Genome-wide association reveals limited benefits of pyramiding the 1B and 1D loci with the 2NS translocation for wheat blast control

Authors: CRUPPE, GIOVANA - Kansas State University; SILVA, PAULA - Kansas State University; DA SILVA, CRISTIANO - Kansas State University; Peterson, Gary; Pedley, Kerry; CRUZ, CHRISTIAN - Purdue University; ASIF, MOHAMMAD - Kansas State University; LOLLATO, ROMULO - Kansas State University; FRITZ, ALLAN - Kansas State University; VALENT, BARBARA - Kansas State University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/23/2020
Publication Date: 12/22/2020
Citation: Cruppe, G., Silva, P., Da Silva, C.L., Peterson, G.L., Pedley, K.F., Cruz, C.D., Asif, M., Lollato, R.P., Fritz, A., Valent, B. 2020. Genome-wide association reveals limited benefits of pyramiding the 1B and 1D loci with the 2NS translocation for wheat blast control. Crop Science. 61:1089-1103. https://doi.org/10.1002/csc2.20397.
DOI: https://doi.org/10.1002/csc2.20397

Interpretive Summary: Wheat spike blast, caused by the fungus Magnaporthe oryzae pathotype Triticum, is a devastating disease of wheat. Currently, resistance to the pathogen is limited to wheat lines that contain a region of the genome referred to as 2NS. The 2NS region was introduced into wheat lines from a wild relative of wheat. The resistance provided by the 2NS region is partial and populations of the pathogen appear to be overcoming this resistance. The goal of this study was to identify new sources of resistance using a diverse panel of wheat genotypes and three strains of the pathogen. Novel markers associated with potential sources of resistance to one of the pathogen isolates were identified, but these markers mapped to the 2NS region. Further analysis is needed to fully assess the potential of these newly discovered markers as tools for breeding more durable wheat. Breeding for durable resistance is vital to sustainable wheat production especially with the emergence of new and more virulent races of this pathogen.

Technical Abstract: Wheat spike blast (WSB), caused by Magnaporthe oryzae pathotype Triticum (MoT), has relied upon a single major source of resistance: the 2NvS translocation introgressed from the wild relative Aegilops ventricosa. However, this resistance is partial and recently partially overcome by newer MoT races. To characterize potential novel loci conferring resistance to WSB, we conducted a genome-wide association study (GWAS) using a diverse panel of 384 wheat genotypes phenotyped under three controlled-environment conditions using MoT isolates T-25, B-71, and 008. Genotyping-by-sequencing identified 13,175 SNPs after filtering. Principal components analysis (PCA) identified two clusters based on the presence/absence of the 2NvS translocation and the first three PCAs explained 13% of the genetic variation. Three individual analyses were performed [full (all genotypes combined), 2NvS genotypes only, and non-2NvS genotypes only] using a linear mixed model and a threshold of significance of false discovery rate at 5%. Association analysis detected 25 significant SNPs for the full GWAS with isolate T-25, in which 21 were mapped on 2A chromosome in the same physical position as the 2NvS translocation. Highly significant linkage disequilibrium among these SNPs suggested they might tag the same QTL. No significant associations were identified with isolates B-71 and 008. QTL pyramiding analysis showed that the combination of multiple QTL was not statistically different from the individual effect of the 2A QTL. Further validation of these genomic regions can aid breeding for broad spectrum and durable WSB resistance.