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

Ramie is one of the most ancient cellulose fiber crops, having been used for at least 6000 years. It is also one of the strongest and longest natural fine textile fibers in the world and is principally used for fabric production. Although ramie is very important and has a high economic value, the genetic basis of its yield-related and fiber quality traits remains poorly understood and is insufficient owing to the lack of assessment in multiple environments. Here, we evaluated the population structure and genomic variation in ramie based on resequencing of 319 core accessions and detected several candidate genes associated with fiber yield and quality traits by combining them with linkage mapping. We obtained approximately 3.49 million high-quality single nucleotide polymorphisms (SNPs), 2,089,798 insertions and deletions (Indels), and 88,087 structure variations (SVs). The investigation of phenotypes for plant height (PL), stem diameter (SD), bark thickness (BT), fiber diameter (FD), fiber fineness (FF), and ramet number (RN) found these traits showed abundant variation and correlation. Several genetic loci and candidate genes were identified associated with three yield-related traits and fiber fineness. A gene within pleiotropic loci encoding NAC domain containing protein (BnNAC29) was found to be significantly correlated with stem diameter and bark thickness. Another variation of large fragment insertions and deletions in two candidate genes, BnVIT1 and BnAEP, may also be responsible for the increase of stem diameter and bark thickness, respectively. Favorable gene haplotypes were identified as having the same tendency in stem diameter and bark thickness. Moreover, we presumed that plant height-related genes had undergone selection from landraces to breeding cultivars, even though there was minor differentiation during domestication. Our study provides new insights into the genetic architecture of yield and fiber quality traits in ramie. Moreover, the identification of fiber yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this fiber crop.