Single-reaction for SNP Genotyping on Agarose Gel by Allele-specific PCR in Black Poplar (Populus nigra L.)

Gaudet, Muriel; Fara, Anna-Giulia; Sabatti, Maurizio; Kuzminsky, Elena; Mugnozza, Giuseppe Scarascia

doi:10.1007/s11105-007-0003-6

Cited by 39 publications

(22 citation statements)

References 28 publications

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“…Gaudet et al (2008) have reported the construction of a genetic map using three SNPs together with other markers (AFLP and SSR). A new method for SNP genotyping has also been developed for this species (Gaudet et al 2007). However, patterns of DNA sequence variation at nuclear genes are still largely unknown, and SNP-based association studies have not been systematically performed in P. nigra.…”

Section: Introductionmentioning

confidence: 99%

Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms

Chu

Huang

et al. 2009

Genetica

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Black poplar (Populus nigra L.) is an economically and ecologically important tree species and an ideal organism for studies of genetic variation. In the present work, we use a candidate gene approach to infer the patterns of DNA variation in natural populations of this species. A total of 312 single nucleotide polymorphisms (SNPs) are found among 8,056 bp sequenced from nine drought-adaptation and photosynthesis-related gene loci. The median SNP frequency is one site per 26 bp. The average nucleotide diversity is calculated to be theta(W) = 0.01074 and pi(T) = 0.00702, higher values than those observed in P. tremula, P. trichocarpa and most conifer species. Tests of neutrality for each gene reveal a general excess of low-frequency mutations, a greater number of haplotypes than expected and an excess of high-frequency derived variants in P. nigra, which is consistent with previous findings that genetic hitchhiking has occurred in this species. Linkage disequilibrium is low, decaying rapidly from 0.45 to 0.20 or less within a distance of 300 bp, although the declines of r(2) are variable among different loci. This is similar to the rate of decay reported in most other tree species. Our dataset is expected to enhance understanding of how evolutionary forces shape genetic variation, and it will contribute to molecular breeding in black poplar.

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Section: Introductionmentioning

confidence: 99%

Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms

Chu

Huang

et al. 2009

Genetica

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“…The matrix is usually a gel, which allows migration of the markers under an applied voltage. Most early methods used polyacrylamide (PA) gel, but it is cumbersome to prepare, toxic, and costly; therefore, simpler, cheaper, and non-toxic agarose, from seaweed has been preferred for many applications (White and Kusukawa, 1997;Guilliatt, 2002;Gaudet et al, 2007;Eschholz et al, 2008;Raji et al, 2009). However, the lower separation capacity of the latter, usually for size differences of <4 bp, is a drawback in some applications (Perumal et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Recycling of superfine resolution agarose gel

Seng¹,

Singh²,

Faridah³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Genetic markers are now routinely used in a wide range of applications, from forensic DNA analysis to marker-assisted plant and animal breeding. The usual practice in such work is to extract the DNA, prime the markers of interest, and sift them out by electrically driving them through an appropriate matrix, usually a gel. The gels, made from polyacrylamide or agarose, are of high cost, limiting their greater applications in molecular marker work, especially in developing countries where such technology has great potential. Trials using superfine resolution (SFR) agarose for SSR marker screening showed that it is capable of resolving SSR loci and can be reused up to 14 times, thus greatly reducing the cost of each gel run. Furthermore, for certain applications, low concentrations of agarose sufficed and switching to lithium borate buffer, instead of the conventional Trisborate-ethylenediaminetetraacetic acid buffer, will further save time and cost. The 2.5% gel was prepared following the Agarose SFR TM

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“…Ten SNP loci were selected for the test of genetic diversity in three populations of common carp (108 individuals in total) in China, specifically, 36 from the southern Dongting Lake; 36 from Hongze Lake; and 36 from the Yellow River. PCR-SSCP (Tong et al 2002) and FLDAS-PCR (Gaudet et al 2007) were used for genotyping (Table S1). Minor allele frequency (MAF), observed heterozygosity (H o ), expected heterozygosity (H e ), and F is (inbreeding coefficient) for each locus were calculated using Popgene version 1.32 (Yeh et al 2000) (Table 1).…”

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Isolation and characterization of single nucleotide polymorphisms in the common carp (Cyprinus carpio L.) genome

Liu

Zhu

et al. 2012

Conservation Genet Resour

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In this study, we constructed a genomic library to identify a set of new SNPs from the common carp (Cyprinus carpio L.) genome. Putative SNPs were validated by amplification of 41 fragments from the library using unrelated individuals. A total of 211 SNPs, 18 Indels and 6 microsatellites were identified from a total length of 18,244 bp genomic sequences. A/G was the most common substitution, and the ratio of transitions to transversions was 2.3:1. Ten validated SNPs were selected for genetic diversity analysis in three wild populations of common carp, and all loci were polymorphic, with the average observed (H o ) and expected (H e ) heterozygosities were 0.2154 and 0.3321, respectively. These new SNPs would be good resources for population genetics, parentage analysis and conservation genetics in common carp.Keywords Cyprinus carpio L. Á Single nucleotide polymorphisms (SNPs) Á Validation Á Genetic diversityAs an important aquaculture species, common carp (Cyprinus carpio L.) has been domesticated for about 4,000 years, and widely distributed from Asia to Europe with huge number of varieties, strains or breeds. During the past decades, owing to habitat degradation, commercial overexploitation and water pollution, population resources of common carp have declined in China leading to the sharp reduction of natural fisheries in the rivers and lakes. Genetic variations of common carp populations, varieties or strains worldwide have been extensively studied using such molecular markers as mitochondrial DNA, AFLP and microsatellite DNA. Single nucleotide polymorphisms (SNPs) are the most abundant DNA variation in the vertebrate genome, and this type of marker is increasingly important in population genetics, linkage analysis and genome-wide association studies (Elahi et al. 2004). Nowadays, only a limited number of SNPs from expressed sequence tags (ESTs) were identified and utilized in the common carp (Kongchum et al. 2010;Zheng et al. 2011). SNPs discovery on a large scale throughout the entire genome was not reported for this species. In this study, we isolated and characterized a set of new SNPs in common carp for further genetics and conservation studies.An SNP-enriched genomic library was constructed for common carp, primarily following the method described by Xu et al. (2009). DNA from ten unrelated individuals from the Yangtze River was mixed equally as a DNA pool and was digested with MseI. The fragmented DNAs were ligated to specific adapters (5 0 -TACTCAGGACTCAT-3 0 / 5 0 -GACGATGAGTCCTGAG-3 0 ). Ligated fragments were amplified with MseI adaptors pecific primers. Heteroduplex of PCR products, formed by denaturation and annealing, was digested by CEL I nuclease and elongated by Bst. Target DNA containing SNPs were ligated into a pMD18-T vector (TaKaRa) and transformed into E. coli DH5a cells. After PCR confirmation, 50 random positive clones, ranging from 400 to 1,000 bp, were sequenced. Primer Premier 5 was used to design primers for 49 unique (Table S1) for 45 s and 72°C for 1 min, with last el...

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Single-reaction for SNP Genotyping on Agarose Gel by Allele-specific PCR in Black Poplar (Populus nigra L.)

Cited by 39 publications

References 28 publications

Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms

Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms

Recycling of superfine resolution agarose gel

Isolation and characterization of single nucleotide polymorphisms in the common carp (Cyprinus carpio L.) genome

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