Table 2.

Quantitative trait loci (QTL) linked markers used as fixed effects in the least-squares (LS) model for the 46th international bread wheat screening nursery (IBWSN)

Dataset	Marker	Marker synonyma	Chromosome	Genetic position in cM (Popseq map)	Physical position in bps (Popseq map)	Expected genes	Average p value	Average R 2	Frequencyb
Leaf rust
Seedling 2012	GBS_19971	WCSS1_contig1905752_1DS-4628	1DS	5.4	2,073,708	Lr42	<E−16	0.33	1
	GBS_28186	gbsHWWAMP44231	3B	25.3	15,366,258	–	<E−16	0.26	1
	GBS_28376	WCSS1_contig1898017_1DS-2235	1DS	11.0	3,306,922	Lr42	<E−16	0.39	0.9
El Batan 2011	GBS_40747	gbsHWWAMP55344	2D	17.3	8,198,944	–	3.08E−07	0.10	0.8
	GBS_38496	–	–	–	–	–	2.27E−07	0.10	0.7
El Batan 2013	GBS_18425	WCSS1_contig3419689_3AS-1090	3AS	60.6	61,387,121	–	5.08E−10	0.14	1
	GBS_2400	WCSS1_contig3361063_3AS-2705	3AS	53.4	14,901,099	–	2.83E−10	0.13	0.6
	GBS_1491	gbsHWWAMP1393	3AL	63.1	133,091,112	-	3.70E−10	0.14	0.5
Stem rust
Njoro 2011 main	GBS_23856	gbsHWWAMP37196	1AL	86.5	220,028,370	–	3.44E−08	0.12	0.9
	GBS_1505	–	3B	–	91,939	Sr2	6.79E−08	0.11	0.5
Njoro 2011 off	GBS_28025	WCSS1_contig3042477_6BS-5453	6BS	65.1	70,672,093	–	1.18E−08	0.13	1
	GBS_1505	–	3B	–	91,939	Sr2	1.03E−07	0.11	0.6
	GBS_20060	WCSS1_contig2078323_6DS-22,086	6DS	2.5	2,067,639	SrTmp	1.33E−08	0.12	0.5
Stripe rust
Seedling 2013	GBS_702	WCSS1_contig5304580_2AS-10,182	2AS	0	944,474	Yr17	<E−16	0.58	1
Quito 2012							<E−16	0.26	1
Njoro 2011							<E−16	0.27	1
Toluca 2011							<E−16	0.41	1
Toluca 2013							<E−16	0.41	1

^aMarkers prefixed by gbsHWWAMP are from the hard winter wheat association mapping panel available in T3  database and markers prefixed by WCSS1_contig are from the CSS GBS 2014 physical map, where ‘WCSS1’ stands for wheat chromosome survey sequence

^bThe frequency of the marker in the ten cross-validation folds