High-throughput genotyping of unknown genomic terrain in complex plant genomes: lessons from a case study
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Novel high-throughput genotyping technologies have facilitated rapid genotyping of single nucleotide polymorphisms in non-model organisms. Most plant species have complex genomes with a large proportion of their genes having one or more paralogous copies due to single gene duplications and ancient or recent polyploidization events. These paralogous gene copies are potential sources of genotyping errors, and hence genotyping of plant genomes is inherently difficult. Here we present a case study that exemplifies paralog-related problems in high-throughput genotyping of plant genomes. We used the MassARRAY genotyping platform to genotype the LpIRI locus in L. perenne populations; this gene is thought to be involved in low-temperature stress tolerance. The dissection of the molecular genetics underlying the genotyping results provides a good example of how unknown paralogs can mask the true genotype of the locus, instructive to the non-specialist plant researcher and breeder.
KeywordsGenotyping error Paralogs Plant MassARRAY
We thank Kjetil Fosnes for technical assistance, and Odd-Arne Olsen, Torben Asp, and reviewers for valuable comments on the manuscript. We thank Magnus Dehli Vigeland for help with statistical modelling. The Bayesian phylogenetic analysis was carried out through the Bioportal server at University of Oslo. This work was funded through the KMB project Festulolium with Improved Forage Quality and Winter Survival for Norwegian Farming, project number 173319/I10, funded by the Research Council of Norway and Graminor AS.
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