Genome-wide association analysis uncovers candidate genes for forage quality traits in Brassica napus stems

Abstract

Background Brassica napus (rapeseed) is an important oilseed crop and its leaves and stems can also be used as animal feed. Lignocellulose content is closely related to the nutritional quality and palatability of animal feed. However, quantitative trait loci (QTLs) associated with acid detergent fiber (ADF) and neutral detergent fiber (NDF) contents in rapeseed stems have not yet been mapped. Results In this study, we used 494 B. napus accessions to perform genome-wide association studies (GWAS) of ADF and NDF contents. Ninety-two single-nucleotide polymorphisms (SNP) and 35 simple-sequence repeat (SSR) loci were significantly correlated with ADF and NDF contents, respectively, and six genetic loci associated with ADF and NDF contents were detected using both types of markers. We identified three candidate genes on chromosome A05 related to ADF content, including genes encoding chitinase-like protein 2 (CTL2) and two trichome birefringence-like 41 s (TBL41s). Seven genes on chromosomes A03 and A04 were related to NDF content, including genes encoding glycosyl hydrolase (GH), reversibly glycosylated polypeptide 1 (RGP), irregular xylem 12 (IRX12), trichome birefringence-like 34 (TBL34), galacturonosyltransferase 7 (GAUT7), cytokinesis defective 1 (CYT1), and LOB domain-containing protein 15 (LBD15). These candidate genes encode factors that likely participate in secondary cell wall formation and lignocellulose biosynthesis. Conclusions These findings lay the foundation for identifying genes related to forage quality traits and improving the efficiency of forage utilization in rapeseed, which will be beneficial for breeding new varieties for high-quality forage with low lignocellulose content.