ArticleGenetics2016
Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 61 citations in OpenAlex.
- Haplotyped genome mapping and functional characterization of a blueberry anthocyanin acetyltransferase (AAT) controlling the accumulation of acylated anthocyanins.Journal of experimental botany · 2025Article
- Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum).The New phytologist · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- There and back again; historical perspective and future directions forHorticulture research · 2022Article
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- Article
- Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty.Heredity · 2021Article
- A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species.The New phytologist · 2021Article
- HICANCER: accurate and complete cancer genome phasing with Hi-C reads.Scientific reports · 2021Article
- A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses.Frontiers in plant science · 2021Article
- Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.G3 (Bethesda, Md.) · 2020Article
- QTL Mapping for Resistance to Cankers Induced byPathogens (Basel, Switzerland) · 2020Article
- Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations.Nature genetics · 2020Article
- Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population.Genetics · 2020Article
- Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping.G3 (Bethesda, Md.) · 2020Article
- Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids.The plant genome · 2019Article
- Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models.G3 (Bethesda, Md.) · 2019Article
- Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models.G3 (Bethesda, Md.) · 2019Article
- Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato.Euphytica: Netherlands journal of plant breeding · 2019Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For both plant (e.g., potato) and animal (e.g., salmon) species, unveiling the genetic architecture of complex traits is key to the genetic improvement of polyploids in agriculture. F1 progenies of a biparental cross are often used for quantitative trait loci (QTL) mapping in outcrossing polyploids, where haplotype reconstruction by identifying the parental origins of marker alleles is necessary. In this paper, we build a novel and integrated statistical framework for multilocus haplotype reconstruction in a full-sib tetraploid family from biallelic marker dosage data collected from single-nucleotide polymorphism (SNP) arrays or next-generation sequencing technology given a genetic linkage map. Compared to diploids, in tetraploids, additional complexity needs to be addressed, including double reduction and possible preferential pairing of chromosomes. We divide haplotype reconstruction into two stages: parental linkage phasing for reconstructing the most probable parental haplotypes and ancestral inference for probabilistically reconstructing the offspring haplotypes conditional on the reconstructed parental haplotypes. The simulation studies and the application to real data from potato show that the parental linkage phasing is robust to, and that the subsequent ancestral inference is accurate for, complex chromosome pairing behaviors during meiosis, various marker segregation types, erroneous genetic maps except for long-range disturbances of marker ordering, various amounts of offspring dosage errors (up to ∼20%), and various fractions of missing data in parents and offspring dosages.
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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.