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Figure S1. The genetic linkage maps constructed based on 144 simple sequence repeats (SSRs) by using 118 recombinant inbred lines (RILs) from the cross of Yanzhan 1 x Xichang 76-9.

Locus name and corresponding location are indicated on the right hand side, and genetic distances (cM) between them are indicated on the left hand side. Asterisks at the end of the markers denote the significantly distorted loci (*significant distortion at P < 0.05, **P < 0.01 and ***P < 0.001 levels, respectively). The ``Y'' letter indicates marker exhibiting an excess of Yanzhan 1 alleles.

Figures S2. Infection types of `0-9' scales at the adult-plant stage (pictures taken in 2010).

Descriptions of levels:

0 = no visible signs or symptom.

1 = necrotic and/or clorotic flecks; no sporulation.

2 = necrotic and/or chlorotic blotches or stripes; no sporulation.

3 = necrotic and/or chlorotic blotches or stripes; trace sporulation.

4 = necrotic and/or chlorotic blotches or stripes; light sporulation.

5 = necrotic and/or chlorotic blotches or stripes; intermediate sporulation.

6 = necrotic and/or chlorotic blotches or stripes; moderate sporulation.

7 = necrotic and/or chlorotic blotches or stripes; abundant sporulation.

8 = chlorosis behind sporulating area; abundant sporulation.

9 = no necrosis or chlorosis.

Figure S3. Likelihood plots of quantitative trait locus (QTLs) for slow-rusting resistance on chromosomes 2DS, 3AS, 6A and 7BL identified by composite interval mapping in the cross of Yanzhan 1/Xichang 76-9.

(A) Yrq1 on chromosome 2D; (B) Yrq2 on chromosome 3A; (C) Yrq3 on chromosome 6A; and (D) Yrq4 on chromosome 7B. The LOD plot of each trait (LP1S, LP50S and ITA) is represented separately. The LOD score is the log base 10 of the likelihood ratio under the hypotheses of linkage and non-linkage. LOD threshold for each dataset was established by conducting a permutation test with 1 000 permutations. Marker loci are listed to the right and centiMorgan (cM) distances are shown to the left. p, proximal flanking marker; pk, QTL peak marker (i.e. the locus associated with the highest LOD score); d, distal flanking marker.

Figure S4. Collinearity of chromosomal region harboring the newly developed SSRs on chromosome 2DS in wheat between the corresponding genomic region of Brachypodium chromosome 5.

Physical locations corresponding to the SSR-derived scaffolds on the genetic map of 2DS are indicated as million pairs on the genomic region of Brachypodium. Marker loci are listed to the right and centiMorgan (cM) distances are shown to the left. The red shaded region indicates the chromosomal interval harboring Yrq1.

Table S1. Pearson's linear correlation coefficients (r) among traits in 118 recombinant inbred lines (RILs) (F8) derived from the cross Yanzhan1 x Xichang 76-9.

Table S2. Summary of quantitative trait locus (QTL) for slow-rusting resistance to stripe rust in wheat detected by composite interval mapping (CIM).

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