ArticleBMC bioinformatics2017
PERGOLA: fast and deterministic linkage mapping of polyploids.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).BMC biology · 2025Article
- Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks.Plants (Basel, Switzerland) · 2023Article
- High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content.Frontiers in plant science · 2022Article
- Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes.Frontiers in plant science · 2022Article
- Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map.Frontiers in plant science · 2021Article
- QTL Mapping for Resistance to Cankers Induced byPathogens (Basel, Switzerland) · 2020Article
- Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance.Scientific reports · 2020Article
- Preferential Disomic Segregation andFrontiers in plant science · 2020Article
- Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models.G3 (Bethesda, Md.) · 2019Article
- polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.Bioinformatics (Oxford, England) · 2018Article
- Tools for Genetic Studies in Experimental Populations of Polyploids.Frontiers in plant science · 2018Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creation for polyploid species is not supported by standard tools. We want to overcome this limitation and validate our results with simulation studies.
resultsWe developed PERGOLA, a deterministic and heuristic method that addresses this problem. We show that it creates correct linkage groups, marker orders and distances for simulated and real datasets. We compare it to existing tools and demonstrate that it overcomes limitations in ploidy and outperforms them in computational time and mapping accuracy. We represent linkage maps as dendrograms and show that this has advantages in the comparison of different maps.
conclusionsPERGOLA can be used successfully to calculate linkage maps for diploid and polyploid species and outperforms existing tools.
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