PERGOLA: fast and deterministic linkage mapping of polyploids

BMC Bioinformatics

Methodology Article

Dirk Metzler¹  Soumya Ranganathan¹  Nikkie van Bers²  Jorn R. de Haan²  Fabian Grandke³ 

[1] Fakultät für Biologie, University of Munich (LMU), Munich, Germany;Genetwister Technologies B.V., Wageningen, The Netherlands;Genetwister Technologies B.V., Wageningen, The Netherlands;Fakultät für Biologie, University of Munich (LMU), Munich, Germany;

关键词: Linkage mapping;    Polyploids;    Heuristic;   

DOI  :  10.1186/s12859-016-1416-8

 received in 2016-07-22, accepted in 2016-12-09,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s) 2017

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