Comparative genomic analysis of mitogen activated protein kinase gene family in grapevine

Abstract

Mitogen activated protein kinases (MAPKs) are important proteins involved in the signal transduction of extracellular information to intracellular targets, and play a crucial role in the response to biotic and abiotic stresses. Although Arabidopsis MAPKs are used for identification of the putative MAPKs in higher plants, no grapevine MAPK gene nomenclature has yet been appeared in the literature. In this study, we have identified 12 members of grapevine MAPK gene (VvMPK) family via In-silico analysis of current grapevine genome database. The structural comparison of 12 VvMPKs through the analysis of chromosome locations, sequence annotation and paralogous gene pair indicated that VvMPKs have evolved by segmental duplication, rather than by tandem amplification. Although further functional analysis of VvMPKs through in vivo and in vivo experiments will be required, our study provides the basis for future research on the diverse signaling pathways medicated by MAPKs in grapevine.

Validation by isolation and expression analyses of the mitogen-activated protein kinase gene family in the grapevine (Vitis vinifera L.)

“…By scanning the V1 genome sequence (http://genomes.cribi .unipd.it/grape/), we confirmed the 12 VvMPK genes previously reported in grapevine based on 8× coverage (Hyun et al 2010). These genes were renamed following the new international naming convention based on the gene order of their chromosomal locations: from VvMPK1 to VvMPK12.…”

“…A few other VvMPKs (VvMPK4, 6 and 11) were expressed at a much lower level in certain organs or stages: VvMPK4 was poorly expressed in senescing leaves and winter nodes; VvMPK6 was strongly expressed in stems but much less in flower organs, nodes and seeds; while VvMPK11 expression decreased during berry maturation and postharvest and in senescing leaves. The genes VvMPK5 and VvMPK6 cluster together in the expression analysis as well as the corresponding genes in the previously reported phylogenetic analysis (Hyun et al 2010), although VvMPK5 expression level is mostly higher than that of VvMPK6 in all examined organs. A parallelism with this observation was also reported in poplar -another perennial crop -for the two closest homologues PtMPK6 and 3 respectively, with a relatively higher abundance of the first over the second gene, especially in nodes .…”

“…In the present study, we validated 12 earlier identified (Hyun et al 2010) non-redundant MPK genes using the 12× sequence coverage of the grapevine genome by polymerase chain reaction (PCR)-based cloning. We then examined the expression pattern of VvMPK genes in tissues/organs at several developmental stages and in response to biotic and abiotic stresses, and related chemical signals.…”

“…This has greatly facilitated the grapevine comparative and functional genomics studies at the whole genome-, gene-family-or individual gene level, similarly to those of Arabidopsis and rice (Jaillon et al 2007, Nonis et al 2008. Recent preliminary data indicated that the grapevine possesses 12 MPK genes based on the genome scan of the 8× sequence coverage, but without experimental verification (Hyun et al 2010). In addition, no gene-family expression analysis and few functional analyses of each MPK gene have been undertaken in terms of their roles in biotic and abiotic stress responses in grapevine.…”

EST-SSRs characterization and in-silico alignments with linkage map SSR loci in grape (Vitis L.) genome

“…On the other hand, efficient sequence comparison (e.g., BlastN), and in silico mapping tools (e.g., e-PCR) had been efficiently used for markers mapping in Sorghum (Ramu et al, 2010), comparative gene sequences mapping in grape (Hyun et al, 2010), and SSR loci assignment in barley (Varshney et al, 2006), as well as markers anchoring in grape physical map (Lamoureux et al, 2006;Di Gaspero et al, 2007). The genetic linkage maps were built with most of the SSR markers (Dalbo et al, 2000;Doligez et al, 2002;Grando et al, 2003;Adam-Blondon et al, 2004;Doucleff et al, 2004;Riaz et al, 2004;Lowe and Walker 2006;Di Gaspero et al, 2007;Vezzulli et al, 2008).…”