Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history

Vos, Peter G.; Uitdewilligen, Jan G. A. M. L.; Voorrips, Roeland E.; Visser, R.G.F.; Eck, Herman J. van

doi:10.1007/s00122-015-2593-y

Cited by 178 publications

(250 citation statements)

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“…The genetic positions of markers were compared with their physical positions, as defined in Vos et al (2015). It was found that some markers did not map to the same chromosome as expected from the physical map; a list of such markers is included in Supporting Information, Table S1.…”

Section: Comparison Of Genetic and Physical Mapsmentioning

confidence: 99%

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

“…An example of the four homolog maps of chromosome 1 in parent 2 is shown in Figure 1. In total, 30 mapped markers were found to have a discrepancy between their assignment to a linkage group in this population and their assigned chromosome on the physical sequence (Felcher et al 2012;Vos et al 2015). Of these, two SolCAP markers (solcap_snp_c2_42265 and solcap_snp_c2_32337) were found to have positions at two physical locations but mapped to a single genetic position.…”

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confidence: 93%

“…The concentration of DNA was measured using a NanoDrop ND-1000 Spectrophotometer (Thermo Scientific), and the DNA concentration was adjusted to 50 ng/ml (Vos et al 2015). For DNA concentrations in the range of 25-50 ng/ml, the sample also was used; samples having concentrations lower than 25 ng/ml were discarded, and DNA isolation was performed again.The samples were genotyped on the SolSTW Infinium SNP array, which assayed 17,987 SNPs, as described by Vos et al (2015). Of these SNPs, 4179 also form part of the SolCap SNP array (Felcher et al 2012).…”

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confidence: 99%

“…Of these, two SolCAP markers (solcap_snp_c2_42265 and solcap_snp_c2_32337) were found to have positions at two physical locations but mapped to a single genetic position. A further 25 mapped markers were found to have an unknown physical position from the published data sets of marker positions (Felcher et al 2012;Vos et al 2015). We provide a list of these markers with their mapped positions in Table S1.…”

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confidence: 99%

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The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map

et al. 2015

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The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.KEYWORDS linkage mapping; tetraploid; double reduction; potato; multivalents P OLYPLOID species constitute a very important group among cultivated crops. Polyploids themselves can be further divided into auto-and allopolyploids, with autopolyploids showing random association between homologous chromosomes and allopolyploids showing nonrandom or preferential pairing during meiosis. Linkage mapping in autopolyploid species remains a challenging exercise despite recent advances in genotyping technology and mapping methodology. Breeding work in many autopolyploid crops has yet to benefit from the use of markers in breeding programs. This is partly due to the lack of software to perform linkage mapping and QTL analysis in polyploids but is also due to the complicated nature of autopolyploid genomes and genetics. The software program TetraploidMap (Hackett and Luo 2003) is a notable exception to this but is constrained by the relatively low numbers of markers it can handle (currently 800 is the maximum) and the need to manually assign marker phase, which may become infeasible with large data sets.One autopolyploid species in which large advances in genetic analysis have been made is tetraploid potato (Solanum tuberosum L.), in terms of the availability of a high-quality reference sequence (Potato Genome Sequencing Consortium 2011), many published linkage maps (Meyer et al. 1998;van Os et al. 2006;Felcher et al. 2012;Hackett et al. 2013) as well as methods for performing linkage mapping at the polyploid level (Luo et al. 2001;Bradshaw et al. 2004;Hackett et al. 2013). In comparison with other economically important autotetraploid species such as alfalfa, rose, and leek, the pairing behavior of potato is thought to be relatively well understo...

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Section: Comparison Of Genetic and Physical Mapsmentioning

confidence: 99%

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

mentioning

confidence: 93%

mentioning

confidence: 99%

mentioning

confidence: 99%

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