Abstract
Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with BN were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.
Highlights
Rapeseed (Brassica napus L., AACC, 2n = 38) is a globally significant oilseed crop used in the production of vegetable oil and oil meals, and ∼95% of its total cultivation is in Asia, Europe, and North America
Extensive phenotypic variations for plant height (PH), branch initiation height (BIH), and branch number (BN) were observed in the 333 accessions that were grown over the course of 4 years (2012–2015)
A mixed linear model (MLM) was used to calculate the association in the genome-wide association study (GWAS) analysis, while incorporating a Q matrix and kinship data to control the false discovery rate, this model was an improvement relative to the naïve GLM (Figure 3; Larsson et al, 2013)
Summary
Rapeseed (Brassica napus L., AACC, 2n = 38) is a globally significant oilseed crop used in the production of vegetable oil and oil meals, and ∼95% of its total cultivation is in Asia, Europe, and North America. According to a new report from the United States Department of Agriculture (USDA), rapeseed production in 2015/16 is estimated at 66.9 million tons, down 4.7% from the previous year. Harvested area is estimated at 32.9 million hectares, down 5.5% from the previous year (http://www.pecad.fas.usda.gov/). To meet growing demands for both edible products and biofuel, it is critical to increase rapeseed productivity through efficient breeding. Rapeseed productivity is determined by three components: number of siliques per plant (NSP), number of seeds per silique (NSS), and seed weight per plant (Clarke and Simpson, 1978). GWAS for Plant Architecture Traits in Rapeseed
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