基于种子发育转录组的豌豆bZIP基因家族分析及种子发育候选基因的鉴定

doi:10.3724/SP.J.1006.2025.44123

Abstract

Abstract:

The bZIP gene is widely involved in physiological processes such as seed development, light signal regulation, and stress response. However, little is known about the regulation of seed development by pea PastbZIP gene. In order to identify the PastbZIP gene family related to pea seed development and reveal its evolutionary relationship, this study used bioinformatics methods and seed development transcriptome data to identify and analyze the PastbZIP gene family, and mined the candidate PastbZIP genes related to seed development through comparative genomics, at the same time, it was verified by protein interaction network and qRT-PCR. A total of 62 PastbZIP genes were identified from the transcriptome data of pea seed development, and PastbZIP genes were divided into 9 groups according to phylogenetic characteristics, Different subfamilies showed evolutionary diversity and differences in protein physicochemical properties, gene structure, conserved motifs, etc. Collinearity analysis showed that pea had 54, 23, 8, and 22 pairs of collinearity gene with soybean, Medicago truncatula, Arabidopsis and faba bean, respectively. More important, it was found that the fragment replication was the main driving force for the expansion of the PastbZIP gene family, and the evolution of these genes was achieved through purification selection. KEGG enrichment analysis showed that PastbZIP was mainly enriched in plant hormone signal transduction pathways. The same is that the cis-acting elements of the PastbZIP promoter contain a large number of hormone response elements, and 60 PastbZIP (96.8%) genes contained five hormone response elements. Ten candidate genes related to seed development were found in pea by homologous comparison, and protein interaction genes also regulated seed development. In conclusion, this study was the first to identify and analyze the members of the PastbZIP family related to seed development in pea, and excavated the candidate genes related to seed development through homologous alignment. These results will provide important reference for the study of PastbZIP gene regulation of seed development.

Key words: pea, PastbZIP, gene family, seed development, evolutionary analysis, protein interaction network

ZHOU En-Qiang, MIAO Ya-Mei, ZHOU Yao, YAO Meng-Nan, ZHAO Na, WANG Yong-Qiang, ZHU Yu-Xiang, XUE Dong, LI Zong-Di, SHI Yu-Xin, LI Bo, WANG Kai-Hua, GU Chun-Yan, WANG Xue-Jun, WEI Li-Bin. Analysis of bZIP gene family and identification of seed development candidate genes in pea based on seed development transcriptome[J].Acta Agronomica Sinica, 2025, 51(4): 914-931.

Figures/Tables 14

Table 1

Table 2

Information of bZIP family members in pea"

基因 Gene	bZIP名称 bZIP name	氨基酸长度 Amino acid length (aa)	相对分子量 Molecular weight (Da)	等电点 Isoelectric point	不稳定指数 Instability index	脂肪系数 Aliphatic index	亲疏水性 Grand average of hydropathicity
Psat6g192360.1	PsatbZIP1	227	25,102.05	5.22	37.05	66.12	-0.68
Psat6g192360.2	PsatbZIP2	246	27,463.83	5.50	45.81	69.72	-0.70
Psat6g192360.3	PsatbZIP3	246	27,248.60	5.32	41.50	71.71	-0.54
Psat6g192360.4	PsatbZIP4	224	24,654.51	5.03	38.59	67.01	-0.64
Psat5g042560.3	PsatbZIP5	326	34,559.98	9.32	36.04	73.59	-0.42
Psat5g042560.4	PsatbZIP6	378	40,577.77	6.87	40.73	71.75	-0.47
Psat7g122760.1	PsatbZIP7	403	44,435.37	9.68	51.96	77.59	-0.56
Psat7g122760.2	PsatbZIP8	403	44,435.37	9.68	51.96	77.59	-0.56
Psat3g033680.1	PsatbZIP9	422	46,093.33	8.24	61.59	63.55	-0.73
Psat4g141680.1	PsatbZIP10	325	36,171.72	6.88	53.62	67.85	-0.77
Psat4g141680.2	PsatbZIP11	325	36,171.72	6.88	53.62	67.85	-0.77
Psat1g087440.1	PsatbZIP12	320	36,160.67	7.91	53.79	70.03	-0.82
Psat1g087440.2	PsatbZIP13	316	35,770.23	7.91	54.34	70.00	-0.84
Psat1g087440.3	PsatbZIP14	320	36,160.67	7.91	53.79	70.03	-0.82
Psat1g087440.4	PsatbZIP15	316	35,770.23	7.91	54.34	70.00	-0.84
Psat3g083400.1	PsatbZIP16	326	36,292.51	6.91	52.21	63.47	-0.85
Psat3g083400.2	PsatbZIP17	281	30,930.51	7.18	46.51	65.98	-0.71
Psat0s2281g0240.2	PsatbZIP18	270	29,959.73	8.65	50.86	79.07	-0.67
Psat0s2281g0240.3	PsatbZIP19	248	27,402.87	9.00	42.79	82.14	-0.62
Psat5g225680.1	PsatbZIP20	324	36,114.68	6.62	52.36	71.30	-0.74
Psat5g257120.1	PsatbZIP21	322	36,421.87	8.76	62.27	70.53	-0.86
Psat5g257120.2	PsatbZIP22	297	33,475.32	5.77	63.92	69.56	-0.84
Psat5g257120.3	PsatbZIP23	305	34,524.56	5.46	60.96	70.92	-0.75
Psat6g006040.1	PsatbZIP24	342	37,238.98	5.14	42.49	68.36	-0.58
Psat6g006040.2	PsatbZIP25	275	30,254.58	5.85	47.73	70.15	-0.63
Psat3g007160.1	PsatbZIP26	371	40,638.86	6.57	55.38	62.13	-0.85
Psat3g007160.2	PsatbZIP27	268	29,590.67	7.69	56.35	67.76	-0.89
Psat6g144640.1	PsatbZIP28	422	45,401.27	5.59	60.53	65.85	-0.65
Psat3g079000.1	PsatbZIP29	455	50,296.26	6.69	56.63	70.48	-0.65
Psat3g079000.2	PsatbZIP30	438	48,682.51	7.09	58.00	68.74	-0.69
Psat3g079000.3	PsatbZIP31	438	48,682.51	7.09	58.00	68.74	-0.69
Psat3g079000.4	PsatbZIP32	455	50,296.26	6.69	56.63	70.48	-0.65
Psat5g257080.1	PsatbZIP33	483	54,318.93	6.29	52.82	67.47	-0.64
Psat5g135880.1	PsatbZIP34	357	40,077.79	7.09	46.11	87.45	-0.31
Psat2g076800.4	PsatbZIP35	318	36,387.11	5.12	61.05	89.56	-0.51
Psat4g145320.1	PsatbZIP36	466	51,591.52	5.99	56.20	74.81	-0.56
Psat4g145320.2	PsatbZIP37	466	51,591.52	5.99	56.20	74.81	-0.56
Psat4g145320.3	PsatbZIP38	503	56,110.78	6.29	52.34	75.69	-0.50
Psat6g229520.1	PsatbZIP39	428	47,858.61	6.11	50.76	84.60	-0.44
Psat6g121080.1	PsatbZIP40	451	50,390.06	6.98	63.60	78.38	-0.53
Psat7g166600.1	PsatbZIP41	326	37,331.21	5.54	63.83	61.35	-1.04
Psat0s1431g0080.5	PsatbZIP42	333	35,244.92	8.91	59.93	46.07	-0.84
Psat0s1431g0080.6	PsatbZIP43	333	35,244.92	8.91	59.93	46.07	-0.84
Psat4g091720.6	PsatbZIP44	238	25,483.68	5.74	64.89	46.05	-1.17
Psat4g158440.1	PsatbZIP45	463	50,338.88	6.08	50.80	62.63	-0.82
Psat4g178600.1	PsatbZIP46	656	72,876.78	5.18	38.10	78.52	-0.46
Psat5g115640.1	PsatbZIP47	312	34,010.34	6.56	42.06	55.35	-1.05
Psat3g145920.1	PsatbZIP48	161	18,535.46	8.76	57.28	50.81	-1.35
Psat2g051040.1	PsatbZIP49	370	40,257.45	6.31	58.07	59.70	-0.82
Psat5g148760.1	PsatbZIP50	383	41,879.97	6.15	49.13	53.86	-0.89
Psat7g181680.1	PsatbZIP51	531	59,049.13	6.89	65.93	57.91	-1.01
Psat7g181680.2	PsatbZIP52	531	59,049.13	6.89	65.93	57.91	-1.01
Psat7g181680.3	PsatbZIP53	474	52,589.17	7.32	63.37	59.30	-0.88
Psat7g181680.4	PsatbZIP54	474	52,589.17	7.32	63.37	59.30	-0.88
Psat0s3019g0160.2	PsatbZIP55	254	28,439.06	6.33	49.05	70.71	-0.65
Psat5g289760.1	PsatbZIP56	455	49,629.29	6.06	57.55	54.35	-0.96
Psat5g005640.1	PsatbZIP57	156	17,899.07	6.12	49.51	74.36	-0.68
Psat6g009600.1	PsatbZIP58	162	18,982.69	8.37	53.05	66.85	-0.77
Psat7g140160.1	PsatbZIP59	159	17,638.69	8.03	56.57	71.70	-0.60
Psat1g064080.1	PsatbZIP60	186	22,013.34	6.13	62.22	70.22	-1.04
Psat0s2991g0040.1	PsatbZIP61	140	15,986.20	6.86	56.55	87.21	-0.72
Psat3g034880.1	PsatbZIP62	483	54,474.93	8.97	73.68	63.85	-0.92

Table 2

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6

Fig. 7

Table 3

Fig. 8

Table 4

Table 5

Fig. 9

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基因名称 Gene name	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
PsatbZIP9	AGCAGGTGTGGTTAGGGAAC	CCAATAGCGAAAGGAGCAG
PsatbZIP21/22/23	CCGAAACGAGACACTCAAG	AAACAACACCGCCACTATG
PsatbZIP47	ACATCAGGTCCTTTGGGTC	AACCAGTGCCTTTACGAGAG
PsatbZIP59	GAAACAGAAGCACTTGGATG	TCATAACCCCAACAATCTC
PsatbZIP61	CGAACAGGTTACAAAGCGAG	CCATAATCCGTTGAATCGG
PsatACTIN	CACAATTGGCGCTGAAAGAT	TAATTGAGTTAAATGTCGTCTCATGGAT

基因对 Gene pairs		非同义替换K_a	同义替换K_s	K_a/K_s	分离时间 Diversification time (Mya)	复制类型 Duplication type
PsatbZIP49	PsatbZIP50	0.201	0.922	0.218	30.73	片段复制Segmental
PsatbZIP35	PsatbZIP34	0.261	0.750	0.348	25.00	片段复制Segmental
PsatbZIP9	PsatbZIP21	0.458	1.356	0.338	45.20	片段复制Segmental
PsatbZIP26	PsatbZIP28	0.279	0.757	0.368	25.23	片段复制Segmental
PsatbZIP33	Psat7g188240.1	0.206	0.872	0.236	29.07	片段复制Segmental
Psat5g275000.1	PsatbZIP41	0.199	0.982	0.202	32.73	片段复制Segmental

豌豆 Pea	大豆 Soybean	苜蓿 Medicago truncatula	拟南芥 Arabidopsis	蚕豆 Faba bean
PsatbZIP2	KRH35126	Medtr1g098590.1	—	Vf3g103200.1
PsatbZIP9	KRH32738, KRG96191	Medtr7g104480.1	AT2G36270.3	Vf5g119200.1
PsatbZIP10	—	Medtr8g043960.1	—	—
PsatbZIP12	KRG94991, KRH57716	Medtr7g088090.1	—	—
PsatbZIP16	KRG94991, KRH64894	Medtr7g088090.1	—	—
PsatbZIP20	KRH62689, KRH56273	—	—	Vf2g005920.1
PsatbZIP21	KRH22688, KRG96191	Medtr2g086340.1	—	Vf1g043440.1
PsatbZIP24	—	—	AT1G75390.1	—
PsatbZIP26	KRH34085, KRG96973, KRH68733	Medtr1g080920.1 Medtr7g115120.1	—	Vf5g145520.1
PsatbZIP29	KRG95102, KRH66771	Medtr7g089800.3	—	Vf5g083400.3
PsatbZIP33	KRH30432, KRH26635, KRH25227	Medtr4g053250.2	—	Vf1g043400.2 Vf6g014200.1
PsatbZIP34	KRH18833, KRH16629, KRH64780, KRH53140	Medtr3g073560.1	AT1G77920.1	Vf1g163320.2 Vf2g068160.2
PsatbZIP38	KRH20680, KRH13334	Medtr8g040120.1	—	Vf4g029640.1
PsatbZIP39	KRH75411, KRH35977, KRG90784	Medtr1g111310.1	AT1G68640.1	Vf3g134600.1
PsatbZIP41	KRH25692, KRH27013 KRH22317, KRH55826	Medtr4g079500.1	—	Vf1g031360.1 Vf6g063160.1
PsatbZIP45	—	—	AT2G46270.1	—
PsatbZIP48	—	Medtr7g057160.1	—	Vf5g025920.1
PsatbZIP49	KRH17183, KRG98137, KRH72827	Medtr5g075390.1	—	Vf1g185400.1 Vf2g051160.1
PsatbZIP50	KRH17183, KRG98137, KRH72827	Medtr3g467120.1 Medtr5g075390.1	—	Vf2g051160.1
PsatbZIP51	KRH29330, KRH24356	—	AT4G38900.1	—
PsatbZIP56	KRH29611, KRH24606, KRH10117	Medtr2g099050.1	—	Vf1g018400.1
PsatbZIP57	KRH24436, KRH60802, KRH51497	Medtr3g117120.1	AT4G34590.1	Vf2g175760.1
PsatbZIP58	KRH15149, KRH05862	Medtr1g022495.1	AT1G75390.1	Vf3g189120.1
PsatbZIP59	KRH29414, KRH24436	—	—	—
PsatbZIP60	KRH18312, KRH01443 KRG93749, KRH45160	Medtr6g016375.1	—	Vf1g010720.1
PsatbZIP62	—	Medtr7g104190.1	—	—

候选基因 Candidate gene	功能 Function	拟南芥同源基因 Arabidopsis homologous gene	参考文献 Reference
PsatbZIP9	调控种子成熟和大小Regulating seed maturity and size	AT2G36270 (ABI5)	[38-39]
PsatbZIP21	调节种子脂肪酸组成Regulating fatty acid composition of seeds	AT3G44460 (DPBF2)	[40]
PsatbZIP22
PsatbZIP23
PsatbZIP47	调控淀粉合成Regulating starch synthesis	AT5G11260 (HY5)	[41]
PsatbZIP48	调控淀粉合成Regulating starch synthesis	AT5G11260 (HY5)	[41]
PsatbZIP57	调节糖分含量变化Regulating the change of sugar content	AT4G34590 (bZIP11)	[42]
PsatbZIP58
PsatbZIP59
PsatbZIP61	调控种子成熟Regulating seed maturation	AT3G62420 (bZIP53)	[43]

Analysis of bZIP gene family and identification of seed development candidate genes in pea based on seed development transcriptome

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