豆科作物AOX基因鉴定及其在普通菜豆响应非生物胁迫中的表达模式研究

doi:10.3724/SP.J.1006.2025.44170

Abstract

Abstract:

Alternative oxidase (AOX), a key terminal oxidase in the mitochondrial electron transport chain, plays a pivotal role in plant response to various abiotic stresses. Leguminous crops are not only important sources of plant-based protein but also contribute significantly to sustainable agricultural development. However, their yield and quality have been increasingly compromised by frequent extreme climatic events, highlighting the urgent need to enhance their stress tolerance. In this study, we systematically identified and analyzed the AOX gene family in four leguminous crops: soybean, common bean, tepary bean, and mung bean. Our analysis included assessments of protein structure, physicochemical properties, promoter cis-acting elements, and the expression patterns of AOX genes in common bean under different abiotic stress treatments. We identified four, three, three, and three AOX genes in soybean, common bean, tepary bean, and mung bean, respectively. Phylogenetic analysis grouped these genes into three distinct subfamilies. Cis-element analysis of promoter regions revealed an abundance of hormone-responsive and stress-responsive elements. Expression profiling in common bean demonstrated that AOX genes exhibit differential responses to various abiotic stresses, with distinct temporal expression patterns. Notably, PvAOX1A;2 was strongly upregulated under multiple stress conditions. PvAOX2;2_2 showed high induction under salt and heat stress, while PvAOX2;2_1 was significantly upregulated in response to cold stress. Collectively, these results suggest that AOX genes play important roles in the abiotic stress responses in common bean. This study provides valuable insights into the functional characteristics of AOX genes in leguminous crops and identifies potential candidate genes for the molecular improvement of stress tolerance in common bean.

Key words: common bean, AOX, leguminous crops, abiotic stress, expression pattern

YAN Zhi-Lan, ZHAO Qin, CHANG Tian-Da, WANG Yi-Ming, WANG Bi-Hui, WANG Peng, HUANG Chun-Guo, ZHANG Hui, WANG Li-Xiang, HAO Xiao-Peng, ZHAO Bo. Genome-wide identification and characterization of Alternative oxidase (AOX) genes in leguminous crops and their expression patterns in response to abiotic stresses in common bean[J].Acta Agronomica Sinica, 2025, 51(7): 1769-1783.

Figures/Tables 14

Table S1

Table 1

Table 2

Basic properties of AOX family proteins in the target species"

物种名称 Species name	基因名称 Gene ID	蛋白质长度 Protein length (aa)	相对分子质量 Molecular weight (Da)	等电点 pI	亲水性 GRAVY	不稳定性指数 Instability index	α-螺旋 Alpha helix (%)	延伸链 Extended strand (%)	β-折叠 Beta turn (%)	无规则卷曲 Random coil (%)	亚细胞定位 Subcellular localization
拟南芥Arabidopsis thaliana	AtAOX1D;1	318	36,202.41	8.65	−0.29	36.39	49.06	8.49	7.86	34.59	线粒体Mitochondrion
	AtAOX1B;3	325	37,432.24	8.55	−0.35	42.26	46.46	12.62	6.15	34.77	线粒体Mitochondrion
	AtAOX1A;3	354	39,979.87	8.56	−0.33	35.04	51.41	13.28	4.24	31.07	线粒体Mitochondrion
	AtAOX1C;3	329	37,816.51	6.91	−0.33	47.15	47.42	13.68	6.99	31.91	线粒体Mitochondrion
	AtAOX2;5	353	40,086.65	9.14	−0.17	29.53	43.20	15.41	5.44	35.95	线粒体Mitochondrion
大豆 Glycine max	GmAOX1A;4	321	36,476.17	8.57	−0.24	39.23	48.29	13.08	6.54	32.09	线粒体Mitochondrion
	GmAOX2;5	317	36,007.69	9.01	−0.18	35.81	55.84	9.15	7.26	27.76	线粒体Mitochondrion
	GmAOX2;8_1	326	37,115.48	8.68	−0.32	37.20	49.08	13.19	7.36	30.37	线粒体Mitochondrion
	GmAOX2;8_2	333	38,142.27	9.36	−0.27	38.75	51.95	11.41	8.41	28.23	线粒体Mitochondrion
普通菜豆 Phaseolus vulgaris	PvAOX1A;2	319	36,338.91	8.26	−0.30	40.34	55.17	9.09	5.02	30.72	线粒体Mitochondrion
	PvAOX2;2_2	329	37,772.83	9.04	−0.26	41.88	56.84	10.64	6.99	25.53	线粒体Mitochondrion
	PvAOX2;2_1	332	37,817.18	7.88	−0.38	36.44	53.61	9.94	4.82	31.63	线粒体Mitochondrion
绿豆 Vigna radiata	VrAOX2;9_1	332	37,952.48	8.67	−0.34	40.98	50.30	9.34	3.01	37.35	线粒体Mitochondrion
	VrAOX2;9_2	369	42,303.71	6.72	−0.27	41.53	46.07	13.55	6.50	33.88	线粒体Mitochondrion
	VrAOX1A;11	321	36,426.04	8.26	−0.28	37.00	47.35	10.59	5.61	36.45	线粒体Mitochondrion
宽叶菜豆Phaseolus acutifolius	PaAOX1A;2	319	36,369.90	8.22	−0.30	42.00	52.98	9.09	4.39	33.54	线粒体Mitochondrion
	PaAOX2;2_2	329	37,789.92	9.13	−0.23	41.09	48.02	11.55	6.99	33.43	线粒体Mitochondrion
	PaAOX2;2_1	332	37,802.21	8.36	−0.36	34.45	57.83	9.34	5.12	27.71	线粒体Mitochondrion

Table 2

Fig. 1

Fig. 2

Fig. S1

Fig. 3

Table S2

Table S3

Fig. 4

Table S4

Fig. 5

Fig. 6

Fig. 7

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物种名称 Species name	基因名称 Gene ID	登录号 Accession no.
拟南芥Arabidopsis thaliana	AtAOX1D;1	AT1G32350
	AtAOX1B;3	AT3G22360
	AtAOX1A;3	AT3G22370
	AtAOX1C;3	AT3G27620
	AtAOX2;5	AT5G64210
大豆Glycine max	GmAOX1A;4	GLYMA_04G123800
	GmAOX2;5	GLYMA_05G117200
	GmAOX2;8_1	GLYMA_08G072200
	GmAOX2;8_2	GLYMA_08G072300
普通菜豆Phaseolus vulgaris	PvAOX1A;2	PHAVU_002G127100g
	PvAOX2;2_2	PHAVU_002G209100g
	PvAOX2;2_1	PHAVU_002G209200g
绿豆Vigna radiata	VrAOX2;9_1	Vradi09g03140
	VrAOX2;9_2	Vradi09g03150
	VrAOX1A;11	Vradi11g08000
宽叶菜豆Phaseolus acutifolius	PaAOX1A;2	Phacu.CVR.002G149400
	PaAOX2;2_2	Phacu.CVR.002G238600
	PaAOX2;2_1	Phacu.CVR.002G238900
玉米Zea mays	ZmAOX4;2_1	Zm00001eb071880
	ZmAOX4;2_2	Zm00001eb071870
	ZmAOX5;2	Zm00001eb071890
	ZmAOX5;5	Zm00001eb251680
谷子Setaria italica	SiAOX4;VII_1	SETIT_010566mg
	SiAOX4;VII_2	SETIT_010539mg
	SiAOX5;VII_1	SETIT_010540mg
	SiAOX5;I	SETIT_017726mg
小麦Triticum aestivum	TaAOX3;3B	TraesCS3B02G087900
	TaAOX4;2B_1	TraesCS2B02G459000
	TaAOX4;2A_1	TraesCS2A02G438300
	TaAOX4;2A_2	TraesCS2A02G439100
	TaAOX4;2D_1	TraesCS2D02G436100
	TaAOX4;2B_2	TraesCS2B02G459100
	TaAOX4;2D_2	TraesCS2D02G43620
	TaAOX4;2A_3	TraesCS2A02G438200
	TaAOX5;2D	TraesCS2D02G436700
	TaAOX5;2B	TraesCS2B02G459300
	TaAOX5;2A	TraesCS2A02G439400
	TaAOX5;6D	TraesCS6D02G245800
	TaAOX5;6B	TraesCS6B02G296400
	TaAOX5;6A	TraesCS6A02G269100
高粱Sorghum bicolor	SbAOX4;6_1	SORBI_3006G202600
	SbAOX4;6_2	SORBI_3006G203000
	SbAOX5;6	SORBI_3006G202500
	SbAOX5;4	SORBI_3004G270500
水稻Oryza sativa	OsAOX3;2	Os02g0318100
	OsAOX4;4	Os04g0600300
	OsAOX5;4	Os04g0600200
	OSAOX5;2	Os02g0700400

基因名称Gene name	正向引物Forward primer (5'-3')	反向引物Reverse primer(5'-3')
PvAOX1A;2	TGACGTTCATGGAAGTGGCA	CCCTTAAAGTGGCGTCTGGT
PvAOX2;2_2	AGAGTGTGGTGGAGTCCAGT	ACATCCCTCCTACCATGCCA
PvAOX2;2_1	CACCTCCCAACAGCGAAGAT	ACAGTTCCATGGCCACTCAG
PvActin	GAAGTTCTCTTCCAACCATCC	TTTCCTTGCTCATTCTGTCCG

物种 Species	基因 ID Gene ID	转录本长度 Transcript length (bp)	染色体 Chr.	基因组位置 Genomic location	5'UTR数 Number of 5'UTR	3'UTR数 Number of 3'UTR	外显子数 Number of exon	内含子数 Number of intron
拟南芥 Arabidopsis thaliana	AtAOX1D;1	1429	1	11,666,886-11,668,690	1	1	4	3
	AtAOX1B;3	1229	3	7,904,097-7,905,576	1	1	4	3
	AtAOX1A;3	1764	3	7,906,521-7,908,746	1	1	4	3
	AtAOX1C;3	1346	3	10,229,045-10,230,707	1	1	4	3
	AtAOX2;5	1324	5	25,683,770-25,685,731	1	1	5	4
大豆 Glycine max	GmAOX1A;4	2448	4	16,009,828-16,014,505	1	1	4	3
	GmAOX2;5	954	5	31,012,789-31,015,519	0	0	5	3
	GmAOX2;8_1	1487	8	5,530,937-5,533,495	1	1	4	3
	GmAOX2;8_2	1527	8	5,534,625-5,537,952	1	1	4	3
普通菜豆 Phaseolus vulgaris	PvAOX1A;2	1353	2	25,631,296-25,635,132	1	1	4	3
	PvAOX2;2_2	1496	2	36,912,163-36,915,354	1	1	4	3
	PvAOX2;2_1	1263	2	36,916,649-36,918,323	1	1	4	3
绿豆 Vigna radiata	VrAOX2;9_1	1513	9	3,689,595-3,691,839	1	1	4	3
	VrAOX2;9_2	1133	9	3,719,512-3,724,510	1	0	6	5
	VrAOX1A;11	1282	11	8,412,330-8,414,861	1	1	4	3
宽叶菜豆Phaseolus acutifolius	PaAOX1A;2	1601	2	21,877,429-21,879,874	1	1	3	2
	PaAOX2;2_2	1024	2	32,731,956-32,734,686	0	1	4	3
	PaAOX2;2_1	1671	2	32,745,753-32,747,820	1	1	4	3

miRNA序号 miRNA accession	靶基因 ID Target accession	E值 Expectation	抑制作用 Inhibition	miRNA起始 miRNA start	miRNA终止 miRNA end	基因起始 Target start	基因终止 Target end
ath-miR863-3p	AtAOX1C;3	3.5	裂解Cleavage	1	21	1119	1139
ath-miR5021	AtAOX1C;3	2.5	裂解Cleavage	1	20	6	25
ath-miR414	GmAOX1A;4	2.5	裂解Cleavage	1	21	260	280
gra-miR8787	GmAOX1A;4	2.5	裂解Cleavage	1	23	2370	2392
osa-miR414	GmAOX1A;4	2.5	裂解Cleavage	1	21	260	280
mtr-miR2619b-5p	GmAOX1A;4	3.0	裂解Cleavage	1	21	2386	2406
aly-miR838-3p	PaAOX1A;2	2.5	裂解Cleavage	1	21	1493	1513
ptc-miR7814	PaAOX1A;2	2.5	裂解Cleavage	1	21	1244	1264
ata-miR1432-3p	PaAOX1A;2	3.0	裂解Cleavage	1	21	264	284
ath-miR414	PaAOX1A;2	3.0	裂解Cleavage	1	21	248	268
osa-miR414	PaAOX1A;2	3.0	裂解Cleavage	1	21	248	268
ppt-miR414	PaAOX1A;2	3.0	裂解Cleavage	1	21	248	268
ppt-miR1211-5p	PaAOX2;2_2	2.5	裂解Cleavage	1	21	1911	1931
gma-miR4392	PaAOX2;2_2	3.0	裂解Cleavage	1	22	715	736
sbi-miR6218-3p	PaAOX2;2_2	3.0	裂解Cleavage	1	21	2061	2081
ptc-miR6462c-5p	PaAOX2;2_1	3.0	裂解Cleavage	1	22	1513	1534
aly-miR838-3p	PvAOX1A;2	2.5	裂解Cleavage	1	21	657	677
ath-miR414	PvAOX1A;2	3.0	裂解Cleavage	1	21	119	139
osa-miR414	PvAOX1A;2	3.0	裂解Cleavage	1	21	119	139
-miR414	PvAOX1A;2	3.0	裂解Cleavage	1	21	119	139
aly-miR838-3p	VrAOX1A;11	3.0	裂解Cleavage	1	21	646	666
ath-miR1886.3	VrAOX1A;11	3.0	裂解Cleavage	1	21	1168	1188
sbi-miR5385	VrAOX1A;11	3.0	翻译Translation	1	22	172	193

Genome-wide identification and characterization of Alternative oxidase (AOX) genes in leguminous crops and their expression patterns in response to abiotic stresses in common bean

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物种1 AOX AOXs in species1	染色体编号 Chr.	物种2 AOX AOXs in species2	染色体编号 Chr.	非同义替换率K_a	同义替换率 K_s	非同义替换/同义替换 K_a/K_s
AtAOX1D;1	1	AtAOX1B;3	3	0.29	2.04	0.14
AtAOX1D;1	1	AtAOX1C;3	3	0.29	1.64	0.18
AtAOX1B;3	3	AtAOX1A;3	3	0.13	1.04	0.13
AtAOX1B;3	3	AtAOX1C;3	3	0.09	0.57	0.15
AtAOX1B;3	3	AtAOX2;5	5	0.27	1.66	0.16
AtAOX1A;3	3	AtAOX1C;3	3	0.15	1.30	0.11
AtAOX1A;3	3	AtAOX2;5	5	0.32	2.67	0.12
AtAOX1C;3	3	AtAOX2;5	5	0.29	1.47	0.20
VrAOX2;9_1	9	VrAOX2;9_2	9	0.22	2.23	0.10
VrAOX2;9_1	9	PaAOX2;2_1	11	0.29	3.26	0.09
PaAOX2;2_1	11	AtAOX1D;1	1	0.26	3.53	0.07
VrAOX2;9_1	9	GmAOX2;5	5	0.22	1.53	0.14
VrAOX2;9_1	9	GmAOX2;8_1	8	0.04	0.50	0.08
PaAOX2;2_1	11	GmAOX1A;4	4	0.06	0.43	0.14
GmAOX1A;4	4	GmAOX2;8_1	8	0.31	3.26	0.10
GmAOX2;5	5	GmAOX2;8_1	8	0.24	1.54	0.15
GmAOX2;5	5	GmAOX2;8_2	8	0.04	0.18	0.19
GmAOX2;8_1	8	GmAOX2;8_2	8	0.23	1.39	0.16
GmAOX2;5	5	AtAOX2;5	5	0.27	2.42	0.11
GmAOX1A;4	4	PvAOX1A;2	2	0.05	0.37	0.13
GmAOX2;5	5	PvAOX2;2_2	2	0.06	0.29	0.20
GmAOX2;8_1	8	PvAOX2;2_2	2	0.20	1.47	0.14
PvAOX2;2_2	2	AtAOX2;5	5	0.25	3.41	0.07
PvAOX1A;2	2	PvAOX2;2_1	2	0.30	2.69	0.11
PvAOX1A;2	2	PaAOX2;2_1.1	11	0.09	0.57	0.15
PvAOX2;2_2	2	PvAOX2;2_1	2	0.23	1.53	0.15
PvAOX2;2_2	2	VrAOX2;9_1	9	0.22	1.59	0.14
PaAOX2;2_2	2	PaAOX2;2_1	2	0.23	1.55	0.15
PaAOX2;2_2	2	AtAOX2;5	5	0.24	2.80	0.09
PaAOX1A;2	2	GmAOX1A;4	4	0.04	0.36	0.12
PaAOX2;2_2	2	GmAOX2;5	5	0.05	0.29	0.18
PaAOX2;2_2	2	GmAOX2;8_1	8	0.20	1.58	0.13
PaAOX2;2_2	2	PvAOX2;2_2	2	0.01	0.03	0.45
PaAOX1A;2	2	PvAOX1A;2	2	0.01	0.08	0.13
PaAOX1A;2	2	PaAOX2;2_1	11	0.04	0.23	0.19
PaAOX2;2_2	2	VrAOX2;9_1	9	0.21	1.72	0.12

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