Dissecting the Genetic Mechanisms of Hemicellulose Content in Rapeseed Stalk

Polysaccharides such as hemicellulose in rapeseed can be used as an abundant resource to develop biomass energy. In the present study, the hemicellulose content in the middle stalk and taproot of a rapeseed core population of 139 accessions in Guizhou, Hubei and Anhui provinces was determined. Genotyping of the core population was carried out by a 60 K single nucleotide polymorphism chip, and a genome-wide association study (GWAS) was performed to reveal the associated sites of hemicellulose content in rapeseed. The results of the GWAS showed that 28 SNPs (<i>p</i> ≤ 0.001) were significantly associated with hemicellulose content, and revealed that three sites—qHCs.C02 (contribution rate = 17.20%), qHCs.C05 (10.62%), and qHCs.C08 (8.80%)—are significantly associated with hemicellulose content in the stalk and three sites—qHCt.A09 (9.49%), qHCt.C05 (9.18%) and qHCt.C08 (13.10%)—are significantly associated with hemicellulose content in the taproot. Seven candidate genes associated with hemicellulose synthesis were identified in these major loci. Further RNA-seq analysis showed that two key differentially expressed genes (<i>BnaC05G0092200ZS</i> and <i>BnaC05G0112400ZS</i>) involved in hemicellulose synthesis were identified as having underlying QTL. This study excavated the key loci and candidate genes for regulating hemicellulose synthesis, providing a theoretical basis for developing rapeseed varieties with high hemicellulose content. At the same time, our results will be helpful in producing rapeseed cultivars with high lodging-resistance as well as highlighting the value of rapeseed as a resources for the bioenergy industry.