Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

R J Cody Markelz; Michael F Covington; Marcus T Brock; Upendra K Devisetty; Daniel J Kliebenstein; Cynthia Weinig; Julin N Maloof

doi:10.1534/g3.117.043000

Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

G3 (Bethesda). 2017 Jul 5;7(7):2259-2270. doi: 10.1534/g3.117.043000.

Authors

R J Cody Markelz¹, Michael F Covington¹, Marcus T Brock², Upendra K Devisetty¹, Daniel J Kliebenstein³, Cynthia Weinig², Julin N Maloof⁴

Affiliations

¹ Department of Plant Biology, University of California at Davis, California 95616.
² Department of Botany, University of Wyoming, Laramie, Wyoming 82072.
³ Department of Plant Sciences, University of California at Davis, California 95616.
⁴ Department of Plant Biology, University of California at Davis, California 95616 jnmaloof@ucdavis.edu.

Abstract

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. 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.

Keywords: Brassica rapa; RNA-Seq; genetic map; genome assembly correction.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Brassica rapa / genetics*
Chromosome Mapping*
Genetic Markers
Genome, Plant*
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation*
RNA, Plant / genetics

Substances

Genetic Markers
RNA, Plant