2
NHX4-F	TGGTCATACTGCCGTGCG	60.1
NHX4-R	TTGAGATGTCGGCTGCGG	60.1
NHX5-F	TCGCTGGAGCTGAGCATG	59.8
NHX5-R	CTGCAGCAGGATCCCCAC	60.1
NHX6-F	TGGTGCTCTCCTTCGTGC	60.0
NHX6-R	CCGATGAGGAGGGATGCG	60.0
NHX7-F	GTTCGTGCTCAGCCACCT	60.0
NHX7-R	GCCCTCCCACGATCAACC	60.1
NHX8-F	TCAGAGGACTCCCAGCGT	59.6
NHX8-R	AGCCGATGTGTGACCAGC	60.0
NHX9-F	CCGCGCTGGACAGAAACT	60.4
NHX9-R	TCCACGTCTTGCAGCTCG	60.0
NHX10-F	ATCGCGGCCAGAACATCG	60.6
NHX10-R	AAGCGCAAAAGCCATGGC	60.0

基因名称 Gene name	ID号 Gene identifier	氨基酸数/ aa Amino acids	分子质量/ku Molecular weight	等电点 pI	不稳定系数 Instability index	亲水性平均系数 Grand average of hydropathicity	亚细胞定位 Subcellular localization
ScNHX1	ScWN2R01G102600.1	538	59.03	8.41	34.13	0.612	质膜、液泡
ScNHX2	ScWN4R01G176300.1	541	59.49	8.81	34.85	0.573	质膜、液泡
ScNHX3	ScWN4R01G271700.1	527	58.03	8.41	33.55	0.603	质膜、液泡
ScNHX4	ScWN4R01G477800.1	546	59.72	8.13	31.26	0.679	质膜、液泡、高尔基体
ScNHX5	ScWN5R01G182900.1	534	58.35	5.13	47.85	0.477	质膜
ScNHX6	ScWN5R01G285100.1	533	59.02	5.20	43.63	0.389	质膜
ScNHX7	ScWN6R01G382600.1	527	58.15	5.59	45.89	0.446	质膜、液泡
ScNHX8	ScWN6R01G493000.1	344	37.93	5.17	46.36	0.099	质膜、液泡、内质网
ScNHX9	ScWNUn01G004700.1	533	58.73	5.29	47.70	0.377	质膜、液泡
ScNHX10	ScWNUn01G024600.1	253	27.92	5.36	40.77	0.109	质膜、液泡

基因名称 Gene name	ID号 Gene identifier	氨基酸数/ aa Amino acids	分子质量/ku Molecular weight	等电点 pI	不稳定系数 Instability index	亲水性平均系数 Grand average of hydropathicity	亚细胞定位 Subcellular localization
ScNHX1	ScWN2R01G102600.1	538	59.03	8.41	34.13	0.612	质膜、液泡
ScNHX2	ScWN4R01G176300.1	541	59.49	8.81	34.85	0.573	质膜、液泡
ScNHX3	ScWN4R01G271700.1	527	58.03	8.41	33.55	0.603	质膜、液泡
ScNHX4	ScWN4R01G477800.1	546	59.72	8.13	31.26	0.679	质膜、液泡、高尔基体
ScNHX5	ScWN5R01G182900.1	534	58.35	5.13	47.85	0.477	质膜
ScNHX6	ScWN5R01G285100.1	533	59.02	5.20	43.63	0.389	质膜
ScNHX7	ScWN6R01G382600.1	527	58.15	5.59	45.89	0.446	质膜、液泡
ScNHX8	ScWN6R01G493000.1	344	37.93	5.17	46.36	0.099	质膜、液泡、内质网
ScNHX9	ScWNUn01G004700.1	533	58.73	5.29	47.70	0.377	质膜、液泡
ScNHX10	ScWNUn01G024600.1	253	27.92	5.36	40.77	0.109	质膜、液泡

蛋白 Protein	α-螺旋 Alpha helix	β-转角 Beta turn	无规则卷曲 Random coil	延伸链 Extended strand
ScNHX1	45.54	2.97	33.27	18.22
ScNHX2	40.30	5.18	33.46	21.07
ScNHX3	44.78	4.17	30.36	20.68
ScNHX4	44.51	4.03	33.52	17.95
ScNHX5	46.44	3.93	32.96	16.67
ScNHX6	47.84	2.63	34.52	15.01
ScNHX7	49.34	2.09	33.21	15.37
ScNHX8	45.64	2.03	39.83	12.50
ScNHX9	53.73	3.19	30.39	13.70
ScNHX10	41.50	3.56	39.53	15.42

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