植物学报 ›› 2024, Vol. 59 ›› Issue (2): 231-244.DOI: 10.11983/CBB23065 cstr: 32102.14.CBB23065
段政勇1, 丁敏1, 王宇卓1, 丁艺冰2, 陈凌3, 王瑞云1,3,*(), 乔治军3,*()
收稿日期:
2023-05-21
接受日期:
2023-12-25
出版日期:
2024-03-10
发布日期:
2024-03-10
通讯作者:
* 王瑞云, 山西农业大学农学院教授, 博士生导师, 山西省杂粮产业技术体系岗位专家, 中国作物学会粟类作物专业委员会委员。长期从事糜子种质资源遗传多样性研究。以通讯作者和第一作者身份发表学术论文80篇(其中SCI收录期刊8篇, 国家一级学术期刊11篇); 独著1部, 参编合著论著2部。E-mail: 基金资助:
Zhengyong Duan1, Min Ding1, Yuzhuo Wang1, Yibing Ding2, Ling Chen3, Ruiyun Wang1,3,*(), Zhijun Qiao3,*()
Received:
2023-05-21
Accepted:
2023-12-25
Online:
2024-03-10
Published:
2024-03-10
Contact:
* E-mail: 摘要: SBP (squamosa promoter binding protein)家族广泛参与植物生长发育、信号转导及多种生理生化过程。从糜子(Panicum miliaceum)全基因组中筛选并鉴定到25个SBP基因。系统发育分析表明, PmSBP家族成员分为6个亚家族。同一亚家族成员具有相似的基因结构和保守基序。共线性分析表明, PmSBP与拟南芥(Arabidopsis thaliana) AtSBP和水稻(Oryza sativa) OsSBP分别形成7对和31对直系同源基因。顺式作用元件分析表明, PmSBP启动子区富含逆境胁迫、光反应及激素信号响应元件。基因表达模式分析表明, PmSBP基因表达具有明显的组织特异性、品种特异性及发育阶段特异性, 表明SBP基因在糜子生长发育中发挥重要作用。研究结果为揭示SBP基因在糜子生长发育中的生物学功能奠定了基础, 也为其它作物SBP基因研究提供了借鉴参考。
段政勇, 丁敏, 王宇卓, 丁艺冰, 陈凌, 王瑞云, 乔治军. 糜子SBP基因家族全基因组鉴定及表达分析. 植物学报, 2024, 59(2): 231-244.
Zhengyong Duan, Min Ding, Yuzhuo Wang, Yibing Ding, Ling Chen, Ruiyun Wang, Zhijun Qiao. Genome-wide Identification and Expression Analysis of SBP Genes in Panicum miliaceum. Chinese Bulletin of Botany, 2024, 59(2): 231-244.
Gene name | Forward primer (5′-3′) | Reverse primer (5′-3′) |
---|---|---|
PM13G22100 | CTCATATGGCAGCCAGGGTA | CAGGCATTGACGCAGCAC |
PM10G18000 | AGTTCGACGAGGCCAAGAG | TGGTGTAGGAGCCCGTCAT |
PM07G33040 | GCTTCCCTTTCCTGACCAAT | ACAGTTGCCGTTGCTATGCT |
PM03G01570 | GGTCACAATGAGCGTCGG | CCAGGCTCTTGAAATGATGC |
Actin | CGAAGCCCCTCTTAACCC | GTATGGCTGACACCATCACC |
表1 qRT-PCR引物序列
Table 1 Primer sequences for qRT-PCR
Gene name | Forward primer (5′-3′) | Reverse primer (5′-3′) |
---|---|---|
PM13G22100 | CTCATATGGCAGCCAGGGTA | CAGGCATTGACGCAGCAC |
PM10G18000 | AGTTCGACGAGGCCAAGAG | TGGTGTAGGAGCCCGTCAT |
PM07G33040 | GCTTCCCTTTCCTGACCAAT | ACAGTTGCCGTTGCTATGCT |
PM03G01570 | GGTCACAATGAGCGTCGG | CCAGGCTCTTGAAATGATGC |
Actin | CGAAGCCCCTCTTAACCC | GTATGGCTGACACCATCACC |
Gene name | Gene ID | Number of amino acids | Molecular weight (Da) | Theoretical pI | Instability index | Aliphatic index | Grand average of hydropathicity | Subcellular localization |
---|---|---|---|---|---|---|---|---|
PmSBP1 | PM13G22100 | 389 | 40425.64 | 9.02 | 59.42 | 53.57 | -0.554 | Nucleus |
PmSBP2 | PM15G18460 | 391 | 40589.82 | 9.03 | 59.36 | 51.79 | -0.586 | Nucleus |
PmSBP3 | PM04G19860 | 351 | 36740.87 | 9.15 | 50.66 | 54.27 | -0.508 | Nucleus |
PmSBP4 | PM03G01570 | 373 | 38851.28 | 9.11 | 51.60 | 55.01 | -0.454 | Nucleus |
PmSBP5 | PM07G33040 | 378 | 39705.20 | 9.41 | 50.71 | 58.47 | -0.470 | Nucleus |
PmSBP6 | PM16G15940 | 405 | 40953.59 | 9.61 | 58.23 | 55.11 | -0.442 | Nucleus |
PmSBP7 | PM15G16820 | 398 | 40086.69 | 9.43 | 59.47 | 53.39 | -0.441 | Nucleus |
PmSBP8 | PM10G18000 | 416 | 43996.51 | 9.18 | 63.21 | 57.09 | -0.528 | Nucleus |
PmSBP9 | PM09G20570 | 423 | 45069.55 | 9.14 | 65.80 | 57.07 | -0.590 | Nucleus |
PmSBP10 | PM03G07850 | 181 | 18864.75 | 9.80 | 70.12 | 49.34 | -0.796 | Nucleus |
PmSBP11 | PM11G14200 | 475 | 51028.91 | 9.10 | 45.90 | 60.06 | -0.577 | Nucleus |
PmSBP12 | PM12G02720 | 474 | 51043.79 | 9.10 | 47.15 | 61.22 | -0.573 | Nucleus |
PmSBP13 | PM03G07830 | 195 | 20090.95 | 9.71 | 65.22 | 40.77 | -0.962 | Nucleus |
PmSBP14 | PM12G04460 | 439 | 46205.92 | 6.84 | 59.02 | 61.07 | -0.423 | Nucleus |
PmSBP15 | PM11G16250 | 249 | 27804.58 | 9.66 | 58.67 | 57.27 | -0.726 | Nucleus |
PmSBP16 | PM01G25080 | 953 | 104207.41 | 5.74 | 46.12 | 78.91 | -0.310 | Nucleus |
PmSBP17 | PM12G04270 | 331 | 36135.41 | 8.90 | 58.10 | 58.76 | -0.670 | Nucleus |
PmSBP18 | PM13G22370 | 1107 | 121234.39 | 6.64 | 55.79 | 75.46 | -0.482 | Nucleus |
PmSBP19 | PM15G18240 | 1109 | 121513.62 | 6.55 | 55.94 | 74.96 | -0.491 | Nucleus |
PmSBP20 | PM06G21970 | 855 | 94067.89 | 5.78 | 53.45 | 82.02 | -0.327 | Nucleus |
PmSBP21 | PM05G24780 | 857 | 94363.22 | 5.74 | 54.80 | 82.07 | -0.336 | Nucleus |
PmSBP22 | PM07G07420 | 540 | 60348.18 | 5.60 | 56.90 | 82.19 | -0.396 | Nucleus |
PmSBP23 | PM04G25580 | 105 | 11903.20 | 11.92 | 86.68 | 33.52 | -1.624 | Nucleus |
PmSBP24 | PM11G02690 | 403 | 42276.93 | 6.22 | 57.12 | 61.64 | -0.481 | Nucleus |
PmSBP25 | PM13G17660 | 255 | 27293.16 | 7.92 | 46.21 | 58.31 | -0.555 | Nucleus |
表2 糜子SBP转录因子家族成员理化性质及其亚细胞定位
Table 2 Physicochemical properties and subcellular localization of SBP transcription factor family members in Panicum miliaceum
Gene name | Gene ID | Number of amino acids | Molecular weight (Da) | Theoretical pI | Instability index | Aliphatic index | Grand average of hydropathicity | Subcellular localization |
---|---|---|---|---|---|---|---|---|
PmSBP1 | PM13G22100 | 389 | 40425.64 | 9.02 | 59.42 | 53.57 | -0.554 | Nucleus |
PmSBP2 | PM15G18460 | 391 | 40589.82 | 9.03 | 59.36 | 51.79 | -0.586 | Nucleus |
PmSBP3 | PM04G19860 | 351 | 36740.87 | 9.15 | 50.66 | 54.27 | -0.508 | Nucleus |
PmSBP4 | PM03G01570 | 373 | 38851.28 | 9.11 | 51.60 | 55.01 | -0.454 | Nucleus |
PmSBP5 | PM07G33040 | 378 | 39705.20 | 9.41 | 50.71 | 58.47 | -0.470 | Nucleus |
PmSBP6 | PM16G15940 | 405 | 40953.59 | 9.61 | 58.23 | 55.11 | -0.442 | Nucleus |
PmSBP7 | PM15G16820 | 398 | 40086.69 | 9.43 | 59.47 | 53.39 | -0.441 | Nucleus |
PmSBP8 | PM10G18000 | 416 | 43996.51 | 9.18 | 63.21 | 57.09 | -0.528 | Nucleus |
PmSBP9 | PM09G20570 | 423 | 45069.55 | 9.14 | 65.80 | 57.07 | -0.590 | Nucleus |
PmSBP10 | PM03G07850 | 181 | 18864.75 | 9.80 | 70.12 | 49.34 | -0.796 | Nucleus |
PmSBP11 | PM11G14200 | 475 | 51028.91 | 9.10 | 45.90 | 60.06 | -0.577 | Nucleus |
PmSBP12 | PM12G02720 | 474 | 51043.79 | 9.10 | 47.15 | 61.22 | -0.573 | Nucleus |
PmSBP13 | PM03G07830 | 195 | 20090.95 | 9.71 | 65.22 | 40.77 | -0.962 | Nucleus |
PmSBP14 | PM12G04460 | 439 | 46205.92 | 6.84 | 59.02 | 61.07 | -0.423 | Nucleus |
PmSBP15 | PM11G16250 | 249 | 27804.58 | 9.66 | 58.67 | 57.27 | -0.726 | Nucleus |
PmSBP16 | PM01G25080 | 953 | 104207.41 | 5.74 | 46.12 | 78.91 | -0.310 | Nucleus |
PmSBP17 | PM12G04270 | 331 | 36135.41 | 8.90 | 58.10 | 58.76 | -0.670 | Nucleus |
PmSBP18 | PM13G22370 | 1107 | 121234.39 | 6.64 | 55.79 | 75.46 | -0.482 | Nucleus |
PmSBP19 | PM15G18240 | 1109 | 121513.62 | 6.55 | 55.94 | 74.96 | -0.491 | Nucleus |
PmSBP20 | PM06G21970 | 855 | 94067.89 | 5.78 | 53.45 | 82.02 | -0.327 | Nucleus |
PmSBP21 | PM05G24780 | 857 | 94363.22 | 5.74 | 54.80 | 82.07 | -0.336 | Nucleus |
PmSBP22 | PM07G07420 | 540 | 60348.18 | 5.60 | 56.90 | 82.19 | -0.396 | Nucleus |
PmSBP23 | PM04G25580 | 105 | 11903.20 | 11.92 | 86.68 | 33.52 | -1.624 | Nucleus |
PmSBP24 | PM11G02690 | 403 | 42276.93 | 6.22 | 57.12 | 61.64 | -0.481 | Nucleus |
PmSBP25 | PM13G17660 | 255 | 27293.16 | 7.92 | 46.21 | 58.31 | -0.555 | Nucleus |
图1 糜子、水稻和拟南芥SBP家族蛋白系统进化树 系统进化树的分支颜色及填充底色表示不同的SBP亚家族, 分支颜色一致的为同一亚家族。
Figure 1 Phylogenetic tree of SBP family proteins in Panicum miliaceum, Oryza sativa and Arabidopsis thaliana The branch color and the filling base color of the phylogenetic tree distinguish the subfamilies of the SBP family, and the proteins with the same branch color are represented as the same subfamily.
图8 SBP基因在不同时期不同品种糜子中的表达模式 (A) 抽穗期; (B) 开花期; (C) 单粒品种; (D) 双粒品种。D1-D3/Z1-Z3: 抽穗期/开花期的单粒品种; M1-M3/Y1-Y3: 抽穗期/开花期的双粒品种
Figure 8 Expression patterns of SBP genes in different stages and varieties of Panicum miliaceum (A) Heading stage; (B) Flowering stage; (C) Single grain varieties; (D) Double grain varieties. D1-D3/Z1-Z3: Single grain varieties at heading/flowering stage; M1-M3/Y1-Y3: Double grain varieties at heading/flowering stage
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