A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine (Vitis viniferaL.) Anchoring Pinot Noir Bacterial Artificial Chromosome Contigs

Abstract

The construction of a dense genetic map for Vitis vinifera and its anchoring to a BAC-based physical map is described: it includes 994 loci mapped onto 19 linkage groups, corresponding to the basic chromosome number of Vitis. Spanning 1245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 single-nucleotide polymorphism (SNP)-based genetic markers, 132 simple sequence repeats (SSRs), and 379 AFLP markers in a mapping population of 94 F 1 individuals derived from a V. vinifera cross of the cultivars Syrah and Pinot Noir. Of these markers, 623 were anchored to 367 contigs that are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. On the basis of contigs containing two or more genetically mapped markers, region-dependent estimations of physical and recombinational distances are presented. The markers used in this study include 118 SSRs common to an integrated map derived from five segregating populations of V. vinifera. The positions of these SSR markers in the two maps are conserved across all Vitis linkage groups. The addition of SNP-based markers introduces polymorphisms that are easy to database, are useful for evolutionary studies, and significantly increase the density of the map. The map provides the most comprehensive view of the Vitis genome reported to date and will be relevant for future studies on structural and functional genomics and genetic improvement.

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

“…This is higher than that reported by Troggio et al (2007) and Grando et al (2003), but lower than the 40 % reported by Riaz et al (2011). One region of distortion that stood out was chromosome 15 where all 13 markers showed significant segregation distortion as previously reported for 'Regent' in this region by Welter et al (2007).…”

“…Additional to this major locus, two minor loci were identified on chromosomes 5 and 20, but were not assigned specific names. Several genetic maps have been constructed for grapevine (Dalbó et al 2000;Doligez et al 2002;Grando et al 2003;Adam-Blondon et al 2004;Fischer et al 2004;Riaz et al 2004;Doligez et al 2006;Lowe and Walker 2006;Di Gaspero et al 2007;Troggio et al 2007;Welter et al 2007;Vezzulli et al 2008;Bellin et al 2009;Marguerit et al 2009;Moreira et al 2011;Blasi et al 2011;Blanc et al 2012). The first maps were constructed using mainly AFLP and RAPD markers.…”

A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution

“…In the two latter systems, microsatellite markers developed in closely related domestic animals could be used across species. In sticklebacks, anonymous, species-specific microsatellites were used and random approaches for map development have also included the use of microsatellites, RAPD, or AFLP markers in a number of other species (Reid et al 2007;Troggio et al 2007).The development of the collared flycatcher map represents an application of a new approach to genetic mapping in natural populations. For several reasons, it benefited from an earlier systematic effort to develop a set of conserved reference markers evenly spread across the avian genome (Backström et al 2008).…”

Development of highly polymorphic EST-SSR markers and segregation in F1 hybrid population of Vitis vinifera L.

“…In fact, marker applications to assist breeding are reported both for herbaceous (Huang et al, 1996) and woody plants (Gianfranceschi et al, 1994;Akkurt et al, 2007). In plants, genetic markers provide the framework in breeding programs via marker-assisted selection (Mazur and Tingey, 1995), map-based cloning (Tanksley et al, 1995), and anchoring physical maps (Mun et al, 2006;Troggio et al, 2007). Among the wood plants, poplar (Populus trichocarpa Torr.…”

“…Owing to their quality of following clear Mendelian inheritance, they can provide an anchor or reference point for specific regions of the genome. SSRs are extremely useful for the detection of polymorphisms between closely related genotypes (Sprague, 1966;Paterson et al, 1991;Troggio et al, 2007). With this background knowledge, the present study was undertaken with the following objectives: 1) to develop and validate EST-SSR markers from large EST sequences, and 2) to study the segregation ratio and distribution of SSRs within two grape vine parental lines.…”