Genome-wide analysis of MIKCC-type MADS box genes in grapevine.

María José Carmona,Diego Lijavetzky,José Díaz-Riquelme,José M. Martínez-Zapater

doi:10.1104/pp.108.131052

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.

Highlights

MIKCc-type MADS box genes encode transcription factors that play crucial roles in plant growth and development
MIKC subfamilies like those represented by FLOWERING LOCUS C (FLC; Michaels and Amasino, 1999; Ratcliffe et al, 2003; Searle et al, 2006; Reeves et al, 2007), SUPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1; Lee et al, 2000; Samach et al, 2000; Hepworth et al, 2002; Moon et al, 2003; Schonrock et al, 2006; Liu et al, 2008), and SHORT VEGETATIVE PHASE (SVP; Hartmann et al, 2000; Yu et al, 2002; Michaels et al, 2003; Lee et al, 2007; Liu et al, 2008) are involved in the regulation of flowering transition by the integration of signáis from different flowering pathways
Six additional sequences containing MADS domains characteristic of MIKC genes and mapping to defined chromosomal positions were identified. This suggests that the total number of MIKC genes could rise to 38. Two of those sequences would belong to the AGL17, two to the B-sister (BS), and two to the SVP subfamilies based on the available sequence information

Summary

Introduction

MIKCc-type MADS box genes encode transcription factors that play crucial roles in plant growth and development. MIKCc-type MADS box genes ( on called MIKC genes) are the best characterized group of MADS box genes and have been involved in essential and diverse functions related to plant growth and development (Rounsley et al, 1995; Alvarez-Buylla et al, 2000a; Theissen, 2001; Becker and Theissen, 2003; Kaufmann et al, 2005; Theissen and Melzer, 2007). Expression of MIKC genes has been detected outside reproductive organs, among them those belonging to subfamilies AGL12 and AGL17 (Rounsley et al, 1995; Alvarez-Buylla et al, 2000a; Burgeff et al, 2002) Their expression suggested a role for those genes in vegetative development, which has later been evidenced for some of them in root development (Zhang and Forde, 2000; Tapia-López et al, 2008). Notwithstanding, a role for AGL12 and AGL17 genes as flowering promoters was recently proposed (Han et al, 2008; Tapia-López et al, 2008)

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Conclusion