Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus

Abstract Background Plant height is a key morphological trait of rapeseed, which not only plays an important role in determining plant architecture, but is also an important character related to yield. Presently, improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height have been characterized in rapeseed. Results In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60K Illumina Infinium SNP array in 203 Brassica napus accessions. Eleven haplotypes carrying important candidate genes were detected significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06 and C09. Meanwhile, regional association analysis of 50 resequencing rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermo re, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors, and formed a potential network regulation in plant height of rapeseed. Conclusions Combination of GWAS with haplotype analysis revealed a number of directly or indirectly gene related to plant height and provide insight into the genetic basis of plant height in rapeseed. Otherwise, our results will be favorable to develop haplotype functional markers to further improve plant height in rapeseed.