Fig. 1.
Fig. 1.

Scatter plot showing the linkage disequilibrium (LD) decay across the chromosomes (Chr) for 432 durum wheat accessions. The genetic distance in centimorgan (cM) is plotted against the LD estimate (R2) for pairs of single-nucleotide polymorphisms.

 


Fig. 2.
Fig. 2.

Principal component (PC) analysis obtained from 3067 polymorphic single-nucleotide polymorphisms indicating population structure in 432 durum wheat accessions. PC1, PC2, and PC3 explain 15.5, 5.7, and 4.9% variation, respectively. The colors represent clusters: red = Cluster 1; blue = Cluster 2; green = Cluster 3.

 


Fig. 3.Fig. 3.Fig. 3.
Fig. 3.

Manhattan plots showing P-values for single-nucleotide polymorphism (SNP) markers associated with response to leaf rust at seedling and adult plant stages. (A) Races in Mexico El Batán field; (B) races in Mexico Ciudad Obregón field; (C) BBBQJ; (D) MBDSD; (E) MCDSS; (F) BBBDB; (G) race mixture (MHDSB, MFPSB, MLDSB, TBBGJ, TFBJQ, and TFBGQ); (H) races in Minnesota St. Paul field; (I) races in Minnesota Crookston field; (J) BBBQD (North Dakota); (K) BBBQD (Cereal Disease Laboratory). The horizontal dotted red line indicates significant threshold at P-value = 0.001. The black horizontal line indicates significant threshold at positive false discovery rate (pFDR) = 0.1. The SNPs included in stepwise regression are shown in blue stars.

 


Fig. 4.Fig. 4.Fig. 4.Fig. 4.
Fig. 4.

Chromosome locations of significant single-nucleotide polymorphism (SNP)–leaf rust associations in this study relative to mapped known Lr genes. Marker order and locations (left side of chromosome bars) are as reported by Maccaferri et al. (2015). The association mapping results are reported for Puccinia triticina races used at seedling stage in the greenhouse and at artificially inoculated field trials performed in the United States and Mexico. Markers in red are the significant SNP–leaf rust association observed in this study. † Simple-sequence repeat (SSR) marker associated with leaf rust response in durum wheat in Maccaferri et al. study (2010b). The genetic locations of Lr genes are indicated with arrows. The Lr genes assigned to chromosomes but not yet mapped are in a box at the bottom of each chromosome. Centromere position is indicated with a black circle on the chromosome bar. Not all SSR in the tetraploid consensus map (Maccaferri et al. 2015) are presented in this figure, a more saturated genetic map is presented in Supplemental Table S3.