Abstract
The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries.
Highlights
Harvestable plant organs exhibit significant phenotypic diversity between and within species.This diversity is vital for marketing produce and provides the basis for selection of useful agronomic traits [1].Recent research demonstrated the role of genes that interact with other proteins and link with microtubules, altering cell division patterns that control the specific form of vegetative or reproductive organs [2,3]
In total 49 putative VvIQD genes were identified from the V. vinifera genome and were denominated as VvIQD1 to VvIQD49 depending on their phylogenetic position relative to their associated orthologous gene pair of Arabidopsis (Table S2)
Extensive genome-wide analysis of IQ67 Domain (IQD) gene family was carried out using the advanced bioinformatic analyses, which identified 49 VvIQD genes in the grapevine genome
Summary
Harvestable plant organs exhibit significant phenotypic diversity between and within species.This diversity is vital for marketing produce (fruits, flowers, vegetables, seeds, tubers, and leaves) and provides the basis for selection of useful agronomic traits (size and shape) [1].Recent research demonstrated the role of genes that interact with other proteins and link with microtubules, altering cell division patterns that control the specific form of vegetative or reproductive organs [2,3]. Harvestable plant organs exhibit significant phenotypic diversity between and within species. This diversity is vital for marketing produce (fruits, flowers, vegetables, seeds, tubers, and leaves) and provides the basis for selection of useful agronomic traits (size and shape) [1]. Recent research demonstrated the role of genes that interact with other proteins and link with microtubules, altering cell division patterns that control the specific form of vegetative or reproductive organs [2,3]. Various IQD genes have been shown to control morphology, such as AtIQD11 and AtIQD16 in elongated shape, AtIQD14 in twisted shape, and AtIQD25 in round shape, demonstrating the functional diversity of IQD proteins in the regulation of cellular elongation and the cytoskeleton [8,12,13]
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