title: Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.
abstract: Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL) underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP) density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes.
authors.affiliation: Cargill Specialty Seeds & Oils, Fort Collins, Colorado 80525 richard_fletcher@cargill.com.
authors.forename: Richard S
authors.initials: RS
authors.lastname: Fletcher
authors.affiliation: Cargill Specialty Seeds & Oils, Fort Collins, Colorado 80525.
authors.forename: David
authors.initials: D
authors.lastname: Herrmann
authors.affiliation: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Jack L
authors.initials: JL
authors.lastname: Mullen
authors.affiliation: College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
authors.forename: Qinfei
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, New Jersey 08854.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Schrider
authors.affiliation: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Price
authors.affiliation: Department of Computer Science, University of Toronto, Ontario M5S 2J7, Canada.
authors.forename: Junjiang
authors.initials: J
authors.lastname: Lin
authors.affiliation: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Kelsi
authors.initials: K
authors.lastname: Grogan
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, New Jersey 08854.
authors.forename: Andrew
authors.initials: A
authors.lastname: Kern
authors.affiliation: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: John K
authors.initials: JK
authors.lastname: McKay
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D029688:Brassica napus / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D055864:Droughts; D017343:Genes, Plant; D056726:Genetic Association Studies; D008040:Genetic Linkage; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D054643:INDEL Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
keywords: FLC; canola; flowering time; rapeseed; root pulling force (RPF)