Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Abstract

Tobacco bacterial wilt (TBW) is a devastating soil-borne disease threatening the yield and quality of tobacco. However, its genetic foundations are not fully understood. In this study, we identified 126,602 high-quality single-nucleotide polymorphisms (SNPs) in 94 tobacco accessions using genotyping-by-sequencing (GBS) and a 94.56 KB linkage disequilibrium (LD) decay rate for candidate gene selection. The population structure analysis revealed two subpopulations with 37 and 57 tobacco accessions. Four multi-locus genome-wide association study (ML-GWAS) approaches identified 142 quantitative trait nucleotides (QTNs) in E1–E4 and the best linear unbiased prediction (BLUP), explaining 0.49–22.52% phenotypic variance. Of these, 38 novel stable QTNs were identified across at least two environments/methods, and their alleles showed significant TBW-DI differences. The number of superior alleles associated with TBW resistance for each accession ranged from 4 to 24; eight accessions had more than 18 superior alleles. Based on TBW-resistant alleles, the five best cross combinations were predicted, including MC133 × Ruyuan No. 1 and CO258 × ROX28. We identified 52 candidate genes around 38 QTNs related to TBW resistance based on homologous functional annotation and KEGG enrichment analysis, e.g., CYCD3;2, BSK1, Nitab4.5_0000641g0050, Nitab4.5_0000929g0030. To the best of our knowledge, this is the first comprehensive study to identify QTNs, superior alleles, and their candidate genes for breeding TBW-resistant tobacco varieties. The results provide further insight into the genetic architecture, marker-assisted selection, and functional genomics of TBW resistance, improving future breeding efforts to increase crop productivity.

Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing

“…We compared the expression data of leaves at 1, 6, and 12 h with the control, identifying 10,153, 7,879, 7,662, 13,704, 5,161, and 7,438 DEGs in HS-1h, HS-6h, HS-12h, HT-1h, HT-6h, and HT-12h, respectively (Figures 2A-C). Further, these genes were involved in cell division, cellular process, response to stimulus, primary metabolic process, response to heat, the developmental process involved in reproduction, photosynthesis, detoxification, RNA binding, and auxin homeostasis (Figures 3, S2, S3) in line with previous studies (Wang et al, 2016;Cai et al, 2020;Helal et al, 2021;Lai et al, 2021). In addition, most DEGs were enriched in the MAPK signaling pathwayplant, brassinosteroid biosynthesis, plant-pathogen interaction, plant hormone signal transduction, and circadian rhythm (Figures 3, S4, S5); these results are similar to previous reports (Song et al, 2014a;Song et al, 2021).…”

“…Our previous research identified expressed sequence tagsimple sequence repeat (EST-SSR) markers in flowering Chinese cabbage (Chen et al, 2017) and also detected significant SNPs/ genes for plant height (Ikram et al, 2022a;Ikram et al, 2022b;Li et al, 2022) and wilt resistance (Lai et al, 2021) in tobacco. The present study used RNA-seq based on the Illumina HiSeq2000 platform to undertake a genome-wide analysis of gene expression in leaves of HT (Youlu-501) and HS (3T-6) flowering Chinese cabbage varieties under heat stress (0, 1, 6, and 12 h) to (1) identify DEGs in HS and HT genotypes after 1, 6, and 12 h of heat stress: (2) annotate these genes based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis; (3) identify the expression pattern of genes using Hierarchical clustering analysis; (4) identify TFs associated with the DEGs and their role in heat stress.…”

Genome-wide identification and development of InDel markers in tobacco (Nicotiana tabacum L.) using RAD-seq

“…3-5), indicating some accessions from the same source could not cluster together and confirmed no clear pattern for geographical source, consistent with other reports (Fricano et al 2012;Xia et al 2013;Liu et al 2017). Interestingly, in PCoA, both groups had mixed accessions, indicating that most tobacco varieties examined are of mixed origin (Kalivas et al 2016;Lai et al 2021). Similarly, the pedigree information of 50 tobacco accessions (Table 1) showed that Chinese tobacco accessions originated from USA accessions and have a common ancestry.…”

Intestinal metabolomics in premature infants with late-onset sepsis

“…Glyoxylate and dicarboxylate metabolism bypass the TCA cycle, participate in energy metabolism, and are important in fungal infections 30 . Glutathione metabolism is involved in biological processes such as ferroptosis and antioxidation 31 , and glutathione is a major antioxidant that maintains redox homeostasis, which is closely associated with inflammatory responses 32 . Steroid hormone biosynthesis and primary bile acid biosynthesis involved in pathogenesis of acute and chronic infections in mice 33 .…”