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作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (4): 914-931.doi: 10.3724/SP.J.1006.2025.44123

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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

周恩强(), 缪亚梅, 周瑶, 姚梦楠, 赵娜, 王永强, 朱宇翔, 薛冬, 李宗迪, 石宇欣, 李波, 汪凯华, 顾春燕, 王学军(), 魏利斌()   

  1. 江苏沿江地区农业科学研究所, 江苏南通 226012
  • 收稿日期:2024-07-29 接受日期:2024-12-12 出版日期:2025-04-12 网络出版日期:2024-12-18
  • 通讯作者: 魏利斌, E-mail: libinwei2013@aliyun.com; 王学军, E-mail: wangxj4002@sina.com
  • 作者简介:E-mail: zhouenqiang0526@163.com
  • 基金资助:
    财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-08-Z10);江苏省农业科技自主创新项目[CX(22)2011]和江苏省“双创人才”项目(YSSCRC2022469)

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

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()   

  1. Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226012, Jiangsu, China
  • Received:2024-07-29 Accepted:2024-12-12 Published:2025-04-12 Published online:2024-12-18
  • Contact: E-mail: libinwei2013@aliyun.com; E-mail: wangxj4002@sina.com
  • Supported by:
    China Agriculture Research System of MOF and MARA(CARS-08-Z10);Independent Innovation Project of Agricultural Science and Technology in Jiangsu Province [CX (22) 2011], and the Jiangsu Province “Double Talents” Project(YSSCRC2022469)

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摘要：

bZIP基因广泛参与种子发育、光信号调节和胁迫响应等生理过程。然而, 目前对豌豆PastbZIP基因调控种子发育知之甚少。为鉴定豌豆种子发育相关PastbZIP基因, 揭示其进化关系, 本研究利用生物信息学和种子发育转录组数据对PastbZIP基因家族进行鉴定与进化分析, 并通过比较基因组学挖掘种子发育相关PastbZIP基因, 同时利用蛋白互作网络和qRT-PCR对其验证。在豌豆种子发育转录组数据中共鉴定出62个PastbZIP基因, 根据系统进化特征将PastbZIP基因分为9组, 不同亚家族在蛋白理化性质、基因结构、保守基序等方面表现出进化多样性和差异性。共线性分析发现, 豌豆与大豆、苜蓿、拟南芥和蚕豆分别有54、23、8和22对共线性基因, 并且发现片段复制是PastbZIP基因家族扩张的主要驱动力, 而且这些基因的进化是通过纯化选择来实现的。KEGG富集分析显示, PastbZIP主要富集在植物激素信号转导通路中, 且PastbZIP启动子顺式作用元件中包含大量的激素响应元件, 有60个(96.8%) PastbZIP基因包含5种激素响应元件。通过同源比对在豌豆中发现10个与种子发育相关的候选基因, 且其蛋白互作基因均参与调控种子发育。综上所述, 本研究首次对豌豆种子发育相关PastbZIP家族成员进行了鉴定和进化分析, 并通过同源比对挖掘了种子发育候选基因, 研究结果将为研究豌豆bZIP基因调控种子发育提供重要参考。

关键词: 豌豆, PastbZIP, 基因家族, 种子发育, 进化分析, 蛋白互作网络

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

表1

qRT-PCR引物及其序列"

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

表2

豌豆bZIP家族成员信息"

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

图1

差异PastbZIP基因表达趋势分析 PastbZIP基因在18个profile中的表达趋势; 左上角数字代表profile的数值, 左下角数字代表P值大小, 颜色标注代表是显著趋势集合, 没有颜色代表不是显著趋势集合。"

图2

PastbZIP基因KEGG富集及表达模式分析"

图3

拟南芥和豌豆PastbZIP基因家族系统进化分析"

图4

PastbZIP基因家族成员染色体定位"

图5

PastbZIP家族成员结构域、基序及结构分析 (a): 系统进化树; (b): 保守结构域; (c): 保守基序(Motif); (d): 基因结构, CDS: 编码序列, UTR: 非翻译区, 线条表示内含子。"

图6

PastbZIP启动子顺式作用元件预测"

图7

PastbZIP基因家族物种内共线性分析"

表3

基因对分离时间的估算"

基因对
Gene pairs		 非同义替换Ka 同义替换Ks Ka/Ks 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

图8

bZIP基因家族种间共线性分析"

表4

bZIP基因家族豌豆与其他作物之间共线性基因"

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 — —

表5

豌豆种子发育相关的候选基因"

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
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]

图9

豌豆种子发育候选基因的蛋白互作网络预测及qRT-PCR验证"

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