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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. 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,*()   

  1. 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)

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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

图1

3个不同颜色马铃薯品种的块茎"

表1

qPCR引物序列"

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

图2

拟南芥和马铃薯BBXs基因家族进化树 红色圆表示StBBXs, 蓝色三角表示AtBBXs。"

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

图3

StBBX基因家族的进化关系、基因结构和保守基序分析 A: StBBXs进化树。B: StBBXs基因的外显子/内含子结构。蓝色框表示外显子, 相同长度的黑线表示内含子。上游/下游区域红色方框表示。数字0、1和2表示内含子的剪接阶段。C: StBBXs中保守基序的分布。10个不同颜色的框代表了10个不同的基序。"

图4

BBX基因家族重复事件 红色线表示StBBX基因与AtBBX基因之间具有同源性, 染色体数目显示在每个染色体的底部。"

图5

StBBXs在不同组织部位中的表达 对30个StBBXs基因表达量取以2为底的对数, 以进行标准化处理, 不同颜色的色块表示基因在不同组织中的表达水平。"

图6

StBBXs基因家族不同非生物胁迫和不同激素处理下的表达 对30个StBBXs基因表达量取以2为底的对数, 以进行标准化处理, 不同颜色的色块表示基因在非生物胁迫和激素处理下的表达水平。"

图7

StBBXs不同薯皮薯肉中的表达 对30个StBBX基因表达量取以2为底的对数, 以进行标准化处理, 不同颜色的色块表示基因在不同颜色薯皮薯肉中的表达水平。"

图8

StBBXs在彩色马铃薯不同部位花色素苷含量的相关性分析 *和**分别表示在0.05和0.01水平显著相关。"

图9

8个StBBX基因在白色和彩色薯皮和薯肉里的定量表达分析 对8个StBBXs基因在白色和彩色薯皮和薯肉的定量表达分析。XDS、LTS和HMS分别代表“新大坪”、“红美”和 “黑美人”的薯皮。XDF、LTF和HMF分别代表“新大坪”、“红美”和“黑美人”的薯肉。"

图10

StBBX蛋白互作网络分析 红色圆圈表示StBBXs候选基因, 黄色圆圈表示与花色素苷合成相关的基因。蓝色线条表示综合得分≥400, 紫色线条表示综合得分≥700, 红色线条表示综合得分≥900。"

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