Transcriptome versus Genomic Microsatellite Markers: Highly Informative Multiplexes for Genotyping Abies alba Mill. and Congeneric Species

Postolache, Dragoș; Leonarduzzi, Cristina; Piotti, Andrea; Spanu, Ilaria; Roig, Anne; Fady, Bruno; Roschanski, Anna M.; Liepelt, Sascha; Vendramin, Giovanni G.

doi:10.1007/s11105-013-0688-7

Cited by 65 publications

(58 citation statements)

References 61 publications

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“…These strategies allow to simultaneously amplify more than one locus in a single reaction using multiple primer pairs. Multiplex PCR protocols have been developed and successfully applied for different uses in many species, such as the detection of colorectal tumors in humans (Patil et al 2012), monitoring of rat strains (Bryda and Riley 2008), genetic characterization of different plant species (Jewell et al 2010;Postolache et al 2013;Drašnarová et al 2014), identification of selfed progenies in switchgrass (Liu and Wu 2012), or to facilitate systematic and rapid genetic mapping in soybean (Sayama et al 2011). Multiplex PCR design requires a priori knowledge of the range of allelic sizes for each marker in order to avoid amplicons overlapping and the optimization of PCR conditions to obtain a balanced amplification of all the targeted fragments (Butler 2005a).…”

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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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: 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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“…The ratio of polymorphic primers (16.1 %) is also as low as some typical coniferous trees(Postolache et al 2014). The coniferous trees with huge genomes have a very high content of repetitive DNA, such as transposable elements, which may lead to the low polymorphism rate(Kovach et al 2010;Wagner et al 2012).…”

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confidence: 99%

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

et al. 2015

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Taxodium 'zhongshansa', an extremely floodtolerant tree species, has been widely planted in eastern China due to its environmental attributes. Although much progress has been made in understanding its physiological response to flooding stress, as well as its rapid propagation and variety selection, little is known regarding its molecular genetics due primarily to a lack of reliable molecular markers. In this paper, 108,692 expressed sequence tags (ESTs) with a total size of 69.3 Mb derived from T. 'zhongshansa' were analyzed. And 10,038 simple sequence repeat (SSR) loci were identified from 8137 SSR-containing EST sequences. The average SSR frequency in the transcriptome was one in 6.90 kb of EST sequences. The most abundant repeat type was mononucleotide (6581, 65.56 %), followed by trinucleotide (2246, 22.37 %) and dinucleotide (1080, 10.76 %). After filtering unqualified SSR loci, loci with mononucleotide repeats and compound SSRs, 1958 EST-SSR loci were selected to design SSR makers. To validate this set of SSR markers, 503 primer pairs were randomly selected to amplify across 12 genomic DNA templates from three Taxodium species. Two hundred fifty-seven (51.09 %) out of 503 primer pairs amplified the expected products, of which 81 and 176 could amplify polymorphic and monomorphic bands, respectively. The functional categorization of EST sequences containing randomly selected markers revealed that 264 (52.49 %) had homology with known proteins. This set of EST-SSR markers will provide a valuable genetic and genomic tool for further genetic research in Taxodium, such as genetic map construction, quantitative trait loci mapping, and marker assisted selection.

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“…The highest number of alleles was found in locus SF78 (32) and the minimum in loci SF239 and SF333 (8, see Table I). A recent survey on 192 silver fir individuals from northern and southern Italy, Romania and Bulgaria found 25 alleles at locus SFb4 with an observed and expected heterozygosity of 0.667 and 0.865, respectively (Postolache et al 2014). A previous study on 17 individuals mainly from central Europe (Cremer et al 2006) found only five alleles for the same locus, with an observed heterozygosity of 0.294.…”

Section: Resultsmentioning

confidence: 95%