马铃薯ARM基因家族的全基因组鉴定及表达分析

doi:10.3724/SP.J.1006.2024.34121

作物学报 ›› 2024, Vol. 50 ›› Issue (6): 1451-1466.doi: 10.3724/SP.J.1006.2024.34121

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

马铃薯ARM基因家族的全基因组鉴定及表达分析

刘震¹(), 陈丽敏², 李志涛², 朱金勇², 王玮璐², 齐喆颖², 姚攀锋¹, 毕真真², 孙超², 白江平³, 刘玉汇¹^,^*()

¹甘肃农业大学省部共建干旱生境作物学国家重点实验室, 甘肃兰州 730070
²甘肃农业大学农学院, 甘肃兰州 730070
³甘肃省教育厅, 甘肃兰州 730030

收稿日期:2023-07-14 接受日期:2024-01-12 出版日期:2024-06-12 网络出版日期:2024-02-19
通讯作者: * 刘玉汇, E-mail: lyhui@gsau.edu.cn
作者简介:E-mail: pepsipyy@126.com
基金资助:
甘肃省科技计划资助项目(22JR5RA870);甘肃省科技计划资助项目(22JR5RA834);财政部和农业农村部国家现代农业产业技术体系建设项目(CARS-09-P14);甘肃省科技重大专项(22ZD6NA009);中央引导地方科技发展资金项目(23ZYQJ304);省部共建干旱生境作物学国家重点实验室开放基金课题(GSCS-2021-Z02);甘肃农业大学“伏羲人才”计划项目(Gaufx-02Y04);甘肃农业大学公招博士科研启动基金项目(GAU-KYQD-2020-11)

Genome-wide identification and expression analysis of ARM gene family in potato (Solanum tuberosum L.)

LIU Zhen¹(), CHEN Li-Min², LI Zhi-Tao², ZHU Jin-Yong², WANG Wei-Lu², QI Zhe-Ying², YAO Pan-Feng¹, BI Zhen-Zhen², SUN Chao², BAI Jiang-Ping³, LIU Yu-Hui¹^,^*()

¹State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, Gansu, China
²College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China
³Department of Education of Gansu Province, Lanzhou 730030, Gansu, China

Received:2023-07-14 Accepted:2024-01-12 Published:2024-06-12 Published online:2024-02-19
Contact: * E-mail: lyhui@gsau.edu.cn
Supported by:
Science and Technology Program of Gansu Province(22JR5RA870);Science and Technology Program of Gansu Province(22JR5RA834);China Agriculture Research System of MOF and MARA(CARS-09-P14);Major S&T Special Projects of Gansu Province(22ZD6NA009);Central government guidance for local scientific and technological development projects(23ZYQJ304);State Key Laboratory of Aridland Crop Science of China(GSCS-2021-Z02);Fuxi Talent Project of Gansu Agricultural University(Gaufx-02Y04);Scientific Research Startup Funds for Openly-recruited Doctors Agricultural University(GAU-KYQD-2020-11)

摘要/Abstract

摘要：

ARM蛋白重复序列(Armadillo repeats)广泛存在于高等植物中, 它们参与多种细胞过程, 如信号转导、核转运以及对多种生物/非生物胁迫的响应。本研究在马铃薯(Solanum tuberosum L.)全基因组水平下鉴定出了54个马铃薯ARM基因家族成员(StARMs), 它们不均匀的分布在12条染色体上。根据其蛋白结构和系统发育特征, 将54个StARMs分为3个亚家族。片段重复事件在马铃薯ARM基因家族的扩展中起主要作用。共线性分析发现, StARMs与番茄(Solanum lycopersicum)、拟南芥(Arabidopsis)、甘蓝(Brassica oleracea)、水稻(Oryza sativa)、玉米(Zea mays)分别有51对、17对、25对、6对和10对直系同源基因, 这些基因均在纯化选择下进化。RNA-seq数据分析发现, 4个StARM基因在匍匐茎中特异表达, 2个StARM基因在根和心皮中特异表达, 1个StARM基因在块茎中特异表, 还有一些StARM基因参与了马铃薯对生物/非生物胁迫的响应。此外, 本研究对3个不同颜色马铃薯块茎组织(薯皮和薯肉)进行了RNA-seq测序, 分析了54个StARMs在不同颜色马铃薯块茎组织中的表达模式, 并利用qPCR分析了StARMs 在3个不同颜色块茎杂交子代薯肉中的相对表达量, 筛选出了4个可能参与马铃薯块茎花色素苷生物合成的候选基因。本研究为进一步了解StARM基因家族的特征, 深入分析StARM基因在马铃薯抵御生物/非生物胁迫和调控块茎花色素苷生物合成中的功能提供了理论依据。

关键词: 马铃薯, ARM基因家族, 生物/非生物胁迫, 花色素苷生物合成, 表达分析

Abstract:

The armadillo repeats (Armadillo repeats) are widely distributed in higher plants and are involved in a variety of cellular processes such as signal transduction, nuclear transport, and the response to various biotic/abiotic stresses. In this study, 54 potato ARM gene family members (StARMs) were identified at the genome-wide level of potato (Solanum tuberosum L.), and they were unevenly distributed on 12 chromosomes. Based on their protein structure and phylogenetic characteristics, 54 StARMs were divided into three subfamilies. Segmental duplication events play a major role in the expansion of potato StARM gene family. Collinearity analysis showed that there were 51, 17, 25, 6, and 10 orthologous gene pairs between StARMs and tomato, Arabidopsis, cabbage, rice, and maize, respectively, which evolved under purification selection. RNA-seq data analysis showed that four StARMs genes were specifically expressed in the stolon, two StARMs were specifically expressed in the root and carpel, and one StARM gene was specifically expressed in the tuber. Some StARM genes were involved in potato response to biotic/abiotic stresses. In addition, we performed RNA-seq on three different colored potato tuber tissues (skin and flesh) and analyzed the relative expression pattern of 54 StARMs genes in different colored potato tuber tissues and the StARMs in potato flesh in three different colored potatoes by qPCR. Four candidate genes that may be involved in anthocyanin biosynthesis in potato tubers were screened. This study provides a theoretical basis for further understanding the characteristics of the StARM gene family and further analyzing the function of the StARM gene in potato resistance to biotic/abiotic stresses and regulation of anthocyanin biosynthesis in tubers.

Key words: potato, ARM gene family, biotic/abiotic stress, anthocyanin biosynthesis, the relative expression pattern

刘震, 陈丽敏, 李志涛, 朱金勇, 王玮璐, 齐喆颖, 姚攀锋, 毕真真, 孙超, 白江平, 刘玉汇. 马铃薯ARM基因家族的全基因组鉴定及表达分析[J]. 作物学报, 2024, 50(6): 1451-1466.

LIU Zhen, CHEN Li-Min, LI Zhi-Tao, ZHU Jin-Yong, WANG Wei-Lu, QI Zhe-Ying, YAO Pan-Feng, BI Zhen-Zhen, SUN Chao, BAI Jiang-Ping, LIU Yu-Hui. Genome-wide identification and expression analysis of ARM gene family in potato (Solanum tuberosum L.)[J]. Acta Agronomica Sinica, 2024, 50(6): 1451-1466.

图/表 12

图1

图2

附表1

附表2

马铃薯ARM基因家族成员及理化性质分析"

基因ID Gene ID	染色体定位 Chromosome localization (bp)			外显子 Exon			内含子 Intron	氨基酸长度 Amino acid length (aa)	相对分子量 Molecular weight (kD)	理论等电点Theoretical isoelectric point	亚家族分类 Subfamily cluster
Soltu01G020170	Chr.01	30,143,970-30,150,717		-		10	9	529	58.65	5.13	C2
Soltu01G040470	Chr.01	55,223,708-55,229,173		-		10	9	534	59.07	5.13	C2
Soltu01G031070	Chr.01	438,010-444,508		-		12	11	916	98.09	6.50	C3
Soltu01G010740	Chr.01	79,037,941-79,055,022		+		4	3	818	89.26	5.53	C3
Soltu01G032480	Chr.01	70,856,440-70,871,600		-		1	0	555	59.92	8.90	C2
Soltu01G035340	Chr.01	50,713,909-50,724,362		-		4	3	993	110.63	5.53	C3
Soltu01G050860	Chr.01	58,701,505-58,709,231		+		2	1	653	71.93	6.10	C1
Soltu01G032130	Chr.01	54,289,424-54,297,721		-		19	18	880	97.60	6.42	C1
Soltu01G035640	Chr.01	782,037-787,228		+		1	0	311	33.47	5.84	C3
Soltu02G032560	Chr.02	56,324,108-56,329,652		+		1	0	486	53.47	6.85	C3
Soltu02G015230	Chr.02	40,233,405-40,241,625		-		1	0	724	79.30	8.49	C3
Soltu02G018740	Chr.02	16,606,559-16,610,036		+		1	0	576	63.72	7.03	C2
Soltu02G023810	Chr.02	55,687,773-55,696,671		-		1	0	552	60.44	6.22	C1
Soltu02G026750	Chr.02	64,221,992-64,224,506		-		3	2	373	40.65	5.63	C2
Soltu02G010520	Chr.02	50,159,071-50,164,293		-		3	2	330	36.38	5.82	C2
Soltu02G005840	Chr.02	4,301,877-4,305,373		-		1	0	631	69.44	6.41	C1
Soltu02G007220	Chr.02	5,051,243-5,053,770		-		2	1	377	41.25	5.89	C2
Soltu03G003650	Chr.03	4,055,247-4,059,698		-		2	1	664	73.06	8.53	C1
Soltu03G027770	Chr.03	56,643,739-56,649,254		+		1	0	535	58.83	8.63	C3
Soltu03G026010	Chr.03	2,781,211-2,784,877		+		1	0	600	66.39	8.24	C1
Soltu03G004990	Chr.03	72,282,608-72,287,380	-		2		1	310	33.62	6.36	C2
Soltu04G022240	Chr.04	68,531,733-68,541,389	-		6		5	2120	226.50	5.27	C1
Soltu04G032610	Chr.04	44,072,182-44,075,864	+		2		1	356	37.96	5.92	C3
Soltu04G002630	Chr.04	9,543,436-9,546,506	+		4		3	647	69.90	8.44	C3
Soltu04G037650	Chr.04	721,136-723,844	+		8		7	959	107.06	6.63	C3
Soltu04G019300	Chr.04	46,654,769-46,658,455	+		4		3	488	52.67	6.17	C3
Soltu04G009290	Chr.04	44,283,632-44,286,388	+		2		1	451	48.78	5.65	C3
Soltu05G004720	Chr.05	9,441,561-9,453,160	+		4		3	650	70.58	7.85	C3
Soltu05G008330	Chr.05	29,865,050-29,868,218	+		1		0	685	76.06	8.07	C3
Soltu05G008150	Chr.05	30,635,738-30,637,944	+		1		0	685	76.25	7.45	C3
Soltu05G008220	Chr.05	3,610,488-3,613,859	+		3		2	588	65.09	6.03	C3
Soltu05G001590	Chr.05	3,872,355-3,875,948	+		5		4	1046	117.25	5.86	C3
Soltu06G000080	Chr.06	33,056,989-33,059,510	-		10		9	527	58.59	5.00	C2
Soltu06G034720	Chr.06	74,816,160-74,822,802	+		19		18	709	78.08	5.79	C3
Soltu06G031430	Chr.06	87,386,346-87,388,491	-		4		3	572	62.02	5.59	C3
Soltu06G010080	Chr.06	39,654,170-39,673,090	+		1		0	679	74.43	7.14	C3
Soltu07G016540	Chr.07	37,187,439-37,189,097	-		1		0	569	61.74	8.21	C2
Soltu07G014990	Chr.07	52,407,155-52,409,531	-		2		1	393	42.84	5.52	C2
Soltu07G011050	Chr.07	39,584,532-39,587,890	+		2		1	138	15.01	9.27	C2
Soltu08G010180	Chr.08	4,359,566-4,377,252	-		10		9	529	58.40	5.15	C2
Soltu08G026240	Chr.08	25,399,342-25,401,770	+		19		18	906	99.87	6.85	C1
Soltu09G019780	Chr.09	55,879,333-55,890,916	-		19		18	708	78.34	5.86	C3
Soltu09G021390	Chr.09	44,771,850-44,776,570	-		5		4	744	81.58	6.11	C3
Soltu10G023900	Chr.10	19,369,067-19,371,435	-		11		10	520	56.66	5.36	C2
Soltu11G020370	Chr.11	8,313,930-8,316,243	+		4		3	664	72.58	6.01	C3
Soltu11G004340	Chr.11	8,090,829-8,093,283	+		2		1	480	51.92	5.89	C3
Soltu11G000490	Chr.11	71,963,673-71,973,849	-		2		1	458	48.93	6.29	C3
Soltu11G009750	Chr.11	75,124,289-75,125,823	-		6		5	2133	229.40	5.37	C1
Soltu11G020000	Chr.11	8,222,752-8,224,810	-		9		8	704	75.78	7.73	C3
Soltu11G004370	Chr.11	50,992,861-50,995,959	+		22		21	1081	121.90	6.49	C1
Soltu12G000800	Chr.12	21,277,440-21,282,530	-		4		3	821	89.69	5.92	C3
Soltu12G021220	Chr.12	1,207,881-1,212,427	-		1		0	469	51.13	5.71	C2
Soltu12G006210	Chr.12	5,402,137-5,406,934	-		2		1	358	38.41	5.91	C3
Soltu12G004840	Chr.12	35,005,661-35,007,289	-		4		3	645	72.83	5.45	C3

附表2

图3

附图1

图4

图5

图6

图7

图8

图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°)
StEF-1α	GGTCGTGTTGAGACTGGTGTGATC	GCTTCGTGGTGCATCTCTACAGAC
Soltu01G035340	CCAGATATGATTTGTGGTCCTTTTG	CAGGGTGTGGAATCAGTAATGTTCT
Soltu02G015230	ATGGCATCTGCTGCAATTTTCT	CAACCCAACATCTGTCAGATCCAC
Soltu02G032560	TGTAACCTGGCAGCGAGTTCTG	GCAGCAAGACAATTCTCACGAGTC
Soltu03G004990	ATGCTTCGTAATTCGCCGTCA	GGCACCAGCATCTATGATACTTTTC
Soltu04G009290	TGGTTTCGCTAGAAAATTCTCATTC	TGGTACAAATTGGACCGGATAGTG
Soltu04G032610	TGGAGACTGAAGTTCAATCGAATTT	TATCACTGTTGCAATCGCTGAAA
Soltu06G031430	TGTGTTGCGGAGCCTCATAGC	ACTACCTGGTCGTTTGGGTGATTC
Soltu07G016540	GTCTAAGGCACAAACCCTAGACCA	CCTGCCAGCGAGAAGTAAAAGACT
Soltu08G026240	CAGCTTACAGAAACGGAACACTTCC	GCGGTTTTTGATTTGAAAGAAGC
Soltu11G020370	CTCAAGTTGTTGACTCCAATGTTCG	GAGCAATTCCTTAGCAGATTCAAGA

马铃薯ARM基因家族的全基因组鉴定及表达分析

Genome-wide identification and expression analysis of ARM gene family in potato (Solanum tuberosum L.)

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