Genome-wide analysis of Aux/IAA genes in Vitis vinifera: cloning and expression profiling of a grape Aux/IAA gene in response to phytohormone and abiotic stresses

Çakır, Birsen; Kılıçkaya, Ozan; Olcay, Ahmet Can

doi:10.1007/s11738-012-1079-7

Cited by 38 publications

(37 citation statements)

References 66 publications

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“…1), which was more than two groups obtained with Arabidopsis (Remington et al 2004) and rice (Jain et al 2006), and less than 4 groups observed in angiosperm (Cakir et al 2013). Furthermore, AtAUX/IAAs and CitAUX/IAAs were significantly distributed uniformly in tree groups, which was consistent with the result reported by Wu et al (2014).…”

Section: Discussionsupporting

confidence: 86%

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Xie

Pang

et al. 2015

Mol Genet Genomics

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Completion of the whole genome sequencing of citrus enabled us to perform genome-wide identification and functional analysis of the gene families involved in agronomic traits and morphological diversity of citrus. In this study, 22 CitARF, 11 CitGH3 and 26 CitAUX/IAA genes were identified in citrus, respectively. Phylogenetic analysis revealed that all the genes of each gene family could be subdivided into three groups and showed strong evolutionary conservation. The GH3 and AUX/IAA gene families shrank and ARF gene family was highly conserved in the citrus genome after speciation from Arabidopsis thaliana. Tissue-specific expression profiles revealed that 54 genes were expressed in at least one tissue while just 5 genes including CitARF07, CitARF20, CitGH3.04, CitAUX/IAA25 and CitAUX/IAA26 with very low expression level in all tissues tested, suggesting that the CitARF, CitGH3 and CitAUX/IAA gene families played important roles in the development of citrus organs. In addition, our data found that the expression of 2 CitARF, 4 CitGH3 and 4 AUX/IAA genes was affected by IAA treatment, and 7 genes including, CitGH3.04, CitGH3.07, CitAUX/IAA03, CitAUX/IAA04, CitAUX/IAA18, CitAUX/IAA19 and CitAUX/IAA23 were related to fruitlet abscission. This study provides a foundation for future studies on elucidating the precise role of citrus ARF, GH3 and AUX/IAA genes in early steps of auxin signal transduction and open up a new opportunity to uncover the molecular mechanism underlying citrus fruitlet abscission.

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Section: Discussionsupporting

confidence: 86%

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Xie

Pang

et al. 2015

Mol Genet Genomics

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“…VvARF7 and VvARF8 were previously reported as VvIAA24 and VvIAA7, respectively [54]. Using several plant transcription databases and PROSITE and Pfam, the VvARF7 amino acid sequence was deduced to contain an N-terminal B3-type DNA-binding domain (DBD; amino acids 126–228), a middle region (MR), two C-terminal Aux/IAA dimerization domains, domain III (amino acids 753–788), and domain IV (amino acids 797–839), needed for typical ARF protein activities.…”

Section: Resultsmentioning

confidence: 99%

Gibberellin Application at Pre-Bloom in Grapevines Down-Regulates the Expressions of VvIAA9 and VvARF7, Negative Regulators of Fruit Set Initiation, during Parthenocarpic Fruit Development

Jung

Hur

et al. 2014

PLoS ONE

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Fruit set is initiated only after fertilization and is tightly regulated primarily by gibberellins (GAs) and auxins. The application of either of these hormones induces parthenocarpy, fruit set without fertilization, but the molecular mechanism underlying this induction is poorly understood. In the present study, we have shown that the parthenocarpic fruits induced by GA application at pre-bloom result from the interaction of GA with auxin signaling. The transcriptional levels of the putative negative regulators of fruit set initiation, including Vitis auxin/indole-3-acetic acid transcription factor 9 (VvIAA9), Vitis auxin response factor 7 (VvARF7), and VvARF8 were monitored during inflorescence development in seeded diploid ‘Tamnara’ grapevines with or without GA application. Without GA application, VvIAA9, VvARF7, and VvARF8 were expressed at a relatively high level before full bloom, but decreased thereafter following pollination. After GA application at 14 days before full bloom (DBF); however, the expression levels of VvIAA9 and VvARF7 declined at 5 DBF prior to pollination. The effects of GA application on auxin levels or auxin signaling were also analyzed by monitoring the expression patterns of auxin biosynthesis genes and auxin-responsive genes with or without GA application. Transcription levels of the auxin biosynthesis genes Vitis anthranilate synthase β subunit (VvASB1-like), Vitis YUCCA2 (VvYUC2), and VvYUC6 were not significantly changed by GA application. However, the expressions of Vitis Gretchen Hagen3.2 (VvGH3.2) and VvGH3.3, auxin-responsive genes, were up-regulated from 2 DBF to full bloom with GA application. Furthermore, the Vitis GA signaling gene, VvDELLA was up-regulated by GA application during 12 DBF to 7 DBF, prior to down-regulation of VvIAA9 and VvARF7. These results suggest that VvIAA9 and VvARF7 are negative regulators of fruit set initiation in grapevines, and GA signaling is integrated with auxin signaling via VvDELLA during parthenocarpic fruit development in grapevines.

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“…Promoter analyses illustrated that all maize Aux/IAA genes contain canonical auxin-response elements or their core sequence. In contrast, in the promoter region of Aux/IAA genes of Vitis vinifera no AuxRE motifs were identified [47]. Similarly, in Arabidopsis only the promoters of AtIAA26 and AtIAA29 contain an AuxRE motif [48].…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, in Arabidopsis only the promoters of AtIAA26 and AtIAA29 contain an AuxRE motif [48]. Consequently, auxin-induced gene expression may be directed by tissue-specific factors different than Aux/IAA proteins in these plants [47,48]. Other promoter elements like MYB and bZIP related binding sites play a role in auxin-mediated transcription [49,50].…”

Section: Discussionmentioning

confidence: 99%

The Maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID Gene Family: Phylogeny, Synteny, and Unique Root-Type and Tissue-Specific Expression Patterns during Development

2013

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The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

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Genome-wide analysis of Aux/IAA genes in Vitis vinifera: cloning and expression profiling of a grape Aux/IAA gene in response to phytohormone and abiotic stresses

Cited by 38 publications

References 66 publications

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

Gibberellin Application at Pre-Bloom in Grapevines Down-Regulates the Expressions of VvIAA9 and VvARF7, Negative Regulators of Fruit Set Initiation, during Parthenocarpic Fruit Development

The Maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID Gene Family: Phylogeny, Synteny, and Unique Root-Type and Tissue-Specific Expression Patterns during Development

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