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Synteny-based Mapping-by-Sequencing enabled by Targeted Enrichment.
Plant J. 2012 Mar 12;
Authors: Galvão VC, Nordström KJ, Lanz C, Sulz P, Mathieu J, Posé D, Schmid M, Weigel D, Schneeberger K
Abstract
Mapping-by-sequencing, as implemented in SHOREmap ("SHOREmapping"), is greatly accelerating the identification of causal mutations. The original SHOREmap approach enabled by resequencing of bulked segregants required a highly accurate and complete reference sequence. Current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms, however, do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed on a reduced number of markers and how the associated decrease in the number of markers can be compensated by enrichment of marker sequences. As a proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, which has a genome with several large scale rearrangements relative to A. thaliana. Our approach outlines an alternative roadmap for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.
PMID: 22409706 [PubMed - as supplied by publisher]
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Synteny-based Mapping-by-Sequencing enabled by Targeted Enrichment.
Plant J. 2012 Mar 12;
Authors: Galvão VC, Nordström KJ, Lanz C, Sulz P, Mathieu J, Posé D, Schmid M, Weigel D, Schneeberger K
Abstract
Mapping-by-sequencing, as implemented in SHOREmap ("SHOREmapping"), is greatly accelerating the identification of causal mutations. The original SHOREmap approach enabled by resequencing of bulked segregants required a highly accurate and complete reference sequence. Current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms, however, do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed on a reduced number of markers and how the associated decrease in the number of markers can be compensated by enrichment of marker sequences. As a proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, which has a genome with several large scale rearrangements relative to A. thaliana. Our approach outlines an alternative roadmap for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.
PMID: 22409706 [PubMed - as supplied by publisher]
More...