Identification of QTLs Associated With Agronomic Traits in Tobacco via a Biparental Population and an Eight-Way MAGIC Population

Abstract

Agronomic traits such as plant height (PH), leaf number (LN), leaf length (LL), and leaf width (LW), which are closely related to yield and quality, are important in tobacco (Nicotiana tabacum L.). To identify quantitative trait loci (QTLs) associated with agronomic traits in tobacco, 209 recombinant inbred lines (RILs) and 537 multiparent advanced generation intercross (MAGIC) lines were developed. The biparental RIL and MAGIC lines were genotyped using a 430 K single-nucleotide polymorphism (SNP) chip assay, and their agronomic traits were repeatedly evaluated under different conditions. A total of 43 QTLs associated with agronomic traits were identified through a combination of linkage mapping (LM) and association mapping (AM) methods. Among these 43 QTLs, three major QTLs, namely qPH13-3, qPH17-1, and qLW20-1, were repeatedly identified by the use of various genetically diverse populations across different environments. The candidate genes for these major QTLs were subsequently predicted. Validation and utilization of the major QTL qLW20-1 for the improvement of LW in tobacco were investigated. These results could be applied to molecular marker-assisted selection (MAS) for breeding important agronomic traits in tobacco.

The allotetraploidNicotiana tabacumgenome and GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits

“…P values and additive effects for the quantitative trait loci (QTLs) are summarized in Supplementary Table 10. Although linkage disequilibrium (LD) is too extensive to directly pinpoint the candidate genes underlying each association peak, we found a few genes previously identified as QTLs 12,[14][15][16][17][18] or annotated as potential candidates near eight peaks (dashed lines in Fig 3B). In addition, we conducted a review of the literature 12,[14][15][16][17][18] to determine the relative position of previously reported QTLs (Supplementary Table 11) in the ZY300 genome assembly and discovered that 95% of the QTLs detected in our study were novel.…”

“…Although linkage disequilibrium (LD) is too extensive to directly pinpoint the candidate genes underlying each association peak, we found a few genes previously identified as QTLs 12,[14][15][16][17][18] or annotated as potential candidates near eight peaks (dashed lines in Fig 3B). In addition, we conducted a review of the literature 12,[14][15][16][17][18] to determine the relative position of previously reported QTLs (Supplementary Table 11) in the ZY300 genome assembly and discovered that 95% of the QTLs detected in our study were novel. Altogether, these marker trait associations constitute a comprehensive genotype-tophenotype map (Fig 3D, Supplementary Table 12), providing a roadmap for future genetic studies in this model plant species.…”

Potential of Molecular Plant Breeding for Sustaining the Global Food Security

“…In Africa, MAS has resulted in the recognition of quantitative trait loci (QTLs) that affects the productivity and nutritional quality of maize. Also many potential QTLs linked to good agronomic traits have been mapped which show better performance in MAS breeding programs 32 .…”

Construction of a high-density genetic map and dissection of genetic architecture of six agronomic traits in tobacco (Nicotiana tabacum L.)

“…black shank, brown spot and soilborne disease) ( Tong et al., 2012 ; Drake-Stowe et al., 2017 ; Zhang et al., 2018 ; Cheng et al., 2019 ; Ma et al., 2019 ), agronomic performance (e.g. various morphological traits) ( Lewis et al., 2007 ; Wu et al., 2014 ; Cheng et al., 2015 ; Tong et al., 2021 ; Liu et al., 2022 ) and leaf quality (e.g. chemical components and smoke properties) ( Julio et al., 2006 ; Vijay et al., 2010 ).…”

“…chemical components and smoke properties) ( Julio et al., 2006 ; Vijay et al., 2010 ). Particularly, for important agronomic traits associated with yield, few QTLs of tobacco have been reported so far ( Lewis et al., 2007 ; Cheng et al., 2015 ; Tong et al., 2021 ; Liu et al., 2022 ). Moreover, those studies of QTL mapping mainly focused on the QTL effects, epistatic effects were barely investigated as well as their interactions with environments.…”