Abstract
BackgroundBrassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type.ResultsFlowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC.ConclusionsThese findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
Highlights
Brassica napus is an important oilseed crop cultivated worldwide
Flowering time genetic pathways have been elucidated in Arabidopsis and most flowering time genes are known to be conserved between Arabidopsis and B. napus [21,22,23]
We present candidate regions for flowering time and budding time and discuss the use of errorprone double digest restriction-site associated DNA sequencing (ddRAD) genotyping in heterozygous breeding populations
Summary
Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Genotyping-by-sequencing (GBS) is a powerful tool for high-throughput discovery of genetic polymorphisms in crops [1,2,3,4,5]. GBS has been used for marker discovery, linkage mapping and QTL analysis in a range of crops [12,13,14], including the important oilseed crop Brassica napus. Flowering time genetic pathways have been elucidated in Arabidopsis and most flowering time genes are known to be conserved between Arabidopsis and B. napus [21,22,23] On this basis, many QTL and associated SNPs for flowering time have been detected in B. napus [24,25,26,27,28,29,30,31]. Despite progress in understanding the genetic underpinnings of B. napus flowering time, a substantial proportion of flowering time variation remains to be explained
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