QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time

Abstract

Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.

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.…”

Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies

“…The Illumina 60K Brassica SNP Bead Chip array (Clarke et al, 2016 ) has previously been used in QTL analysis in Brassica napus to study flowering time, seeds per silique, silique length, seed weight, and other traits (Yang et al, 2017 ; Wu et al, 2018 ; Wang et al, 2019 ; Song et al, 2021 ) but has not yet been utilized in genetic mapping of heterotic loci. Because B. juncea and B. napus share A genome, therefore using common markers, an attempt was made to align QTL for yield-related traits detected in the present study with those detected in previous studies undertaken in B. napus .…”

Identification and Validation of Quantitative Trait Loci Mapping for Spike-Layer Uniformity in Wheat

“…Quantitative trait loci (QTL) mapping can provide usable molecular markers that are linked to a gene of interest. Up to now, QTL mapping has been widely applied to discover the locations of loci underlying traits in plants [4][5][6][7][8][9][10][11][12][13]. With the development of high-throughput sequencing technology, single nucleotide polymorphism (SNP) arrays, including the 9K, 55K, 90K, 660K, and 820K arrays, have been successfully used for constructing high-density genetic maps of wheat [14][15][16][17][18].…”