Genome-Wide Association Study reveals novel genetic loci for quantitative resistance to Septoria tritici blotch in wheat (Triticum aestivum L.)

Authors: MEKONNEN, TILAHUN - Addis Ababa University; SNELLER, CLAY - International Livestock Research Institute (ILRI) - Kenya; HAILESELASSIE, TEKLEHAIMANOT - Addis Ababa University; ZIYOMO, CATHERINE - International Livestock Research Institute (ILRI) - Kenya; ABEYU, BEKELE - International Maize & Wheat Improvement Center (CIMMYT); Goodwin, Stephen - Steve; LULE, DAGNACHEW - Oromia Agriculture Research Institute; TESFAYE, KASSAHUN - Addis Ababa University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2021
Publication Date: 9/24/2021
Citation: Mekonnen, T., Sneller, C.H., Haileselassie, T., Ziyomo, C., Bekele, A.G., Goodwin, S.B., Lule, D., Tesfaye, K. 2021. Genome-Wide Association Study reveals novel genetic loci for quantitative resistance to Septoria tritici blotch in wheat (Triticum aestivum L.). Frontiers in Plant Science. 12:671323. https://doi.org/10.3389/fpls.2021.671323.
DOI: https://doi.org/10.3389/fpls.2021.671323

Interpretive Summary: The fungal leaf disease Septoria tritici blotch (STB) poses serious and persistent challenges to wheat cultivation in Ethiopia and elsewhere in the world. Analysis of genome-wide associations is a promising and widely used technique to identify molecular markers near genes of interest. To identify genomic regions associated with resistance to STB in wheat, 178 lines of bread wheat were scored for molecular markers, growth traits and resistance at field trials in Ethiopia during the 2015 and 2016 growing seasons. Significant genetic variations in resistance to STB with strong genetic linkages were found, suggesting the possibility to improve the resistance through plant breeding. In addition to picking up numerous previously known STB genes, 10 potential new genes were identified. These analyses discovered genomic markers underlying STB resistance and important growth traits in bread wheat that could be used by plant breeders for marker-assisted selection in wheat improvement programs. The results may make it easier for these powerful genetic techniques to be applied by wheat breeders in Africa where high-throughput molecular tools so far are used rarely.

Technical Abstract: Septoria tritici blotch (STB) caused by the fungus Zymoseptoria titici poses serious and persistent challenges to wheat (Triticum aestivum L.) cultivation in Ethiopia and elsewhere in the world. Genome-Wide Association Studies (GWAS) is a promising and widely used technique to decipher genomic loci underlying phenotypic traits of interest. The present study was targeted to elucidate the population structure, linkage disequilibrium (LD), and genomic architecture of STB resistance in an association panel of 178 bread wheat accessions using 7,776 genome-wide scanned DArTSeq Single-Nucleotide Polymorphisms (SNPs). Moreover, the relations of STB resistance with other agronomic traits were explored. The association panel was phenotyped for STB resistance, phenology, yield and yield-related traits at three locations (Holetta, Kulumsa and Bekoji) in 2015 and 2016 growing seasons. Marker-trait associations were calculated using a FarmCPU algorithm implemented in GAPIT. The genotypes exhibited significant genetic variations to STB infestation with broad-sense heritabilities of 0.58 - 0.97 and 0.72 - 0.81 at individual and across environment levels, respectively, suggesting the presence of STB resistance alleles in the association panel with great possibility to improve the trait through selection. Population structure analysis detected two sub-groups (delta K = 2) with greater degree of genetic admixture. Principal component analysis also confirmed population stratification where the first two PCs captured the highest (65%) proportion of the total variance. LD analysis in 338,125 marker pairs confirmed the existence of significant (p = 0.01) linkage between 27.6% marker pairs. In all chromosomes, LD between SNPs declined within 2.26 - 105.62 Mbp, with an overall mean of 31.44 Mbp. GWAS identified 53 loci that were significantly (FDR <0.05) associated with STB resistance pointing to 33 putative QTL. Most of these putative QTL had a similar map position with already published Septoria resistance genes and QTL. However, 10 of the putative resistance loci did not overlap with previously published genes, and hence could be considered as novel. The identified marker-trait associations (MTAs) explained 2.7 - 13.2 % of the total phenotypic variation. Seven of the MTAs for agronomic traits co-mapped with putative QTL for Septoria resistance. Therefore, the present analysis discovered genomic loci underlying STB resistance and important agronomic traits in bread wheat that could be helpful for marker assisted selection in wheat breeding programs. The finding provides new insight into the phenotype-to-genotype relationships for in bread wheat in Africa where the application of high- throughput molecular tools in plant breading is rare.