An integrated SSR map of grapevine based on five mapping populations

Abstract

A grapevine (mainly Vitis vinifera L., 2n = 38) composite genetic map was constructed with CarthaGene using segregation data from five full-sib populations of 46, 95, 114, 139 and 153 individuals, to determine the relative position of a large set of molecular markers. This consensus map comprised 515 loci (502 SSRs and 13 other type PCR-based markers), amplified using 439 primer pairs (426 SSRs and 13 others) with 50.1% common markers shared by at least two crosses. Out of all loci, 257, 85, 74, 69 and 30 were mapped in 1, 2, 3, 4 and 5 individual mapping populations, respectively. Marker order was generally well conserved between maps of individual populations, with only a few significant differences in the recombination rate of marker pairs between two or more populations. The total length of the integrated map was 1,647 cM Kosambi covering 19 linkage groups, with a mean distance between neighbour loci of 3.3 cM. A framework-integrated map was also built, with marker order supported by a LOD of 2.0. It included 257 loci spanning 1,485 cM Kosambi with a mean inter-locus distance of 6.2 cM over 19 linkage groups. These integrated maps are the most comprehensive SSR-based maps available so far in grapevine and will serve either for choosing markers evenly scattered over the whole genome or for selecting markers that cover particular regions of interest. The framework map is also a useful starting point for the integration of the V. vinifera physical and genetic maps.

Towards a unified genetic map for diploid roses

“…Thus for our F 1 populations, the accuracy of marker order and distance strongly depends on the population size, especially when dominant markers are used. This has previously been reported for F 2 and RIL populations (Ferreira et al 2006;Huhn and Piepho 2008 Doligez et al 2006), which means that few recombination events exist in large regions of the map, in combination with scoring errors and/or artifacts of the consensus mapping algorithm (Isobe et al 2009). Based on these experiences, we are currently increasing the number of genotyped individuals to several hundred in the populations 97/7 and HW for the sequence-based markers and some of the AFLP markers.…”

“…But the beneWts from the linkage map information remain limited by the genetic background of the population that was mapped. To overcome this restriction consensus or integrated linkage maps have been constructed for many cultivated plant species including peach (Dirlewanger et al 2004), apple (N'Diaye et al 2008, grapevine (Doligez et al 2006;Vezzulli et al 2008), soybean (Cregan et al 1999), rapeseed (Lombard and Delourme 2001), barley (Wenzl et al 2006), red clover (Isobe et al 2009), eucalyptus (Brondani et al 2006), and loblolly pine (Sewell et al 1999). Integrated maps not only increase the genome coverage but also make it possible to compare locations of major genes controlling important phenotypic traits or QTL positions between populations from multiple crosses.…”

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

“…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.…”

“…The number of markers used to construct these maps varies dramatically and ranges from as little as 84 to more than 400. The reference map by Doligez et al (2006) was constructed using 537 loci with an average intermarker distance of 3.3 cM as well as five individual mapping populations. However, between 200 and 450 markers are typically used in QTL mapping studies (Marguerit et al 2009;Moreira et al 2011;Blasi et al 2011;Blanc et al 2012).…”

“…However, between 200 and 450 markers are typically used in QTL mapping studies (Marguerit et al 2009;Moreira et al 2011;Blasi et al 2011;Blanc et al 2012). While most maps to date have been constructed for V. vinifera, Blanc et al (2012) recently published an SSR based map for M. rotundifolia that showed a high degree of similarity to the V. vinifera reference map of Doligez et al (2006). These maps were used in QTL mapping of disease resistance, leaf morphology, seedlessness, veraison, and fruit quality.…”