马铃薯PYL基因家族的全基因组鉴定及表达分析

doi:10.3724/SP.J.1006.2022.14183

作物学报 ›› 2022, Vol. 48 ›› Issue (10): 2533-2545.doi: 10.3724/SP.J.1006.2022.14183

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

马铃薯PYL基因家族的全基因组鉴定及表达分析

贾小霞¹^,²(), 齐恩芳¹^,², 马胜¹^,², 黄伟¹^,², 郑永伟¹^,², 白永杰¹^,², 文国宏¹^,²^,^*()

¹甘肃省农业科学院马铃薯研究所 / 甘肃省马铃薯种质资源创新工程实验室, 甘肃兰州 730070
²国家种质资源渭源观测实验站, 甘肃渭源 748201

收稿日期:2021-10-11 接受日期:2022-01-05 出版日期:2022-10-12 网络出版日期:2022-02-09
通讯作者: 文国宏
作者简介:第一作者联系方式: E-mail: jiaxx0601@163.com
基金资助:
甘肃省自然科学基金重点项目(21JR7RA728);甘肃省农业科学院科技创新专项(2020GAAS16);甘肃省农业科学院生物技术育种专项(2020GAAS10);国家自然科学基金项目(31560412);国家自然科学基金项目(31860401);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-09-P06)

Genome-wide identification and expression analysis of potato PYL gene family

JIA Xiao-Xia¹^,²(), QI En-Fang¹^,², MA Sheng¹^,², HUANG Wei¹^,², ZHENG Yong-Wei¹^,², BAI Yong-Jie¹^,², WEN Guo-Hong¹^,²^,^*()

¹Potato Research Institute of Gansu Academy of Agricultural Sciences / Gansu Engineering Laboratory of Potato Germplasm resources Innovation, Lanzhou 730070, Gansu, China
²National Germplasm Resources Agricultural Experimental Station, Weiyuan 748201, Gansu, China

Received:2021-10-11 Accepted:2022-01-05 Published:2022-10-12 Published online:2022-02-09
Contact: WEN Guo-Hong
Supported by:
Key Project of Natural Science Foundation of Gansu Province(21JR7RA728);Science and Technology Support Program of Gansu Academy of Agricultural Sciences(2020GAAS16);Special Project of Biotechnology Breeding of Gansu Academy of Agricultural Sciences(2020GAAS10);National Natural Science Foundation of China(31560412);National Natural Science Foundation of China(31860401);China Agriculture Research System of MOF and MARA(CARS-09-P06)

摘要/Abstract

摘要：

作为关键信号分子, 脱落酸(ABA)通过其核心信号通路PYLs-PP2Cs-SnRK2s广泛调控植物的生长发育和逆境响应过程, PYLs蛋白作为ABA信号传导的核心组件, 在ABA信号传导中发挥着不可替代的作用。为探究PYLs (PYR/PYL/RCARs) 基因在马铃薯中的进化以及表达模式, 本研究从马铃薯全基因组‘DM-v 6.1’共鉴定到17个StPYLs基因, 并对其分布、蛋白理化性质、系统进化、基因结构特征以及基因表达模式进行了分析。结果表明, 17个StPYLs基因不均匀分布在8条染色体上, 其氨基酸大小在163~231 aa之间, 等电点在4.5~8.6之间, 相对分子量在18.71~25.29 kD之间。根据基因结构和蛋白的系统发育特征, StPYL家族成员共分为3个亚组, motif 1存在于本家族所有基因中, 说明它在StPYLs的进化过程中较为保守。基因表达模式分析表明, StPYL家族成员具有明显的组织表达特异性, 且除StPYL1在外源激素(BAP、ABA和IAA)和非生物胁迫(高温、盐和干旱)下均上调表达外, 其余基因存在功能分化, 不同胁迫下的表达模式各异。本研究结果为进一步阐明StPYLs基因在马铃薯中的功能奠定了理论基础。

关键词: 马铃薯, PYL基因家族, 脱落酸, 基因表达分析

Abstract:

As a key signalling molecule, abscisic acid (ABA) extensively regulates plant growth and development, and stress response processes through its core signalling pathway PYLs-PP2Cs-SnRK2s. As a core component of ABA signalling transduction, PYLs protein plays an irreplaceable role. In order to explore the evolution and expression pattern of PYL (PYR/PYL/RCARs) genes in potato, 17 PYL genes were identified from the whole potato genome ‘DM-v 6.1’, and their distribution, protein physical and chemical properties, system evolution, structural characteristics, and the relative expression patterns were analysed. The results showed that the 17 StPYL genes were unevenly distributed on 8 chromosomes, with amino acids of 163-231 aa, isoelectric points of 4.5-8.6, and relative molecular weights of 18.71-25.29 kD. According to the gene structure and protein phylogenetic characteristics, the members of the StPYL family were divided into three subgroups. Motif 1 existed in all genes in this family, indicating that it was relatively conserved in the evolution of StPYLs. Gene expression patterns showed that the members of the StPYL family had obvious tissue expression specificity, and except for the up-regulation of StPYL1 under exogenous hormones (BAP, ABA, and IAA) and abiotic stress (high temperature, salt and drought), the rest of the StPYL genes were functionally differentiated and their relative expression patterns were different under different stresses. The results of this study lay a theoretical foundation for further elucidating the function of StPYLs gene in potato.

Key words: potato, PYL gene family, abscisic acid (ABA), gene expression analysis

贾小霞, 齐恩芳, 马胜, 黄伟, 郑永伟, 白永杰, 文国宏. 马铃薯PYL基因家族的全基因组鉴定及表达分析[J]. 作物学报, 2022, 48(10): 2533-2545.

JIA Xiao-Xia, QI En-Fang, MA Sheng, HUANG Wei, ZHENG Yong-Wei, BAI Yong-Jie, WEN Guo-Hong. Genome-wide identification and expression analysis of potato PYL gene family[J]. Acta Agronomica Sinica, 2022, 48(10): 2533-2545.

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基因编号 Gene ID	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
EF1α	ATTGGAAACGGATATGCTCCA	TCCTTACCTGAACGCCTGTCA
Soltu.DM.05G022460	TCCTCAAGAGCTGCCACG	GCCGCCGACTATACTAATGC
Soltu.DM.10G022490	CTCCCGTCTCCACCGTATG	CCCCACCAACAACGCTAAA
Soltu.DM.03G013340	CGTCATTAGTTTCAGCGTCATC	CGTTTCTTCCTTTGTATTCCCT
Soltu.DM.10G019340	CAATCCCACCAATCACTACAGC	TTTGTACGCTTGAGGGTTGTC
Soltu.DM.02G024820	ATCGAACCTGTTTATCCTCCTG	AAATAGCCATCTGGCAAGTCA
Soltu.DM.02G001580	TGAAGACGATGTTTTCCCAGAC	TGAAGGCAGTGAAGCGGTAT
Soltu.DM.04G027470	GCATTGCTTCCTCCTCATTACT	TGAACTCTTCTGCCCTATCCC
Soltu.DM.01G033740	GTTGCCTGACGGGACATTT	CATATCCTTGGACCAGCATTAA

基因名称 Gene name	基因编号 Gene ID	染色体定位 Chromosome localization	亚组分类Subgroup	氨基酸数量 Number of amino acids (aa)	等电点 Isoelectric point (pI)	相对分子量 Molecular weight (kD)
StPYL1	Soltu.DM.01G034800	Chr.01: 74327768-74330316	I	186	6.30	20.79
StPYL2	Soltu.DM.03G013340	Chr.03: 35693624-35694662	II	201	5.95	22.16
StPYL3	Soltu.DM.03G022780	Chr.03: 47692175-47694992	I	185	5.61	20.96
StPYL4	Soltu.DM.05G022460	Chr.05: 50931814-50932956	II	208	7.15	22.89
StPYL5	Soltu.DM.06G010300	Chr.06: 31336857-31338048	II	218	6.40	23.99
StPYL6	Soltu.DM.06G018570	Chr.06: 45115651-45116827	III	213	4.98	23.72
StPYL7	Soltu.DM.08G013560	Chr.08: 39726166-39727508	III	188	6.65	21.08
StPYL8	Soltu.DM.08G014660	Chr.08: 41607872-41608584	I	183	4.93	20.17
StPYL9	Soltu.DM.08G014670	Chr.08: 41614500-41615633	I	176	4.50	19.78
StPYL10	Soltu.DM.08G014680	Chr.08: 41634425-41635105	I	163	5.32	18.71
StPYL11	Soltu.DM.08G022790	Chr.08: 52187476-52188465	III	231	5.12	25.29
StPYL12	Soltu.DM.08G028930	Chr.08: 58181068-58185195	I	189	6.75	21.57
StPYL13	Soltu.DM.09G009100	Chr.09: 10398942-10400047	II	214	8.60	23.39
StPYL14	Soltu.DM.10G019340	Chr.10: 50673639-50674710	II	207	7.10	22.82
StPYL15	Soltu.DM.10G022490	Chr.10: 54650751-54652125	II	213	6.79	23.49
StPYL16	Soltu.DM.12G004400	Chr.12: 3523014-3524941	III	190	5.12	21.24
StPYL17	Soltu.DM.12G008390	Chr.12: 7357759-7362992	I	181	5.97	20.68

序号 No.	基因1 Gene 1	基因2 Gene 2	非同义替换率 Ka	同义替换率 Ks	非同义替换率/同义替换率 Ka/Ks
1	AtPYL1	StPYL11	0.252113	2.46901	0.102111
2	AtPYL10	StPYL1	0.209896	2.62041	0.0801006
3	AtPYL10	StPYL3	0.203876	3.47713	0.0586336
4	AtPYL2	StPYL16	0.199507	3.38436	0.0589498
5	AtPYL2	StPYL7	0.202235	3.41170	0.0592768
6	AtPYL4	StPYL14	0.277640	3.19545	0.0868861
7	AtPYL4	StPYL15	0.251724	3.78848	0.0664447
8	AtPYL5	StPYL2	0.337324	3.20802	0.10515
9	AtPYL5	StPYL5	0.358874	3.08254	0.116422
10	AtPYL6	StPYL14	0.391640	2.85503	0.137175
11	AtPYL6	StPYL2	0.335979	3.04837	0.110216
12	AtPYL6	StPYL5	0.310522	3.18218	0.0975815
13	AtPYL7	StPYL1	0.228439	2.12794	0.107352
14	AtPYL7	StPYL12	0.214102	3.49394	0.0612782
15	AtPYL8	StPYL1	0.148691	4.52157	0.0328847
16	AtPYL8	StPYL12	0.176819	3.71724	0.0475675
17	AtPYL8	StPYL3	0.130553	4.14104	0.0315267
18	AtPYL9	StPYL1	0.163537	1.84526	0.0886251
19	AtPYR1	StPYL11	0.196102	1.34623	0.145668
20	AtPYR1	StPYL6	0.204242	3.81927	0.0534767
21	OsPYL1	StPYL11	0.347476	3.45055	0.100702
序号 No.	基因1 Gene 1	基因2 Gene 2	非同义替换率 Ka	同义替换率 Ks	非同义替换率/同义替换率 Ka/Ks
22	OsPYL12	StPYL1	0.330709	2.89213	0.114348
23	OsPYL12	StPYL12	0.285345	2.94688	0.0968295
24	OsPYL4	StPYL13	0.347064	3.44965	0.100609
25	OsPYL4	StPYL5	0.355825	3.12683	0.113797
26	OsPYL5	StPYL13	0.362471	3.22157	0.112514
27	OsPYL5	StPYL14	0.360063	3.06688	0.117404
28	OsPYL5	StPYL5	0.356826	3.18746	0.111947
29	OsPYL6	StPYL13	0.384219	3.18292	0.120713
30	OsPYL6	StPYL14	0.376110	3.09537	0.121507
31	OsPYL6	StPYL5	0.359420	3.20874	0.112013
32	OsPYL7	StPYL1	0.364590	3.24765	0.112262
33	OsPYL7	StPYL3	0.321310	3.17375	0.10124
34	OsPYL8	StPYL12	0.273630	2.71313	0.100854

基因名称 Gene name	处理Treatment
基因名称 Gene name	T75	T65	T55	T45
StPYL1	82.75±3.26 b	105.73±9.28 a	110.58±13.47 a	101.73±7.90 a
StPYL3	84.46±3.52 a	73.15±4.16 a	73.57±2.17 a	78.06±3.83 a
StPYL12	11.47±2.07 a	15.16±1.26 a	12.43±0.29 a	15.89±2.72 a
StPYL17	38.49±6.22 a	39.70±0.44 a	34.52±1.45 a	27.13±4.26 a
StPYL8	1.53±0.46 ab	1.96±0.04 a	0.99±0.19 b	0.97±0.16 b
StPYL9	2.72±0.32 a	2.91±0.33 a	3.17±0.52 a	3.07±0.09 a
StPYL10	0.46±0.09 b	0.70±0.11 a	0.53±0.15 b	0.52±0.13 b
StPYL2	72.03±3.26 a	58.73±1.45 b	28.23±2.78 c	21.69±5.01 c
StPYL4	17.93±5.37 a	14.44±1.41 a	6.24±1.51 b	5.11±2.19 b
StPYL5	25.90±2.86 a	26.34±4.12 a	17.34±3.35 b	14.46±3.55 b
StPYL13	4.07±0.43 a	2.94±0.48 ab	2.87±0.27 ab	2.54±0.45 b
基因名称 Gene name	处理Treatment
基因名称 Gene name	T75	T65	T55	T45
StPYL14	22.86±2.94 a	18.82±1.06 ab	15.00±1.31 bc	9.44±1.92 c
StPYL15	146.99±4.30 a	121.88±7.18 b	105.61±8.19 b	66.12±9.62 c
StPYL6	40.26±5.09 a	48.10±0.99 a	44.86±3.91 a	48.78±3.15 a
StPYL11	1.00±0.08 c	1.42±0.04 ab	1.47±0.11 a	1.10±0.14 bc
StPYL7	1.68±0.28 b	2.03±0.34 a	1.12±0.20 b	1.14±0.28 b
StPYL16	0	0	0	0

马铃薯PYL基因家族的全基因组鉴定及表达分析

Genome-wide identification and expression analysis of potato PYL gene family

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