Identification of superior haplotypes and candidate genes for yield-related traits in tobacco (Nicotiana tabacum L.) using association mapping

Tobacco is an industrial crop, and its leaves and stems are used to produce cigarettes, cigars, pipe tobacco, and to extract bioethanol and biofuel. However, knowledge of the genetic basis underlying agronomic traits related to quality and yield in tobacco is limited. Therefore, we undertook association mapping to identify quantitative trait nucleotides (QTNs) associated with seven yield-related traits in 94 natural tobacco accessions using 126,602 SNPs and two multi-locus models. The mapping identified 465 QTNs across five environments for stem girth (SG: 84 QTNs), leaf number (LN: 61), SPAD (76), leaf length (LL: 71), leaf width (LW: 71), leaf length to width ratio (LLW: 58), and node distance (ND: 67), with phenotypic variance ranging from 0.46% to 30.99%. Of these, 45 reliable QTNs were found in multiple environments and detected by both methods. In addition, the mapping identified 16 pleiotropic QTNs for different traits, e.g., pQTN-18–13 on Chr18 associated with all traits except SG. For 43 QTNs, yield-related traits significantly differed between superior and alternative alleles, with 13 forming haplotype blocks with 3–5 haplotype groups. We screened 15 putative candidate genes based on the 13 haplotype QTNs for yield-related traits, e.g., PCK1, ECR1, MTACP1, SMC6B, and FH14. To the best of our knowledge, this is the first study to identify superior haplotypes associated with yield-related traits, providing a foundation for genetic studies, map-based cloning, and molecular breeding to improve tobacco varieties with desirable yield-related traits.