Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

Abstract

Background 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. 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. Results Flowering 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. Conclusions These 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.

Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [Sorghum bicolor (L.) Moench]

“…The obtained SNPs were distributed throughout the sorghum genome indicating the effectiveness of this technique, which made it possible to identify a large number of polymorphisms at a low cost ( Peterson et al., 2012 ). The ddRAD-Seq technique has recently been utilized successfully in a variety of plants, including foxtail millet ( Fukunaga et al., 2022 ), Brassica napus ( Chen et al., 2017 ; Scheben et al., 2020 ), and sesame ( Yol et al., 2021 ). To our knowledge, this study is the first to demonstrate that ddRAD-Seq is a suitable approach to detect variants at a genome-wide scale in the sorghum genome.…”

Integrate QTL Mapping and Transcription Profiles Reveal Candidate Genes Regulating Flowering Time in Brassica napus

“…In the northern region of China, winter rapeseed is planted in early autumn and flowers the following spring. Winter is long and frosty; therefore, strong winter rapeseed genotypes are required to avoid premature flowering (Liu et al, 2021) (Fletcher et al, 2015;Jian et al, 2019;Scheben et al, 2020;Xu et al, 2020;Song et al, 2021 and Supplementary Figure 1). Both minor QTLs with small phenotypic contributions and major QTLs accounting for > 10% of the phenotypic variation have been reported.…”

“…Several QTLs associated with flowering time have been reported, and all but three of these (Chr. A01, A09, and C01) are distributed on 16 chromosomes ( Fletcher et al, 2015 ; Jian et al, 2019 ; Scheben et al, 2020 ; Xu et al, 2020 ; Song et al, 2021 and Supplementary Figure 1 ). Both minor QTLs with small phenotypic contributions and major QTLs accounting for > 10% of the phenotypic variation have been reported.…”

QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

“…Several studies have been successfully conducted using F 2 or F 2 -derived F 3 populations to identify major QTLs in bread wheat [ 17 , 18 , 19 ], durum wheat [ 20 ], rice [ 21 ], maize [ 22 ], and other species [ 23 , 24 , 25 , 26 ]. However, unfortunately, F 2 and BC are temporary populations.…”