Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics

Abstract

The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome (n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals (S x G population), successfully amplifying 310 markers. Of these, 88.4% markers were heterozygous for at least one of the two parents. A total of 292 primer pairs were then tested on Riesling, the parent of the RS1 population derived from selfing (96 individuals), successfully amplifying 299 markers among which 207 (62.9%) were heterozygous. Only 6.7% of the markers were homozygous in all three genotypes, stressing the interest of such markers in grape genetics. Four maps were constructed based on the segregation of 245 SSR markers in the two populations. The Syrah map was constructed from the segregations of 177 markers that could be ordered into 19 linkage groups (total length 1,172.2 cM). The Grenache map was constructed with the segregations of 178 markers that could be ordered into 18 linkage groups (total length 1,360.6 cM). The consensus S x G map was constructed with the segregations of 220 markers that were ordered into 19 linkage groups (total length 1,406.1 cM). One hundred and eleven markers were scored on the RS1 population, among them 27 that were not mapped using the S x G map. Out of these 111 markers, 110 allowed to us to construct a map of a total length of 1,191.7 cM. Using these four maps, the genome length of V. vinifera was estimated to be around 2,200 cM. The present work allowed us to map 123 new SSR markers on the V. vinifera genome that had not been ordered in a previous SSR-based map (Riaz et al. 2004), representing an average of 6.5 new markers per linkage group. Any new SSR marker mapped is of great potential usefulness for many applications such as the transfer of well-scattered markers to other maps for QTL detection, the use of markers in specific regions for the fine mapping of genes/QTL, or for the choice of markers for MAS.

Breeding of fungal resistant varieties derived from Grüner Veltliner by chromosomal selection

“…Chromosome 2 is even stable and with 6 SSR markers heritage of chromosomes could be confirmed. OIV 68 is linked to the chromosome and from literature it is known that berry skin color is also coded there [9]. We observed only white berried bunches and could not observe any segregation.…”

“…While AFLP and SNP markers are more abundant in the genome [7] SSR markers are the better choice to anchor an allele [8]. Simple sequence repeat (SSR) markers are more stable than others, they are inherited codominantly and a huge amount of them is already attributed to a chromosome within a linkage group [9,10]. Some of them were already used successfully for marker assisted selection in the grapevine breeding process.…”

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.…”

“…Extracted DNA was quantified using a Nanodrop spectrophotometer and the concentrations were standardised to fall within the range 25-35 ng/ll. SSRs were selected from the literature and the NCBI database (Thomas and Scott 1993;Bowers et al 1996Bowers et al , 1999Scott et al 2000;Decroocq et al 2003;Adam-Blondon et al 2004;Di Gaspero et al 2005;Merdinoglu et al 2005;Doligez et al 2006;Cipriani et al 2008; http://www.ncbi.nlm.nih.gov/) with the aim to achieve comprehensive genome coverage and increased marker density for known minor and major mildew resistance QTL regions on chromosomes 5, 12, 15 and 18. A standard set of PCR conditions (1.8 mM MgCl 2 , 0.75 U Supertherm Taq, 5 mM dNTP and 0.3 pmol/ll of each primer) was used for all reactions.…”

“…The TMAP map was split using the 'split' option in the 'BuilderSplit' programme. The linkage groups were numbered according to the reference V. vinifera map (Adam-Blondon et al 2004). …”