Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fiber yield traits

Ramie is an important fiber-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fiber yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fiber abundance, providing the first evidence for the role of pectin methylesterase in fiber growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focused on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signaling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fiber yield 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 crop.