Genomic variation and candidate genes dissect quality and yield traits in Boehmeria nivea (L.) Gaudich

Abstract Ramie is a perennial and traditional Chinese cellulose fiber crop and accessible for harvesting three times within one year in some region of China. Besides, ramie can also be used in medicine, feed and material industries. The genetic basis over quality- and yield- related traits in ramie is poorly understood and insufficient owing to the lack of assessment in different environments. A core collection comprising 319 accessions with 25.31-fold coverage resequencing depth for evaluating population structure and genomic variation. Combined with linkage mapping method detecting favorable variation and candidate genes associated with yield and quality related traits. We obtained approximately 3.49 million high quality single nucleotide polymorphisms (SNPs), 2,089,798 insertions and deletions (Indels) and 88,087 structure variation (SV) in whole genome. None distinct population structure was found in ramie population based on geographical distribution. Some loci and genes were detected to relate to three yield traits and fiber fineness. A pleiotropic genes encoding NAC domain containing protein (BnNAC29), was identified significantly correlated with stem diameter and bark thickness. The variation of large-fragment deletion and indels in two candidate genes may responsible for the two traits. Moreover, we also detected pleiotropic loci and candidate genes for plant height and stem diameter. Our study provides new insights into the genetic architecture of ramie yield and fiber quality. The identified loci and candidate genes are expected to facilitate genomics-based breeding for higher fiber yield and quality improvement in ramie.