Development of two sets of tobacco chromosome segment substitution lines and QTL mapping for agronomic and disease resistance traits

Chromosome segment substitution lines (CSSLs) represent a powerful genetic resource for quantitative trait loci (QTL) mapping, gene cloning and breeding. Here, we developed two sets of CSSLs consisting of 245 and 128 unique lines, which derived from OX2028 × K326 and Samsun × K326 crosses. On average, each CSSL carried 1.8 and 2.9 introgressed segments in the two sets, with an average physical segment length of approximately 34.3 Mb and 27.6 Mb, respectively. These CSSLs covered ∼97 % and ∼77 % of the genomes of OX2028 and Samsun, respectively. By performing QTL mapping based on best linear unbiased prediction (BLUP) of phenotypic traits, we identified a total of 64 QTLs associated with six agronomic traits and three disease resistance traits. These QTLs explained phenotypic variation ranging from 1.5 % to 50.8 %. Among them, 22 QTLs detected in OX2028 derived population and 42 detected in Samsun derived CSSLs. Notably, a new QTL for tobacco leaf width, qLW1–1 was narrowed down to an 8-Mb interval on chromosome 1, and NtZY01G00114 , encoding an auxin-response factor protein, was considered as the candidate gene. Our study provides valuable genetic resources for tobacco breeding and enhances our understanding of the genetic basis of complex traits in tobacco. • Developed two sets of chromosome segment substitution lines using K326 as the recurrent and two donor parents (OX2028, Samsun) respectively. • Identified more than sixty QTLs associated with agronomic and disease resistance traits. • Genotype-by-environment interaction significantly impacts phenotypes of agronomic traits in tobacco. • qLW1–1 was identified as a new candidate gene for leaf width.