Isolation of (AC)n-microsatellites in Vitis vinifera L. and analysis of genetic background in grapevines under marker assisted selection

Gaspero, Gabriele Di; Cipriáni, G.; Marrazzo, M. T.; Andreetta, D.; Castro, Maria Jesus Prado; Peterlunger, Enrico; Testolin, R.

doi:10.1007/s11032-004-1362-4

Cited by 82 publications

(42 citation statements)

References 27 publications

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“…Moreover, the available information is usually scarce or incomplete, since many of these markers have been developed and/or tested using only a few individuals. For example, in our PCR conditions, five UDV (Di Gaspero et al 2005), four Vitis Microsatellite Consortium (VMC), and one FAM (Huang et al 2011) SSRs amplified in several accessions more than two fragments in a narrow size interval, resulting in unreliable electrophoretic profiles. This could be related to the presence of multiple binding sites for their respective primers in the grapevine genome.…”

Section: Amplification Testsmentioning

confidence: 99%

“…This has allowed the identification of hundreds of them and the design of primers for their analysis throughout the last two decades Bowers et al 1996Bowers et al , 1999Sefc et al 1999;Scott et al 2000;Lefort et al 2002;Decroocq et al 2003;Arroyo-García and Martínez-Zapater 2004;Di Gaspero et al 2005;Merdinoglu et al 2005;Cipriani et al 2008;Huang et al 2011); up to 1,079V. vinifera SSR probes can be currently found at the NCBI database (http://www.…”

Section: Introductionmentioning

confidence: 99%

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Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Zarouri¹,

Vargas²,

Gaforio³

et al. 2015

Tree Genetics & Genomes

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The use of microsatellite markers in large-scale genetic studies is limited by its low throughput and high cost and labor requirements. Here, we provide a panel of 45 multiplex PCRs for fast and cost-efficient genome-wide fluorescencebased microsatellite analysis in grapevine. The developed multiplex PCRs panel (with up to 15-plex) enables the scoring of 270 loci covering all the grapevine genome (9 to 20 loci/chromosome) using only 45 PCRs and sequencer runs. The 45 multiplex PCRs were validated using a diverse grapevine collection of 207 accessions, selected to represent most of the cultivated Vitis vinifera genetic diversity. Particular attention was paid to quality control throughout the whole process (assay replication, null allele detection, ease of scoring). Genetic diversity summary statistics and features of electrophoretic profiles for each studied marker are provided, as are the genotypes of 25 common cultivars that could be used as references in other studies.

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Section: Amplification Testsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Zarouri¹,

Vargas²,

Gaforio³

et al. 2015

Tree Genetics & Genomes

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show abstract

“…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.…”

Section: Molecular Analysismentioning

confidence: 99%

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

et al. 2014

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One hundred and eighty six F 1 plants from a 'Regent' 9 'RedGlobe' cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of 'Regent'. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of 'Regent' in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the 'Regent'-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.

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“…We used 468 pairs of SSR primers, including the VMC series, the VVS series (Thomas and Scott, 1993), the VVMD series (Bowers et al, 1996(Bowers et al, , 1999, the VrZAG series (Sefc et al, 1999), the VVI series (Merdinoglu et al, 2005), the UDV series (Di Gaspero et al, 2005), the Chr series (Blasi et al, 2011), and the VLG series, which were obtained from genomic sequence information. The PCR volume was 16 μL, which contained 10 ng DNA, 2.0 mM Mg 2+ , 100 μM dNTPs, 0.3 μM primer, 0.8 U Taq DNA polymerase, and 1X PCR buffer.…”

Section: Ssr Primers and Polymerase Chain Reaction (Pcr) Amplificationmentioning

confidence: 99%

Quantitative trait locus analysis of grape weight and soluble solid content

Zhao¹,

Guo²,

Lin³

et al. 2015

Genet. Mol. Res.

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ABSTRACT.A grapevine hybrid population was derived from a crossing of the early-maturing female parent cultivar '87-1' and the late-maturing male parent cultivar '9-22'. A total of 149 plants were selected from the hybrid population as the mapping population, and after sequencerelated amplified polymorphism and simple-sequence repeat marker analysis were conducted we constructed molecular genetic maps of the parents. The molecular linkage map of '87-1' had 19 linkage groups that contained 188 markers, with an average interval of 5.7 cM and a total distance of 1074.5 cM; the '9-22' map had 19 linkage groups that contained 175 markers, with an average interval of 7.8 cM and a total distance of 1100.2 cM. The molecular linkage map of both parents had 19 linkage groups that contained 251 markers, with an average interval of 5.0 cM and a total distance of 1264.2 cM. We used the interval mapping method to conduct a quantitative trait locus (QTL) analysis 9873 QTL analysis of grape weight and soluble solid content ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (3): 9872-9881 (2015) of grape weight and soluble solid content of the mapping population. Six QTLs were related to grape weight, and the average contribution to the phenotypic variance was between 11.3 and 33.0%. Seven QTLs were related to soluble solid content, and the average contribution to the phenotypic variance was between 15.7 and 55.8%.

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Isolation of (AC)n-microsatellites in Vitis vinifera L. and analysis of genetic background in grapevines under marker assisted selection

Cited by 82 publications

References 27 publications

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

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

Quantitative trait locus analysis of grape weight and soluble solid content

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