Quantitative trait loci mapping for agronomic and leaf chemistry traits using high density linkage map in flue-cured tobacco (Nicotiana tabacum L.)

Flue-cured tobacco (Nicotiana tabacum L.) is one of the most important economic crops in the world, and is the most important raw material in the cigarette industry. Construction of a high-density linkage map and identification of agronomic and leaf traits quantitative trail loci (QTLs) are prerequisites for molecular marker-assisted selective breeding projects. In the present study, an integrated high-density linkage map for flue-cured tobacco was constructed using a doubled haploid (DH) population based on SSR and SNP markers. The integrated genetic map spans 2618.89 cM and contains 607 SSR marker loci, and 917 SNP marker loci. Using the newly constructed map, QTL mapping was performed using the method of composite interval mapping (CIM) for six plant and six leaf chemistry traits. A total of 102 QTLs associated with 1.77-27.65% of the phenotypic variation were identified on 22 linkage groups in two years (2021 and 2022). Eighty-four and 89 QTLs were detected using 2021 and 2022 field experiments, respectively. Seventy-one QTLs were detected in both years. Most QTLs presented small effects, but six QTLs presented relatively large effects in both two years, with each explaining 15-28% of the phenotypic variation in the DH population. The twelve measured traits were strongly correlated with each other. Consistent with this finding, many QTLs identified for one trait overlapped with those identified for alternative traits.