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| Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population |
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Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. |
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R. J. Cody Markelz, Michael F. Covington, Marcus T. Brock, Upendra K. Devisetty, Daniel J. Kliebenstein, Cynthia Weinig and View Julin N. Maloof G3: Genes, Genomes, Genetics July 1, 2017 vol. 7 no. 7 2259-2270; https://doi.org/10.1534/g3.117.043000 AbstractBrassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1–8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.
See: http://www.g3journal.org/content/7/7/2259?etoc=
Figure 2: An individual plot of a RIL genotyped with the population-based SNP set. Each of the B. rapa 10 chromosomes are displayed (A01–A10) with count coverage of each SNP at each physical position on the chromosome in megabases (Mb). The color indicates the relative ratio of coverage between R500 and IMB211 for each SNP. RIL, recombinant inbred line; SNP, single nucleotide polymorphism. |
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(26).png "Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population")
