ArticleBioinformatics (Oxford, England)2021
Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Physiology and Genetics of Continuous Flowering in Plants.Plant, cell & environment · 2026Review
- Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.).G3 (Bethesda, Md.) · 2026Article
- Genomic history and ecology of local adaptation in sky-islandbioRxiv : the preprint server for biology · 2026Article
- Genome-wide association study of a Guinea grass (Megathyrsus maximus) diversity panel reveals the genetic basis of agronomic and nutritional traits.BMC plant biology · 2025Article
- Local adaptation to climate has facilitated the global invasion of cheatgrass.Nature communications · 2025Article
- QTL mapping for resistance to Pseudomonas syringae pv. actinidiae (Psa) in tetraploid Actinidia.BMC plant biology · 2025Article
- Local adaptation to climate facilitates a global invasion.bioRxiv : the preprint server for biology · 2025Article
- Haplotyped genome mapping and functional characterization of a blueberry anthocyanin acetyltransferase (AAT) controlling the accumulation of acylated anthocyanins.Journal of experimental botany · 2025Article
- Unraveling the genetic architecture of blueberry fruit quality traits: major loci control organic acid content while more complex genetic mechanisms control texture and sugar content.BMC plant biology · 2025Article
- A low-cost dpMIG-seq method for elucidating complex inheritance in polysomic crops: a case study in tetraploid blueberry.Horticulture research · 2024Article
- Article
- Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit.Plant biotechnology journal · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 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
- Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations.Frontiers in plant science · 2022Article
- High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content.Frontiers in plant science · 2022Article
- Dissecting the genetic basis of bioactive metabolites and fruit quality traits in blueberries (Frontiers in plant science · 2022Article
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationThe investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialized tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement.
resultsHere, we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualization tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. AVAILABILITYAND IMPLEMENTATION: polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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