Mapping of Ug99 stem rust resistance in Canadian durum wheat

Figures & data

Table 1. Summary of SNP and DArT markers mapped on different chromosomes in the A9919-BY5C/Strongfield doubled haploid mapping population

Chromosome	Linkage group	Total number of mapped marker	Number of marker used for QTL analysis	Total genetic length (cM)	Map resolution (cM)
1A	1A_1	251	32	58.6	0.2
	1A_2	97	17	19.5	0.2
1B	1B_1	487	41	75.7	0.2
	1B_2	116	18	26.1	0.2
	1B_3	20	3	3.0	0.2
2A	2A_1	117	8	30.4	0.3
	2A_2	188	22	24.8	0.1
2B	2B_1	290	43	51.6	0.2
	2B_2	66	11	20.9	0.3
	2B_3	14	5	16.2	1.2
3A	3A	146	20	53.9	0.4
3B	3B_1	244	44	116.7	0.5
	3B_2	198	18	19.1	0.1
4A	4A	137	32	103.8	0.8
4B	4B_1	109	16	43.5	0.4
	4B_2	23	3	2.9	0.1
5A	5A	241	44	156.4	0.6
5B	5B_1	225	25	41.8	0.2
	5B_2	204	18	39.3	0.2
	5B_3	97	21	35.3	0.4
6A	6A_1	194	22	38.7	0.2
	6A_2	35	8	24.5	0.7
	6A_3	237	38	13.3	0.1
6B	6B	256	27	44.3	0.2
7A	7A_1	445	34	54.8	0.1
	7A_2	6	3	15.1	2.5
	7A_3	40	4	1.6	0.0
7B	7B_1	96	12	49.5	0.5
	7B_2	142	24	32.1	0.2
Total	29	4721	613	1213.4

Note. SNP: single nucleotide polymorphism; DArT: Diversity Array Technology; QTL: quantitative trait locus; cM: centiMorgan.

Fig. 1 Frequency distribution of stem rust infection response (IR) for the doubled haploid mapping population of the cross A9919-BY5C × Strongfield in field nurseries near Njoro, Kenya, during the four consecutive years 2008 to 2011. Stem rust IR for A9919-BY5C and Strongfield are indicated on the graph except A9919-BY5C in 2008 that was missing

Fig. 2 Frequency distribution of stem rust severity (%) for the doubled haploid mapping population of the cross A9919-BY5C × Strongfield in field nurseries near Njoro, Kenya, during the four consecutive years 2008 to 2011. Stem rust severity for A9919-BY5C and Strongfield are indicated on the graph except A9919-BY5C in 2008 that was missing

Fig. 3 Frequency distribution of seedling stem rust infection types (ITs) to Puccinia graminis f. sp. tritici race TTKSK in the biological containment facility at Morden, Manitoba, in March, 2010 for the doubled haploid population of the cross A9919-BY5C × Strongfield. The IT of TTKSK for A9919-BY5C and Strongfield are shown on the graph. The X-axis is the Stakman seedling infection type scale (0–4) where no IT ratings between 2 and 4⁺ occurred and is represented by dashes

Table 2. Quantitative trait loci (QTL) identified for adult plant field infection response (IR) and severity in nurseries in Kenya between years 2008 to 2011, and seedling resistance to stem rust race TTKSK (Ug99) in the A9919-BY5C/Strongfield doubled haploid population, the environment where expressed, chromosome, closest marker or markers to peak LOD and position where located, peak LOD value, percent phenotypic variation explained (R²), additive effect and parental source of favourable allele

QTL designation	Environment	Trait	Chromosome	QTL associated marker-interval	QTL peak (cM)	LOD value^a	R^2 (%)^b	Additive effect^c	Favourable parental allele
QSr.spa-1B	Kenya 2008	IR	1B	wPt-2389 – wPt-3451	2.0	3.7	9.69	−0.65	A9919-BY5C
QSr.spa-1B	Kenya 2008	Severity	1B	BS00062740_51	12.2	4.5	10.19	−10.40	A9919-BY5C
QSr.spa-1B	Kenya 2009	IR	1B	BobWhite_c1456_615 – Ku_c8767_1245	13.1	3.4	8.87	−0.72	A9919-BY5C
QSr.spa-1B	Kenya 2009	Severity	1B	BobWhite_c1456_615 – Ku_c8767_1245	13.1	4.6	13.88	−1.53	A9919-BY5C
QSr.spa-4A	Kenya 2011	Severity	4A	D_GBF1XID01EMISV_148	93.6	3.8	6.48	2.61	Strongfield
QSr.spa-5B	Kenya 2008	IR	5B	Tdurum_contig28868_84 – BobWhite_c7818_278	25.8	4.5	11.95	0.73	Strongfield
QSr.spa-6A	Kenya 2008	Severity	6A	IAAV8377	4.8	12.3	40.68	−13.50	A9919-BY5C
QSr.spa-6A	Kenya 2008	IR	6A	BobWhite_c5092_422	5.0	10.5	35.17	−1.23	A9919-BY5C
QSr.spa-6A	Kenya 2009	Severity	6A	wPt-4589	7.5	9.3	34.20	−2.42	A9919-BY5C
QSr.spa-6A	Kenya 2009	IR	6A	wPt-4589	7.5	7.9	41.84	−1.03	A9919-BY5C
QSr.spa-6A	Kenya 2010	Severity	6A	wPt-7330/wPt-4016 – wPt-0864	6.3	8.0	28.31	−2.91	A9919-BY5C
QSr.spa-6A	Kenya 2010	IR	6A	wPt-7330/wPt-4016 – wPt-0864	6.3	7.6	35.13	−0.37	A9919-BY5C
QSr.spa-6A	Kenya 2011	Severity	6A	wPt-7330/wPt-4016 – wPt-0864	6.3	14.3	46.40	−0.86	A9919-BY5C
QSr.spa-6A	Kenya 2011	IR	6A	wPt-5652	9.1	16.3	45.98	−6.94	A9919-BY5C
QSr.spa-6A	Morden 2010	TTKSK	6A	wPt-7330/wPt-4016 – wPt-0864	6.3	22.2	71.53	−1.02	A9919-BY5C

^amaximum likelihood LOD score for the QTL.

^bphenotypic variation explained by the QTL.

^cpositive values indicate a Strongfield allele, and conversely, negative values indicate an A9919-BY5C allele that minimize the stem rust infection of Puccinia graminis f. sp. tritici (Pgt).

Fig. 4 Correspondence of markers associated with stem rust resistance QTL QSr.spa-6A and markers on genetic maps of chromosome arm 6AS reported in previous studies (Yu et al. 2011, 2014; Guerrero-Chavez et al. 2015; Hiebert et al. 2017). The region corresponds to the location of the Sr8 gene (Bhavani et al. 2008)

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