Genome-wide Identification and Expression Analysis of the ZIP Gene Family in Soybean

doi:10.13560/j.cnki.biotech.bull.1985.2025-0318

Abstract

Abstract:

Objective Identifying and analyzing the expressions of GmZIP family members under aluminum stress in soybean lays the foundation for elucidating the biological function of GmZIP family. Method The members of GmZIP gene family were identified by bioinformatics method, which was used to establish the phylogenetic tree, predict protein network map and analyze the collinearity relationships, gene structure, and promoter cis-acting elements. Based on transcriptome sequencing, the expression patterns of GmZIP gene family in different tissues and under aluminum (Al) stress were analyzed. Result A total of 26 GmZIP were identified in the whole soybean genome, which were unevenly distributed on 14 chromosomes and divided into Ⅰ-Ⅴ subfamilies by phylogenetic analysis. The gene structure of GmZIP members were relatively conservative. All of GmZIP members contained ZIP conserved domain, multiple exons, and significantly different introns. Transcriptome analysis of different soybean tissues showed that most of GmZIP members had high expressions in the soybean root and nodule tissues. Three members of GmZIP (GmZIP6, GmZIP12, and GmZIP25) were up-regulated in Al-tolerant soybean germplasm Nannong 99-6, two members (GmZIP20 and GmZIP25) were up-regulated while one was down-regulated (GmZIP23) in Al-sensitive soybean germplasm soybean Zhongdou 32. The protein prediction results show that 16 of 26 GmZIP have interaction relationships, among which GmZIP23 and GmZIP25 were differentially expressed under Al toxicity stress. Based on fluorescence quantitative PCR detection, the expression of GmZIP25 in Al-resistant germplasm reached the highest at 72 h under aluminum stress treatment, while that in Al-sensitive germplasm reached the highest at 12 h. Conclusion These results suggest that GmZIP25 may play an important role in response to aluminum stress of soybean.

Key words: soybean, GmZIP gene family, bioinformatics, aluminum stress

HUANG Guo-dong, DENG Yu-xing, CHENG Hong-wei, DAN Yan-nan, ZHOU Hui-wen, WU Lan-hua. Genome-wide Identification and Expression Analysis of the ZIP Gene Family in Soybean[J]. Biotechnology Bulletin, 2025, 41(9): 71-81.

Figures/Tables 10

References 40

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基因 Gene	上游引物 Forward primer （5'-3'）	下游引物 Reverse primer （5'-3'）	片段大小 Size （bp）
GmZIP6	GCGTGTTGTGTCCTTCTTTTAC	CTTAACAATGGGAGGCTCACC	167
GmZIP12	AGGAGGAATCAGGGGATGTG	GAAGCTCCCATAGAAATTCC	178
GmZIP20	TCCTTTTACCAACCATGGCCT	TCAACAATGGGAGGCTCACC	150
GmZIP23	TGACCAACCGCGTGATGCTG	GTGATGATGATCAGAGCTAG	127
GmZIP25	GAAGTGTAGGACTACTAGTG	GTCTCATGATGAGCATGGTG	126
Glyma.18G290800（Actin）	GCACCACCGGAGAGAAAATA	GTGCACAATTGATGGACCAG	123

基因 Gene	上游引物 Forward primer （5'-3'）	下游引物 Reverse primer （5'-3'）	片段大小 Size （bp）
GmZIP6	GCGTGTTGTGTCCTTCTTTTAC	CTTAACAATGGGAGGCTCACC	167
GmZIP12	AGGAGGAATCAGGGGATGTG	GAAGCTCCCATAGAAATTCC	178
GmZIP20	TCCTTTTACCAACCATGGCCT	TCAACAATGGGAGGCTCACC	150
GmZIP23	TGACCAACCGCGTGATGCTG	GTGATGATGATCAGAGCTAG	127
GmZIP25	GAAGTGTAGGACTACTAGTG	GTCTCATGATGAGCATGGTG	126
Glyma.18G290800（Actin）	GCACCACCGGAGAGAAAATA	GTGCACAATTGATGGACCAG	123

基因 Gene	基因ID Gene ID	氨基酸数量 Amino acid	相对分子质量 Mw（Da）	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index	亲水性 Hydropathicity	亚细胞定位 Subcellular location
GmZIP1	Glyma.02G126000	360	38 468.30	7.62	26.61	104.06	0.551	细胞膜
GmZIP2	Glyma.05G137400	485	51 989.60	6.00	31.08	95.96	-0.033	细胞膜
GmZIP3	Glyma.06G052000	478	51 484.51	6.57	52.00	94.14	0.340	细胞膜
GmZIP4	Glyma.07G223200	356	38 455.58	8.61	33.40	108.54	0.569	细胞膜
GmZIP5	Glyma.08G092700	485	52 353.64	5.79	35.60	92.95	-0.139	细胞膜
GmZIP6	Glyma.08G164400	361	38 404.85	6.38	40.99	102.16	0.446	细胞膜
GmZIP7	Glyma.08G328000	349	37 559.76	6.06	32.77	107.65	0.668	细胞膜
GmZIP8	Glyma.09G271900	598	62 182.12	7.19	30.11	112.26	0.777	细胞膜
GmZIP9	Glyma.11G132500	272	28 959.34	9.10	47.79	114.38	0.693	细胞膜
GmZIP10	Glyma.11G169300	326	34 776.07	5.81	29.45	113.96	0.769	液泡膜
GmZIP11	Glyma.12G056900	256	27 593.55	9.19	45.62	114.26	0.586	细胞膜
GmZIP12	Glyma.13G004400	347	37 633.21	7.72	37.42	110.55	0.455	细胞膜
GmZIP13	Glyma.13G338300	350	37 989.51	8.43	30.78	105.63	0.549	细胞膜
GmZIP14	Glyma.13G340900	276	29 153.48	8.78	38.44	118.04	0.740	细胞膜
GmZIP15	Glyma.14G094902	135	14 389.27	6.50	43.26	120.00	1.076	液泡膜
GmZIP16	Glyma.14G196200	324	33 863.86	6.35	34.60	114.51	0.773	细胞膜
GmZIP17	Glyma.15G033500	276	29 241.54	7.95	37.60	117.68	0.717	细胞膜
GmZIP18	Glyma.15G036200	345	37 385.49	6.82	32.57	101.22	0.462	细胞膜
GmZIP19	Glyma.15G036300	342	36 681.97	8.18	31.29	106.08	0.617	细胞膜
GmZIP20	Glyma.15G262800	359	38 243.55	6.14	39.12	104.09	0.486	细胞膜
GmZIP21	Glyma.17G228600	393	43 130.94	5.73	40.52	98.52	0.475	细胞膜
GmZIP22	Glyma.18G060300	328	35 036.37	5.96	29.37	112.07	0.742	细胞膜
GmZIP23	Glyma.18G078600	360	38 721.95	6.08	35.02	108.97	0.577	细胞膜
GmZIP24	Glyma.18G217100	598	62 115.03	6.93	29.44	112.59	0.781	细胞膜
GmZIP25	Glyma.20G022500	358	38 705.73	6.86	34.80	105.20	0.548	细胞膜
GmZIP26	Glyma.20G063100	354	38 301.74	6.30	28.63	105.56	0.399	细胞膜

基因 Gene	基因ID Gene ID	氨基酸数量 Amino acid	相对分子质量 Mw（Da）	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index	亲水性 Hydropathicity	亚细胞定位 Subcellular location
GmZIP1	Glyma.02G126000	360	38 468.30	7.62	26.61	104.06	0.551	细胞膜
GmZIP2	Glyma.05G137400	485	51 989.60	6.00	31.08	95.96	-0.033	细胞膜
GmZIP3	Glyma.06G052000	478	51 484.51	6.57	52.00	94.14	0.340	细胞膜
GmZIP4	Glyma.07G223200	356	38 455.58	8.61	33.40	108.54	0.569	细胞膜
GmZIP5	Glyma.08G092700	485	52 353.64	5.79	35.60	92.95	-0.139	细胞膜
GmZIP6	Glyma.08G164400	361	38 404.85	6.38	40.99	102.16	0.446	细胞膜
GmZIP7	Glyma.08G328000	349	37 559.76	6.06	32.77	107.65	0.668	细胞膜
GmZIP8	Glyma.09G271900	598	62 182.12	7.19	30.11	112.26	0.777	细胞膜
GmZIP9	Glyma.11G132500	272	28 959.34	9.10	47.79	114.38	0.693	细胞膜
GmZIP10	Glyma.11G169300	326	34 776.07	5.81	29.45	113.96	0.769	液泡膜
GmZIP11	Glyma.12G056900	256	27 593.55	9.19	45.62	114.26	0.586	细胞膜
GmZIP12	Glyma.13G004400	347	37 633.21	7.72	37.42	110.55	0.455	细胞膜
GmZIP13	Glyma.13G338300	350	37 989.51	8.43	30.78	105.63	0.549	细胞膜
GmZIP14	Glyma.13G340900	276	29 153.48	8.78	38.44	118.04	0.740	细胞膜
GmZIP15	Glyma.14G094902	135	14 389.27	6.50	43.26	120.00	1.076	液泡膜
GmZIP16	Glyma.14G196200	324	33 863.86	6.35	34.60	114.51	0.773	细胞膜
GmZIP17	Glyma.15G033500	276	29 241.54	7.95	37.60	117.68	0.717	细胞膜
GmZIP18	Glyma.15G036200	345	37 385.49	6.82	32.57	101.22	0.462	细胞膜
GmZIP19	Glyma.15G036300	342	36 681.97	8.18	31.29	106.08	0.617	细胞膜
GmZIP20	Glyma.15G262800	359	38 243.55	6.14	39.12	104.09	0.486	细胞膜
GmZIP21	Glyma.17G228600	393	43 130.94	5.73	40.52	98.52	0.475	细胞膜
GmZIP22	Glyma.18G060300	328	35 036.37	5.96	29.37	112.07	0.742	细胞膜
GmZIP23	Glyma.18G078600	360	38 721.95	6.08	35.02	108.97	0.577	细胞膜
GmZIP24	Glyma.18G217100	598	62 115.03	6.93	29.44	112.59	0.781	细胞膜
GmZIP25	Glyma.20G022500	358	38 705.73	6.86	34.80	105.20	0.548	细胞膜
GmZIP26	Glyma.20G063100	354	38 301.74	6.30	28.63	105.56	0.399	细胞膜

Gene	TT_T_vs_TCK_T_Log₂FC	TT_T_vs_TCK_T_regulated	ST_T_vs_SCK_T_Log₂FC	ST_T_vs_SCK_T_regulated
GmZIP6	1.24	Up	0.39	False
GmZIP12	1.82	Up	-0.10	False
GmZIP20	0.898	False	1.14	Up
GmZIP23	-0.73	False	-1.01	Down
GmZIP25	4.25	Up	2.72	Up