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, 149 (1), 354-69

Genome-wide Analysis of MIKCC-type MADS Box Genes in Grapevine

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Genome-wide Analysis of MIKCC-type MADS Box Genes in Grapevine

José Díaz-Riquelme et al. Plant Physiol.

Abstract

MIKC(C)-type MADS box genes encode transcription factors that play crucial roles in plant growth and development. Analysis of the grapevine (Vitis vinifera) genome revealed up to 38 MIKC(C)-type genes. We report here a complete analysis of this gene family regarding their phylogenetic relationships with homologous genes identified in other sequenced dicot genomes, their genome location, and gene structure and expression. The grapevine genes cluster in 13 subfamilies with their Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa) counterparts. The lack of recent whole genome duplications in grapevine allows assigning the gene diversification processes observed within each subfamily either to an ancestral polyploidization event predating the divergence of those three species or to later duplication events within each lineage. Expression profiles of MIKC(C)-type genes in vegetative and reproductive organs as well as during flower and tendril development show conserved expression domains for specific subfamilies but also reflect characteristic features of grapevine development. Expression analyses in latent buds and during flower development reveal common features previously described in other plant systems as well as possible new roles for members of some subfamilies during flowering transition. The analysis of MIKC(C)-type genes in grapevine helps in understanding the origin of gene diversification within each subfamily and provides the basis for functional analyses to uncover the role of these MADS box genes in grapevine development.

Figures

Figure 1.
Figure 1.
Phylogenetic tree of the MIKC gene family in grapevine, Arabidopsis, and poplar. The tree was generated after sequence alignment with Multalin using the neighbor-joining method. Branches with less than 50% bootstrapping support were condensed. MIKC proteins grouped into 13 subfamilies. MIKC*-type MADS box proteins were used as an outgroup.
Figure 2.
Figure 2.
Chromosomal locations of grapevine MIKC genes. Only those chromosomes bearing MIKC genes (13) are represented. Paralogous regions in the putative ancestral constituents of the grapevine genome are depicted in the same color following Jaillón et al. (2007). Black chromosomal regions correspond to random chromosome sequences that are assigned to chromosomes but without a specific physical position. The chromosomal locations of genes VvSVP1 and VvBS1 were derived from NCBI information and appear in red at the bottoms of the assigned chromosomes. Molecular markers to help position the genes are listed in gray.
Figure 3.
Figure 3.
Expression profiles of grapevine MIKC genes in vegetative and reproductive organs. Expression analyses were performed by qRT-PCR, and relative gene expression data were gene-wise normalized. A, Expression pattern related to phylogenetic relationships. Bootstrap support values are shown when over 50. The corresponding subfamilies of each group of genes are indicated at right. B, Cluster analysis of gene expression patterns. Color scales, representing signal values, are shown at bottom.
Figure 4.
Figure 4.
Expression profiles of grapevine MIKC genes during flower and tendril development. Expression analyses were performed by qRT-PCR, and relative gene expression data were gene-wise normalized. Expression of VvSVP4 was not detected at any developmental stage. Color scale, representing signal values, is shown at bottom. At top, photographs from the different developmental stages are shown. Developmental stages correspond to buds from advanced stage B (B2), inflorescences of stage D (D, arrow), and flowers from inflorescences at stage G (G) and early stage H (H1). Tendril 1 (T1, arrow) and tendril 5 (T5, arrow) correspond to the most recently formed tendril by the shoot apex and that in the fifth position from the apex, respectively.
Figure 5.
Figure 5.
Expression profiles of representative MIKC genes in latent buds during flowering transition. Expression analyses were performed using qRT-PCR, and relative gene expression data were gene-wise normalized. Color scale, representing signal values, is shown at bottom. At top, the developmental stages of the shoot apex and derived structures within each bud are illustrated by scanning electron microscopy micrographs. Developmental stages correspond to buds from May to August in the first season as well as advanced stage B (B2) during the second season. In August, the two-branched inflorescence meristems are shown. In stage B2, only a detail of an inflorescence branch meristem, subtended by a bract in which the four flower meristems (asterisks) start to be outlined, is shown. br, Bract subtending each inflorescence branch meristem; ib, inflorescence branch meristem; im, inflorescence meristem; lf, leaf; lp, leaf primordium; sam, shoot apical meristem.

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