芸豆GH3基因家族鉴定、进化与表达分析
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甘肃农业大学

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国家自然科学基金项目(面上项目,重点项目,重大项目)


Identification, evolution, and expression analysis of GH3 gene family in kidney bean
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    摘要:

    【目的】Gretchen Hagen 3(GH3)基因家族是一类生长素早期响应基因,在植物生长发育及抗逆响应中发挥重要作用,为探究GH3基因在芸豆中的功能和作用。【方法】通过生物信息学的方法对芸豆GH3基因家族进行全基因组鉴定,并利用转录组数据(RNA-seq)和荧光定量PCR(RT-qPCR)检测PvGH3基因在不同逆境胁迫下的表达。【结果】在芸豆中共鉴定出19个基因家族成员,其中17个基因不均匀分布于8条染色体上,其余2个基因定位于scafford上无法精确定位。系统进化分析将PvGH3基因家族成员分为3个亚族,各亚族间的成员有相似的基因结构和保守基序。共线性分析发现,PvGH3家族各成员间存在3个旁系同源基因对,PvGHs与拟南芥GH3间有15个直系同源基因对。顺式元件分析发现PvGH3基因家族含有光、激素、胁迫及生长发育相关顺式元件。组织表达分析发现,PvGH3基因家族在花、根、花蕾及茎中表达较高。qRT-PCR分析表明,19个PvGH3在响应干旱(6% PEG)、盐(100 mmol/L NaCl)和低温(4 ℃)逆境胁迫应答方面均上调表达,其中PvGH3.19显著响应干旱胁迫,PvGH3.17响应盐胁迫,PvGH3.11响应低温胁迫。【结论】研究在芸豆中鉴定出19个PvGH3基因,分析其理化性质、染色体位置、共线性、进化关系、保守基序、顺式元件及组织表达,并通过qRT-PCR证明了其功能和作用,研究可为PvGH3的抗逆功能分析提供理论依据。

    Abstract:

    [Objective] The Gretchen Hagen 3 (GH3) gene family is a class of auxin early response genes, which play an important role in plant growth and development and stress resistance. The objective of this study was to investigate the function and effect of GH3 gene in kidney bean. [Methods] The whole genome of kidney bean GH3 gene family was identified by bioinformatics and the expression of PvGH3 gene was detected by transcriptome data (RNA-seq) and fluorescent quantitative PCR (RT-qPCR) under different stress conditions. [Results] A total of 19 gene family members were identified in kidney bean, of which 17 genes were unevenly distributed on 8 chromosomes, and the other 2 genes could not be accurately located on scafford. Phylogenetic analysis divided the PvGH3 gene family into three subfamilies, and the members of each subfamily had similar gene structure and conserved motifs. The collinearity analysis showed that there were 3 para-homologous gene pairs between PvGH3 family members, and 15 direct homologous gene pairs between PvGHs and Arabidopsis GH3.Cis-element analysis showed that PvGH3 gene family contains cis-elements related to light, hormone, stress and growth and development. Tissue expression analysis showed that PvGH3 gene family was highly expressed in flowers, roots, buds and stems. qRT-PCR analysis showed that 19 PvGH3 were up-regulated in response to drought (6% PEG), salt (100 mmol/L NaCl) and low temperature (4 ℃) stress. PvGH3.19 was significantly responsive to drought stress, PvGH3.17 was responsive to salt stress. PvGH3.11 responds to low temperature stress. [Conclusion] In this study, 19 PvGH3 genes were identified in kidney bean. Their physicochemical properties, chromosomal location, collinearity, evolutionary relationship, conserved motif, cis-element and tissue expression were analyzed, and their functions and effects were further demonstrated by qRT-PCR. This study provided a theoretical basis for the analysis of resistance function of PvGH3.

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张晓旭,马媛媛,罗新锐,等.芸豆GH3基因家族鉴定、进化与表达分析[J].西北植物学报,2024,44(9):1433-1444

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  • 收稿日期:2024-02-29
  • 最后修改日期:2024-04-19
  • 录用日期:2024-04-22
  • 在线发布日期: 2024-07-15
  • 出版日期: 2024-09-05