马铃薯BBX基因家族的全基因组鉴定及表达分析

doi:10.3724/SP.J.1006.2022.14199

作物学报 ›› 2022, Vol. 48 ›› Issue (11): 2797-2812.doi: 10.3724/SP.J.1006.2022.14199

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

马铃薯BBX基因家族的全基因组鉴定及表达分析

马文婧¹(), 刘震¹, 李志涛¹, 朱金勇¹, 李泓阳¹, 陈丽敏¹, 史田斌¹, 张俊莲², 刘玉汇¹^,^*()

¹甘肃农业大学农学院 / 省部共建干旱生境作物学国家重点实验室 / 甘肃省作物遗传改良与种质创新重点实验室, 甘肃兰州 730070
²甘肃农业大学园艺学院, 甘肃兰州 730070

收稿日期:2021-10-26 接受日期:2022-02-25 出版日期:2022-11-12 网络出版日期:2022-03-24
通讯作者: 刘玉汇
作者简介:第一作者联系方式: E-mail: 810774875@qq.com
基金资助:
本研究由甘肃省高等学校创新基金项目(2020A-056);国家自然科学基金项目(31860398);甘肃农业大学“伏羲人才”计划项目(Gaufx-02Y04);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(马铃薯);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-P14);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 BBX gene family in potato (Solanum tuberosum L.)

MA Wen-Jing¹(), LIU Zhen¹, LI Zhi-Tao¹, ZHU Jin-Yong¹, LI Hong-Yang¹, CHEN Li-Min¹, SHI Tian-Bin¹, ZHANG Jun-Lian², LIU Yu-Hui¹^,^*()

¹College of Agronomy, Gansu Agricultural University / State Key Laboratory of Aridland Crop Science / Gansu Provincial Key Laboratory of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, Gansu, China
²College of Horticulture, Gansu Agricultural University, Lanzhou 730070, Gansu, China

Received:2021-10-26 Accepted:2022-02-25 Published:2022-11-12 Published online:2022-03-24
Contact: LIU Yu-Hui
Supported by:
The Program for Innovation Ability Improvement of the Higher Education Institutions of Gansu Province(2020A-056);The National Natural Science Foundation of China(31860398);The Fuxi Talent Project of Gansu Agricultural University(Gaufx-02Y04);The China Agriculture Research System of MOF and MARA(马铃薯);The China Agriculture Research System of MOF and MARA(CARS-09-P14);The Scientific Research Startup Funds for Openly-recruited Doctors Agricultural University(GAU-KYQD-2020-11)

摘要/Abstract

摘要：

B-box (BBX)基因家族是一类锌指蛋白转录因子, 在植物生长发育过程中起重要作用。本研究鉴定了30个马铃薯BBXs家族成员, 对其理化性质、染色体定位、基因结构、蛋白保守结构域、基因重复事件、表达模式和蛋白互作网络进行了分析。结果表明, 30个StBBX基因家族成员不均匀的分布在11条染色体上。通过对其基因结构和系统发育特征的分析, 将30个StBBXs分为5个亚类。共线性分析表明, 马铃薯StBBXs与拟南芥AtBBXs间存在15对直系同源基因。利用PGSC数据库下载的RNA-seq数据, 分析了BBX基因家族在双单倍体(DM)马铃薯不同组织部位、非生物胁迫和外源激素处理下的表达。此外, 本研究对3种不同颜色块茎的马铃薯品种的薯皮和薯肉进行了RNA-seq, 研究了StBBXs在不同颜色的薯皮和薯肉中的表达模式, 分析了它们与花色素苷合成关键基因表达之间的相关性。利用String数据库构建了在彩色块茎中差异表达的StBBXs基因的蛋白互作网络。这些结果为进一步了解StBBX基因家族以及进一步分析StBBX基因在马铃薯非生物胁迫耐受和花青素生物合成中的功能提供了理论依据。

关键词: 马铃薯, BBX基因家族, 非生物胁迫, 花青素生物合成, 表达分析

Abstract:

The B-box (BBX) gene family is a type of zinc finger protein transcription factor that plays an important role in the growth and development of plants. In this study, 30 potato BBXs family members (StBBXs) were identified, and their physical and chemical properties, chromosomal location, gene structure, protein conserved domains, gene repetition events, expression patterns, and protein interaction network were analyzed. The results showed that 30 StBBXs were unevenly distributed on 11 chromosomes. According to their gene structures and phylogenetic characteristics, 30 StBBXs were divided into 5 subclasses. Collinearity analysis indicated that there were 15 pairs BBX genes which were orthologous to potato (Solanum tuberosum) and Arabidopsis. We analyzed the relative expression profiles of StBBX genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the PGSC (Potato Genome Sequencing Consortium) database. In addition, to explore the relative expression patterns of the StBBX genes in these tissues, we performed RNA-seq on the tuber skin and flesh of three potato varieties with different colors and analyzed their correlations with the expression of key genes for anthocyanin synthesis. Furthermore, the protein interaction network of StBBXs which differentially expressed in color tuber tissues was constructed using String database. These results provide a theoretical basis for further understanding the StBBX gene family, further function of StBBX genes in abiotic stress tolerance and anthocyanin biosynthesis in potato, and StBBX genes in potato might be related to abiotic stress responses and anthocyanin biosynthesis.

Key words: potato, BBX genes family, abiotic stress, anthocyanin biosynthesis, expression analysis

马文婧, 刘震, 李志涛, 朱金勇, 李泓阳, 陈丽敏, 史田斌, 张俊莲, 刘玉汇. 马铃薯BBX基因家族的全基因组鉴定及表达分析[J]. 作物学报, 2022, 48(11): 2797-2812.

MA Wen-Jing, LIU Zhen, LI Zhi-Tao, ZHU Jin-Yong, LI Hong-Yang, CHEN Li-Min, SHI Tian-Bin, ZHANG Jun-Lian, LIU Yu-Hui. Genome-wide identification and expression analysis of BBX gene family in potato (Solanum tuberosum L.)[J]. Acta Agronomica Sinica, 2022, 48(11): 2797-2812.

图/表 12

图1

表1

图2

表2

StBBX基因家族理化性质及亚细胞定位"

基因名称 Gene name	氨基酸长度 Amino acid length	相对分子量 Molecular weight (kD)	等电点 Point isoelectric (pI)	亚细胞定位 Subcellular localization	染色体定位 Chromosome localization	亚组分类 Class of subgroup
PG0003625	551	44,860.59	5.26	细胞核Nuclear	Chr02	BBX IV
PG0022345	575	46,990.87	5.27	细胞核Nuclear	Chr02	BBX V
PG1010056	1220	100,730.6	5.05	细胞核Nuclear	Chr02	BBX I
PG0007061	899	74,980.43	5.12	细胞核Nuclear	Chr07	BBX IV
PG0017411	1238	102,001	5.08	细胞核Nuclear	Chr07	BBX II
PG0026169	395	32,108.31	5.34	细胞核Nuclear	Chr07	BBX V
PG0026181	776	61,856.12	5.18	细胞核Nuclear	Chr07	BBX V
PG0027475	1160	96,517.16	5.04	细胞核Nuclear	Chr07	BBX I
PG0003109	641	52,158.76	5.22	细胞核Nuclear	Chr01	BBX IV
PG0030958	761	64,412.27	5.20	细胞核Nuclear	Chr01	BBX IV
PG0001263	1271	104,574.6	5.09	细胞核Nuclear	Chr05	BBX II
PG0005325	1244	102,491.8	5.07	细胞核Nuclear	Chr05	BBX II
PG0014566	1346	108,627.7	5.10	细胞核Nuclear	Chr05	BBX III
PG0025414	1364	112,088.5	5.05	细胞核Nuclear	Chr05	BBX II
PG0013178	341	27,626.76	5.50	细胞核Nuclear	Chr12	BBX II
PG0013753	623	49,919.71	5.25	细胞核Nuclear	Chr12	BBX V
PG0019025	902	75,119.83	5.12	细胞核Nuclear	Chr12	BBX IV
PG0028818	1229	100,908.6	5.09	细胞核Nuclear	Chr12	BBX II
PG0029365	1076	88,519.16	5.07	细胞核Nuclear	Chr12	BBX I
PG0029426	995	83,207.43	5.13	细胞核Nuclear	Chr12	BBX IV
PG0011378	1142	94,480.42	5.11	细胞核Nuclear	Chr12	BBX II
PG0005633	1208	97,557.49	5.11	细胞核Nuclear	Chr03	BBX III
PG0026515	782	65,781.32	5.15	细胞核Nuclear	Chr06	BBX V
PG0027017	704	58,425.39	5.17	细胞核Nuclear	Chr06	BBX IV
PG0026311	1046	85,660.46	5.06	细胞核Nuclear	Chr08	BBX I
PG0025024	701	57,480.47	5.21	细胞核Nuclear	Chr10	BBX V
PG0003711	899	75,536.97	5.15	细胞核Nuclear	Chr04	BBX IV
PG0005997	1472	122,076	5.03	细胞核Nuclear	Chr04	BBX V
PG0007749	1694	137,183.7	5.08	细胞核Nuclear	Chr04	BBX III
PG2010056	1244	102,374.8	5.05	细胞核Nuclear	Chr02	BBX I

表2

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图10

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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	ATTGGAAACGGATATGCTCCA	TCCTTACCTGAACGCCTGTCA
PG0011378	ATCATCAGCAGCAGCAGCAAGAG	TCACGGTCACAGGTAAAACAGAGC
PG0029365	CGTCGGCATGAGCGGTTTCC	TCATCATCAGCAGCATCAGCATCG
PG0027475	CGGTGGAATCGGTCGTGAAGTC	CGTGGTCGTGGTCATGGTTGTG
PG0027017	GCAAGGACTGTGACGAAGCAATTC	GCTCAAGGCTACACGGATTCCAG
PG0026311	GACTCCGCCTCCGCCAGATC	GACTCCGCTTCCGCTTCTTCTTC
PG0026181	TGGAGGAGAGTGAGAGCGTGAATG	GCGGTGGAGGCGTCGTATTTG
PG0025024	GGTGCGTTCGGTGAGTTCTTCC	CCTTACTCGCTTCCACGGAGATG
PG0013753	GTCATCAACTCCGCCTCCACAG	CATTCGTCACGCATTCGTTCAAAG

马铃薯BBX基因家族的全基因组鉴定及表达分析

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

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