Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing

G3 : Genes - Genomes - Genetics
Richard S FletcherJohn K McKay

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 sho...Continue Reading

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Citations

Jun 6, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Chao WeiTingdong Fu
Mar 18, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Daniela Quezada-MartinezAnnaliese S Mason

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Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

JoinMap3
SeqMan NGen
SeqMan
PAML
BAM
Burrows Alignment ( BWA )
Tablet
qtl
fastq
R

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