cultivars by the use of the ph1 gene (Riley and Chapman, 1958) that promotes homeologous chromosome Rust resistance genes Lr37, Sr38, and Yr17 are located within a recombination. The ph1 mutation has been extensively segment of Triticum ventricosum (Tausch) Cess. chromosome 2NS translocated to the short arm of bread wheat chromosome 2AS. Char-used to incorporate new disease resistance genes in acterization of this chromosome segment by 13 restriction fragment wheat from wild Triticeae species such as T. monococlength polymorphism (RFLP) markers indicated that the 2NS translocum L., T. speltoides (Tausch) Gren., and T. ventricosum cation replaced approximately half of the short arm of chromosome (McIntosh et al., 1995; Friebe et al., 1996; Dubcovsky 2A (distal 25-38 centimorgans, cM). The objective of this study was et al., 1998). to develop polymerase chain reaction (PCR) assays based on RFLP The Yr17, Lr37, and Sr38 rust resistance genes, which marker cMWG682 to facilitate the transfer of this cluster of rust confer resistance in wheat against stripe rust (caused by resistance genes into commercial wheat (Triticum aestivum L.) culti-Puccinia striiformis West. f. sp. tritici), leaf rust (caused vars. DNA sequence was obtained from the A-, B-, D-, and N-alleles by Puccinia triticina Eriks), and stem rust (caused by of cMWG682 and was used to design N-allele specific primers. The Puccinia graminis Pers. f. sp. tritici Eriks. & E. Henn.), 2NS fragment amplified by PCR primers cosegregated with the presence of the RFLP-2NS band in all backcross populations. A cleaved respectively, have been used by breeders in different amplified polymorphic sequence (CAPS) was used to develop a parts of the world (Dyck and Lukow, 1988; McIntosh marker for the 2A-allele. This marker can be used to differentiate et al., 1995; Robert et al., 1999; Seah et al., 2000). These homozygous and heterozygous plants carrying the 2NS translocation linked resistance genes were initially introgressed in the in the final cycle of backcross introgression or in screenings for homowinter bread wheat 'VPM1' from Triticum ventricosum zygous plants in segregating populations. Finally, a third PCR assay (Maia, 1967) and are located in a 2NS/2AS translocation was developed by means of TaqMan technology as a high-throughput (Bariana and McIntosh, 1993;McIntosh et al., 1995). alternative for selection of the 2NS/2AS translocation in large segre-Rust races with virulence to Yr17 and Lr37 have been gating populations in breeding programs that have access to real time identified in different countries (Robert et al., 1999; PCR equipment. These molecular markers were used to develop four J. Kolmer unpublished data) but this gene cluster still hard red spring isogenic lines homozygous for the 2NS chromosome segment. One of the isogenic lines, derived from 'Anza,' did not show provides resistance to a wide range of races and is useful the expected resistance in spite of the presence of all the RFLP in combination with other rust resistance genes. markers for the ...

BackgroundSingle-nucleotide polymorphisms (SNPs) are the most abundant type of DNA sequence polymorphisms. Their higher availability and stability when compared to simple sequence repeats (SSRs) provide enhanced possibilities for genetic and breeding applications such as cultivar identification, construction of genetic maps, the assessment of genetic diversity, the detection of genotype/phenotype associations, or marker-assisted breeding. In addition, the efficiency of these activities can be improved thanks to the ease with which SNP genotyping can be automated. Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative sequence polymorphisms within and among a reduced number of cultivars. In parallel, the sequence of the grapevine cultivar Pinot Noir is also providing thousands of polymorphisms present in this highly heterozygous genome. Still the general application of those SNPs requires further validation since their use could be restricted to those specific genotypes.ResultsIn order to develop a large SNP set of wide application in grapevine we followed a systematic re-sequencing approach in a group of 11 grape genotypes corresponding to ancient unrelated cultivars as well as wild plants. Using this approach, we have sequenced 230 gene fragments, what represents the analysis of over 1 Mb of grape DNA sequence. This analysis has allowed the discovery of 1573 SNPs with an average of one SNP every 64 bp (one SNP every 47 bp in non-coding regions and every 69 bp in coding regions). Nucleotide diversity in grape (π = 0.0051) was found to be similar to values observed in highly polymorphic plant species such as maize. The average number of haplotypes per gene sequence was estimated as six, with three haplotypes representing over 83% of the analyzed sequences. Short-range linkage disequilibrium (LD) studies within the analyzed sequences indicate the existence of a rapid decay of LD within the selected grapevine genotypes. To validate the use of the detected polymorphisms in genetic mapping, cultivar identification and genetic diversity studies we have used the SNPlex™ genotyping technology in a sample of grapevine genotypes and segregating progenies.ConclusionThese results provide accurate values for nucleotide diversity in coding sequences and a first estimate of short-range LD in grapevine. Using SNPlex™ genotyping we have shown the application of a set of discovered SNPs as molecular markers for cultivar identification, linkage mapping and genetic diversity studies. Thus, the combination a highly efficient re-sequencing approach and the SNPlex™ high throughput genotyping technology provide a powerful tool for grapevine genetic analysis.

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.