SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development

Thiel, Thomas; Kota, Raja; Große, Ivo; Stein, Nils; Graner, Andreas

doi:10.1093/nar/gnh006

Cited by 179 publications

(114 citation statements)

References 11 publications

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“…New CAPS markers were developed by comparing the original length with CAPS length, using SNP2CAPS software [44]. PCR products of CAPS and Indel markers were separated on 1-2% agarose gels.…”

Section: Dna Preparation Pcr Protocol and Dna Marker Analysismentioning

confidence: 99%

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

et al. 2008

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Section: Dna Preparation Pcr Protocol and Dna Marker Analysismentioning

confidence: 99%

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

et al. 2008

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“…de/snp2caps/; Thiel et al 2004), which employs the REBASE database (version 304, March 24, 2003), containing the recognition sequences of 235 non-isoschizomeric and commercially available restriction enzymes. Potentially informative restriction enzymes were validated in vitro, following methods detailed elsewhere (Thiel et al 2004). …”

Section: Conversion Into Cleaved Amplified Polymorphic Sequencesmentioning

confidence: 99%

Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies

et al. 2007

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To elucidate the potential of single nucleotide polymorphism (SNP) markers in rye, a set of 48 barley EST (expressed sequence tag) primer pairs was employed to amplify from DNA prepared from five rye inbred lines. A total of 96 SNPs and 26 indels (insertion-deletions) were defined from the sequences of 14 of the resulting amplicons, giving an estimated frequency of 1 SNP per 58 bp and 1 indel per 214 bp in the rye transcriptome. A mean of 3.4 haplotypes per marker with a mean expected heterozygosity of 0.66 were observed. The nucleotide diversity index (p) was estimated to be in the range 0.0059-0.0530. To improve assay cost-effectiveness, 12 of the 14 SNPs were converted to a cleaved amplified polymorphic sequence (CAPS) format. The resulting 12 SNP loci mapped to chromosomes 1R, 3R, 4R, 5R, 6R, and 7R, at locations consistent with their known map positions in barley. SNP genotypic data were compared with genomic simple sequence repeat (SSR) and EST-derived SSR genotypic data collected from the same templates. This showed a broad equivalence with respect to genetic diversity between these different data types.

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“…These sequences were then aligned and assembled into contigs using BioEdit version 7.0.5.3 (Hall, 1999). SNP2CAPS was used to analyze the potential number of SNPs that could be converted to CAPS markers (Thiel et al, 2004). The SNP primers were designed by Primer3 (Rozen and Skaletsky, 2000) for consensus sequences of contigs containing SNPs with one or more restriction enzyme recognition sites.…”

Section: Development Of Snp-based Caps Markersmentioning

confidence: 99%

Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis)

et al. 2015

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ABSTRACT. The genetic evaluation of oil palm germplasm collections is required for insight into the variability among populations. The information obtained is also useful for incorporating new genetic materials into current breeding programs. Single nucleotide polymorphisms (SNPs) have been widely used in many plant genetic studies due to the availability of large numbers of genomic sequences and expressed sequence tags. The present study examined 219 oil palms collected from two natural Angolan populations, a few hundred kilometers apart. A total of 62 SNPs were designed from oil palm genomic sequences and converted to cleaved amplified polymorphic sequence (CAPS). Of these, nine were found to be informative across the two populations. The nine informative SNPs revealed mean major allele frequency of 0.693. The average expected and observed heterozygosities were 0.398 and 0.400, respectively. The mean polymorphism information content (2015) was 0.315 (ranging between 0.223 and 0.375). None of the loci deviated from Hardy-Weinberg equilibrium and no rare alleles were detected. In cluster analysis using unweighted pair group method with arithmetic, the 219 oil palms fell into two clusters. This was further supported by the population structure analysis result (K = 2), suggesting that the samples were divided into two main genetic groups. However, the two groups did not coincide with the geographic populations. Analysis of molecular variance indicated that within-population variation contributed 93% of the total genetic variation. This study showed that SNP-based CAPS markers are useful for studying the genetic diversity of oil palm and have potential application for marker-trait association studies.

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SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development

Cited by 179 publications

References 11 publications

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies

Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis)

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