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• QTL mapping of six agronomic traits in 341 tobacco genotypes using SSR markers. • A total of 31 single locus and 6 epistatic QTL pairs were identified out of which 5 single locus and 1 epistatic QTL pair showed pleiotropic effects. • The environment-specific superior genotypes (SL) and general superior genotypes (GSL) were predicted using the QTL effects. • Candidate genes associated with major QTL positions and their corresponding proteins were determined. Tobacco is an economically significant industrial crop and model plant for genetic research, yet little is known about its genetic architecture. Quantitative trait loci (QTL) analysis was performed for six agronomic traits on an F_7 population of 341 genotypes, parents, and F 1 plants using 1974 SSR markers across two environments. 31 QTLs contributing single-locus additive effects on 13 linkage groups (LGs) and 6 QTL pairs contributing epistatic effects on 6 LGs, were detected by the QTLNetwork 2.0 which was developed for the mixed-linear-model-based composite interval mapping (MCIM). Notably, 5 QTLs and 1 epistatic QTL pair were found to have pleiotropic effects on some genetically related traits. Moreover, the Broad sense heritability of the detected QTLs ranged from 1.05% to 43.33%, while genotype-by-environment interaction heritability spanned from 27.09% to 56.25%. Based on the results of QTL mapping, the potential superior lines for all or specific environments were designed and evaluated. Five major QTLs were finely dissected based on the tobacco reference genome of K326, and 31 candidate genes were predicted. This study offered new insights into the complicated genetic architecture and QTL resources for efficient breeding design for genetic improvement of agronomic traits in tobacco. [ABSTRACT FROM AUTHOR]

Investigating plant genomes offers crucial foundational resources for exploring various aspects of plant biology and applications, such as functional genomics and breeding practices. With the development in sequencing and assembly technology, several Nicotiana tabacum genomes have been published. In this paper, we reviewed the progress on N. tabacum genome assembly and quality, from the initial draft genomes to the recent high-quality chromosome-level assemblies. The application of long-read sequencing, optical mapping, and Hi-C technologies has significantly improved the contiguity and completeness of N. tabacum genome assemblies, with the latest assemblies having a contig N50 size over 50 Mb. Despite these advancements, further improvements are still required and possible, particularly on the development of pan-genome and telomere-to-telomere (T2T) genomes. These new genomes will capture the genomic diversity and variations among different N. tabacum cultivars and species, and provide a comprehensive view of the N. tabacum genome structure and gene content, so to deepen our understanding of the N. tabacum genome and facilitate precise breeding and functional genomics., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Tong, Huang, Zhu, Fan, Xiao and Shen.)