Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

Neigenfind, Jost; Gyetvai, Gabor; Basekow, Rico; Diehl, Svenja; Achenbach, U.; Gebhardt, Christiane; Selbig, Joachim; Kersten, Birgit

doi:10.1186/1471-2164-9-356

Cited by 42 publications

(47 citation statements)

References 23 publications

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“…The SNP markers are unphased and the SNP allele dosage has to be considered in haplotype models (J. NeigenWnd et al 2008). Instead of haplotype models we used the strong LD observed among several SNPs to distinguish six LD groups, which included the SNPs associated with nematode resistance.…”

Section: Discussionmentioning

confidence: 99%

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

et al. 2008

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The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida conWrmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-Wve SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identiWed. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.Communicated by J. E. Bradshaw. Electronic supplementary materialThe online version of this article

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Section: Discussionmentioning

confidence: 99%

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

et al. 2008

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“…We have studied the decision version of HIPPG and presented it in ASP. We have tested HAPLO-ASP on some real data for cultivated potato genes (described in [11]), and obtained promising results as in [9].…”

Section: Other Variations Of Haplotype Inferencementioning

confidence: 99%

“…HIPAG has been studied by [7] with a greedy algorithm (HAPLO-IHP); [9] studies a variation of HIPAG for polyallelic and polyploid genotypes but does not take into account domain-specific information, and computes a solution using a SAT-based algorithm (SATLOTYPER).…”

Section: Introductionmentioning

confidence: 99%

HAPLO-ASP: Haplotype Inference Using Answer Set Programming

Erdem

Ture

2009

Logic Programming and Nonmonotonic Reasoning

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Abstract. Identifying maternal and paternal inheritance is essential to be able to find the set of genes responsible for a particular disease. However, due to technological limitations, we have access to genotype data (genetic makeup of an individual), and determining haplotypes (genetic makeup of the parents) experimentally is a costly and time consuming procedure. With these biological motivations, we study haplotype inference-determining the haplotypes that form a given set of genotypes-using Answer Set Programming; we call our approach HAPLO-ASP. This note summarizes the range of problems that can be handled by HAPLO-ASP, and its applicability and effectiveness on real data in comparison with the other existing approaches.

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“…Multi-SNP haplotypes can be assembled from single dosage-scored SNPs (originating from SNP array data), although haplotypes are more commonly generated using overlapping sequence reads (Figure 2). A number of different polyploid haplotyping tools (for sequence reads) have been developed in recent years, including polyHap (Su et al, 2008), SATlotyper (Neigenfind et al, 2008), HapCompass (Aguiar and Istrail, 2013), HapTree (Berger et al, 2014), SDhaP (Das and Vikalo, 2015), SHEsisplus (Shen et al, 2016) and TriPoly (Motazedi et al, 2017a). Three of these tools (HapCompass, HapTree and SDhaP) were recently compared and evaluated over a range of different simulated read depths, ploidy levels and insert sizes for paired-end reads (Motazedi et al, 2017b).…”

Section: Haplotype Assemblymentioning

confidence: 99%

Genetic mapping in polyploids

Bourke¹

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Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

Cited by 42 publications

References 23 publications

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

HAPLO-ASP: Haplotype Inference Using Answer Set Programming

Genetic mapping in polyploids

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