Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.)

Abstract

Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

“…According to previous studies, LD decay differs among species and populations. The attenuation distances in Zea mays , Oryza sativa and Brassica napus were <100 kb, <1 and <6 Mb, respectively (Crowell et al ., ; Flint‐Garcia et al ., ; Jamshed et al ., ; Xu et al ., ). In this study, upland cotton in China had a slower LD decay of 6.1 cM (~4 Mb) when r 2 < 0.1 in the whole genome.…”

“…A few accessions were introduced from the Soviet Union (SU) and the United States (USA), such as Deltapine, Coker and Stoneville, which are the founder accessions for cotton breeding in China and have made significant contributions to Chinese cotton production. The relatively larger sample size ensured sufficient genetic variation, and the sample size was similar to the GWAS population sizes used for Arabidopsis thaliana (Zhao et al, 2005), Oryza sativa (Crowell et al, 2016;Famoso et al, 2011), Zea mays (Li et al, 2013a;Wen et al, 2014) and Brassica napus (Xu et al, 2016).…”

Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds

“…Our resource provides 355 536 SNP markers, equivalent to one SNP every 0.33 kb across our B. napus AC pan‐transcriptome reference. The SNP density is much higher than the density of the commercially available 60K Brassica Infinium ® SNP array, which only provided 26 841 or 21 117 SNPs for recent B. napus GWAS studies (Li et al ., ; Xu et al ., ). Although the number of SNPs can even be greater when using whole‐genome resequencing, as shown by Huang et al .…”

Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata

“…Therefore, the genetic diversity of the new‐type B. napus population would likely have been underestimated in terms of introgression of A r, B c and C c polymorphism. Despite this, this ‘new‐type’ B. napus population still presented comparable genetic diversity to the internationally representative germplasm set of 130 traditional B. napus accessions used in this study (Xu et al ., ), as assessed by the number of polymorphic markers, PIC and genetic distance within the population (Tables S3 and ). These results indicate that the rich genetic diversity present within the newly resynthesized population is comparable to the gene pool of traditional B. napus , the latter of which has undergone decades of breeding efforts.…”