Analysis of SSRs derived from grape ESTs

Scott, Keith G.; Eggler, Peter; Seaton, G. G. R.; Rossetto, Maurizio; Ablett, Effie M; Lee, L. S.; Henry, Robert J

doi:10.1007/s001220051344

Cited by 495 publications

(367 citation statements)

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“…For example, Scott et al (2000) tested the transferability of 10 Vitis EST-SSRs among grape cultivars, other grape species and related genera, and found high levels of transferability, with over 60% of markers tested working across taxa. Moreover, all of the transferable markers proved to be polymorphic at the level of cultivars, Vitis species and between related genera.…”

Section: Jr Ellis and Jm Burkementioning

confidence: 99%

EST-SSRs as a resource for population genetic analyses

2007

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Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

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Section: Jr Ellis and Jm Burkementioning

confidence: 99%

EST-SSRs as a resource for population genetic analyses

2007

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“…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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“…Some ESTs contain di-and trinucleotide-repeat motifs, making EST collections a potential source of microsatellite markers. The use of ESTs as a source of SSRs has been reported in a number of crop species including rice (Cho et al 2000), grape (Scott et al 2000), barley (Kota et al 2001), sugarcane (Cordeiro et al 2001), and wheat (Eujayl et al 2002).…”

Section: Introductionmentioning

confidence: 99%