ArticleGenetics2021
Haplotype reconstruction in connected tetraploid F1 populations.
Article in Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 48 citations in OpenAlex.
- Article
- Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy.The plant genome · 2025Article
- A low-cost dpMIG-seq method for elucidating complex inheritance in polysomic crops: a case study in tetraploid blueberry.Horticulture research · 2024Article
- Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.The plant genome · 2024Article
- Molecular breeding of flower load related traits in dioecious autotetraploidMolecular breeding : new strategies in plant improvement · 2024Article
- Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding.The plant genome · 2023Article
- Meta-Analysis of Rose Rosette Disease-Resistant Quantitative Trait Loci and a Search for Candidate Genes.Pathogens (Basel, Switzerland) · 2023Article
- QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations.Frontiers in plant science · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- The genetic architectures of vine and skin maturity in tetraploid potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations.Frontiers in plant science · 2022Article
- Article
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- Understanding the Effectiveness of Genomic Prediction in Tetraploid Potato.Frontiers in plant science · 2021Article
- Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map.Frontiers in plant science · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In diploid species, many multiparental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase the power of QTL detection in comparison with the marker-based association analysis. However, such software tools for polyploid species are few and limited to a single biparental F1 population. In this study, a statistical framework for haplotype reconstruction has been developed and implemented in the software PolyOrigin for connected tetraploid F1 populations with shared parents, regardless of the number of parents or mating design. Given a genetic or physical map of markers, PolyOrigin first phases parental genotypes, then refines the input marker map, and finally reconstructs offspring haplotypes. PolyOrigin can utilize single nucleotide polymorphism (SNP) data coming from arrays or from sequence-based genotyping; in the latter case, bi-allelic read counts can be used (and are preferred) as input data to minimize the influence of genotype calling errors at low depth. With extensive simulation we show that PolyOrigin is robust to the errors in the input genotypic data and marker map. It works well for various population designs with ≥30 offspring per parent and for sequences with read depth as low as 10x. PolyOrigin was further evaluated using an autotetraploid potato dataset with a 3 × 3 half-diallel mating design. In conclusion, PolyOrigin opens up exciting new possibilities for haplotype analysis in tetraploid breeding populations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.