Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.)

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.

Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat

“…The present study revealed highly significant contributions of genotypes, environments, and genotype by environment interactions to the phenotypic variations of the target traits ( p< 0.001 ), which is consistent with the results of previous research on durum wheat ( Mengistu et al., 2015 ; Mohammadi et al., 2018 ; Mekonnen et al., 2021 ). The observed high genotypic variance, genotypic coefficient of variation, and broad-sense heritability for TKW and GFP, strongly suggest that their variation is mainly due to heritable genetic differences among the landraces and cultivars.…”

“…The population clustering inferred by STRUCTURE and PCA divided the genotypes into two sub-populations, similar to the results of earlier research ( Wang et al., 2019 ; Alemu et al., 2020b ; Kumar et al., 2020 ; Mekonnen et al., 2021 ). Based on Q-score values of STRUCTURE analysis (Q > 0.80), 96% of the landraces were pure, and 4% of the genotype were admixtures.…”

“…This decline in LD is far below the results of previous research using Ethiopian durum wheat landraces ( Alemu et al., 2021b ), which reported an average physical distance of 69.1 Mbp. Similarly, Mekonnen et al. (2021) found a higher mean LD decay (31.44 Mbp, r 2 = 0.2) in their study on diverse Ethiopian bread wheat germplasm.…”

“…Association mapping (AM) has been widely used to dissect the genetic architecture behind traits like grain yield, host plant resistance to pathogens, drought and salinity tolerance, phenology, and quality traits ( Maccaferri et al., 2010 ; Tuberosa, 2012 ; Canè et al., 2014 ; Turki et al., 2015 ; Giraldo et al., 2016 ; Mengistu et al., 2016 ; Kidane et al., 2019 ; Mérida-García et al., 2019 ; Mérida-García et al., 2020 ). Moreover, genome-wide association studies (GWAS) have been successfully used to map genetic loci and dissect the genomic regions underlying several vital traits in important food crops, such as barley ( Bellucci et al., 2017 ; Borrego-Benjumea et al., 2021 ), and bread wheat ( Li et al., 2019 ; Gao et al., 2021 ; Mekonnen et al., 2021 ).…”

“…In wheat, GWAS has been successfully applied to identify and dissect QTL associated with grain yield ( Li et al., 2019 ; Gao et al., 2021 ), host plant resistance to pathogens ( Alemu et al., 2021a ; Alemui et al., 2021 ; Mekonnen et al., 2021 ), drought tolerance ( Bhatta et al., 2018 ; Mathew et al., 2019 ), root architecture ( Alemu et al., 2021b ), phenology ( Mekonnen et al., 2021 ), adaptation to salinity ( Quamruzzaman et al., 2021 ), and end-use quality traits ( Chen et al., 2019 ; Talini et al., 2020 ). However, in durum wheat, limited GWAS results have been reported across traits of interest, although some results are present for grain yield ( Wang et al., 2019 ; Anuarbek et al., 2020 ), host plant resistance to pathogens ( Liu et al., 2017b ; Aoun et al., 2021 ), drought tolerance ( Wang et al., 2019 ), root system architecture ( Maccaferri et al., 2016 ; Alemu et al., 2021b ), osmotic adjustment ( Condorell et al., 2022 ), and phenology and quality traits ( Fiedler et al., 2017 ).…”