Abstract
Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26–105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7–13.2% of the total phenotypic variation. Seven of the QTLs (R2 = 2.7–10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.
Highlights
Common wheat (Triticum aestivum L.) is the most widely cultivated and the major staple food crop in the world consumed by human, providing almost 20% of the total calories and 21% of protein demand globally (Arzani and Ashraf, 2017; International Wheat Genome Sequencing Consortium (IWGSC), 2018; Ramadas et al, 2019)
The analysis revealed that the Septoria tritici blotch (STB) infestation showed seasonal fluctuations, but that was still higher during the 2015 growing season (Table 1)
The genetic architecture of adult-plant resistance to STB was explored in bread wheat using high-density, genome-wide single-nucleotide polymorphism (SNP) markers and multi environment-derived phenotype data
Summary
Common wheat (Triticum aestivum L.) is the most widely cultivated and the major staple food crop in the world consumed by human, providing almost 20% of the total calories and 21% of protein demand globally (Arzani and Ashraf, 2017; International Wheat Genome Sequencing Consortium (IWGSC), 2018; Ramadas et al, 2019). Septoria tritici blotch (STB) is a major threat to wheat production in Ethiopia (Getinet et al, 1990; Takele et al, 2015; Kidane et al, 2017; Mekonnen et al, 2019, 2020), causing up to 82% of yield loss in the worst seasons (Getinet et al, 1990; Mengistu et al, 1991; Ayele et al, 2008). Qualitative and quantitative types of resistance to STB have been reported in wheat (Arraiano and Brown, 2006; Arraiano et al, 2009) The former refers to a condition where one or few major Stb genes provide resistance to specific Z. tritici isolates (Brown et al, 2015). Quantitative resistance is the Abbreviations: DH, days to heading; DF, days to flowering; DM, says to maturity; FDR, false discovery rate; FarmCPU, fixed and random model circulating probability unification; GAPIT, genome association and prediction integrated tools; GBS, genotyping by sequencing; GFD, grain-filling duration; GWAS, genome-wide association study; HLW, hectoliter weight; PH, plant height; LD, linkage disequilibrium; MAF, minor allele frequency; MAS, marker-assisted selection; MTAs, marker-trait associations; PCA, principal component analysis; QTL, quantitative trait locus or loci; SL, spike length; SN, seed number per spike; SDS, Septoria disease severity; SDSH, Septoria disease severity at heading; SDSMM, Septoria disease severity at mid-maturity; SDSM, Septoria disease severity at maturity; STB, Septoria tritici blotch; SNP, single-nucleotide polymorphism; SPC, Septoria progress coefficient; TKW, thousand kernel weight
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