Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation

Brassica rapa is a model species for agronomic, ecological, evolutionary and translational studies. Here researchers from the University of California at Davis describe high-density SNP discovery and genetic map construction for a Brassica rapa recombinant inbred line (RIL) population derived from field collected RNA-seq data. This high-density genotype data enables the detection and correction of putative genome mis-assemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated Brassica rapa genome. They 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.

rna-seq

Composite population genotype map with the physical position for each of the ten chromosomes. Each RIL is represented as a single row displaying the genomic region inherited from IMB211 (Orange) or R500 (Blue). Small heterozygous regions are represented in black.

Markelz RJC, Covington MF, Brock MT, Devisetty UK, Kliebenstein DJ, Weinig C, Maloof JN. (2016) Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population. bioRXiv [Epub ahead of print]. [abstract]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.