ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2017
Automated tetraploid genotype calling by hierarchical clustering.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis.The plant genome · 2024Article
- Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines.Frontiers in plant science · 2024Article
- QTL identified that influence tuber length-width ratio, degree of flatness, tuber size, and specific gravity in a russet-skinned, tetraploid mapping population.Frontiers in plant science · 2024Article
- Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Molecular breeding : new strategies in plant improvement · 2023Article
- Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers.Plants (Basel, Switzerland) · 2023Article
- Identification of QTL associated with plant vine characteristics and infection response to late blight, early blight, and Verticillium wilt in a tetraploid potato population derived from late blight-resistant Palisade Russet.Frontiers in plant science · 2023Article
- Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding.Frontiers in plant science · 2023Article
- Analysis of genetic diversity and population structure among cultivated potato clones from Korea and global breeding programs.Scientific reports · 2022Article
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- Linkage and QTL mapping for tuber shape and specific gravity in a tetraploid mapping population of potato representing the russet market class.BMC plant biology · 2021Article
- Using probabilistic genotypes in linkage analysis of polyploids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived FHeredity · 2021Article
- Performing parentage analysis for polysomic inheritances based on allelic phenotypes.G3 (Bethesda, Md.) · 2021Article
- Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population.Genetics · 2020Article
- Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids.The plant genome · 2019Article
- Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Genomic Selection with Allele Dosage inG3 (Bethesda, Md.) · 2019Article
- Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction.G3 (Bethesda, Md.) · 2019Article
- FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support.BMC bioinformatics · 2019Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageNew software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall. In the training phase of the algorithm, hierarchical clustering within an F1 population is used to group samples with similar intensity values, and allele dosages are assigned to clusters based on expected segregation ratios. In the prediction phase, multiple F1 populations and the prediction set are clustered together, and the genotype for each cluster is the mode of the training set samples. A concordance metric, defined as the proportion of training set samples equal to the mode, can be used to eliminate unreliable markers and compare different algorithms. Across three potato families genotyped with an 8K SNP array, ClusterCall scored 5729 markers with at least 0.95 concordance (94.6% of its total), compared to 5325 with the software fitTetra (82.5% of its total). The three families were used to predict genotypes for 5218 SNPs in the SolCAP diversity panel, compared with 3521 SNPs in a previous study in which genotypes were called manually. One of the additional markers produced a significant association for vine maturity near a well-known causal locus on chromosome 5. In conclusion, when multiple F1 populations are available, ClusterCall is an efficient method for accurate, autotetraploid genotype calling that enables the use of SNP data for research and plant breeding.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.