GWAS combined with QTL mapping reveals the genetic loci of leaf morphological traits in Cigar tobacco

Background Tobacco ( Nicotiana tabacum L.) is an important commercial crop. Cigar tobacco plants, which are derived from the same species, possess special leaf characteristics consistent with its industrial usage, including leaf flatness, leaf thickness, lateral vein diameter and leaf vein angle. Exploring the key QTLs determining the quality of cigar leaves and ultimately applying them to the molecular breeding of cigars are therefore highly important. Results In this study, GWAS and QTL mapping were simultaneously performed using a natural population containing 185 accessions collected worldwide and an F 2 population consisting of 240 individuals, respectively. A total of 26 QTLs related to leaf morphological traits were mapped in the F 2 population at three different developmental stages, and some QTL intervals were repeatedly detected for different traits and at different developmental stages. Among the 206 significant SNPs identified in the natural population, several associated with the leaf thickness phenotype were co-mapped via both GWAS and QTL mapping. By analysing linkage disequilibrium and transcriptome data from different tissues combined with gene functional annotations, 7 genes from the co-mapped region were identified as the causal genes associated with leaf thickness traits. Conclusions These results presented a valuable cigar resource showing the genetic diversity regarding its leaf morphological traits at different developmental stages. It also provides valuable information for novel genes and molecular markers that will be useful for further functional verification and for molecular breeding of cigars as well as other crops in the future.