Screening of CIMMYT and South Asian Bread Wheat Germplasm Reveals Marker-Trait Associations for Seedling Resistance to Septoria Nodorum Blotch

Abstract

Wheat (Triticum aestivum L.) production is adversely impacted by Septoria nodorum blotch (SNB), a fungal disease caused by Parastagonospora nodorum. Wheat breeders are constantly up against this biotic challenge as they try to create resistant cultivars. The genome-wide association study (GWAS) has become an efficient tool for identifying molecular markers linked with SNB resistance. This technique is used to acquire an understanding of the genetic basis of resistance and to facilitate marker-assisted selection. In the current study, a total of 174 bread wheat accessions from South Asia and CIMMYT were assessed for SNB reactions at the seedling stage in three greenhouse experiments at CIMMYT, Mexico. The results indicated that 129 genotypes were resistant to SNB, 39 were moderately resistant, and only 6 were moderately susceptible. The Genotyping Illumina Infinium 15K Bead Chip was used, and 11,184 SNP markers were utilized to identify marker-trait associations (MTAs) after filtering. Multiple tests confirmed the existence of significant MTAs on chromosomes 5B, 5A, and 3D, and the ones at Tsn1 on 5B were the most stable and conferred the highest phenotypic variation. The resistant genotypes identified in this study could be cultivated in South Asian countries as a preventative measure against the spread of SNB. This work also identified molecular markers of SNB resistance that could be used in future wheat breeding projects.

Keywords: Parastagonospora nodorum; Septoria nodorum blotch; genome-wide association study; host resistance; marker–trait association.

Figure 1

Phenotypic reactions of the tested genotypes. (A) Boxplot distribution of SNB scores for the 174 wheat genotypes in individual experiments. (B) Histogram distribution of mean disease scores over the three experiments.

Figure 2

The “which-won-where” view (A) and GGE biplot (B) based on the G × E interaction of SNB disease scores in three different experiments.

Figure 3

Population structure (A,B) and PCoA plot (C) of the 174 genotypes.

Figure 4

Heatmap and dendrogram of kinship matrix estimated using Van Randen algorithm based on 11,184 SNP markers and 174 wheat genotypes. Yellow colors represent the haploblocks.

Figure 5

Manhattan plots for MTAs detected from individual experiments such as E1 (A), E2 (B), E3 (C) and the pooled data (D). The red horizontal line indicates the significance threshold (p = 0.001) used in the present study.