%!PS-Adobe-3.1
Supplemental Table 1. Polymorphism in the interspecific BC1, position and linkage information, and parental species assignment of all markers used in the present study																
Marker	Source	Polymorphism type	Heterozygosity in parents	Populus trichocarpa Genome Assembly v2 chromosome assignment 	Populus trichocarpa Genome Assembly v2 position	Linkage group in maternal segregation (BET3)	Linkage group in paternal segregation (J1)	Freq allele 1 (alba/tremula)	Freq allele 2 (alba/tremula)	Odds-ratio allele 1 (alba/tremula)	Odds-ratio allele 2 (alba/tremula)	Test result allele 1	Test result allele 2	Assignment of BET3 alleles		
ORPM 137	(b)	SSR	N	1	9087325	-	-	0.969/0.000	0.969/0.000	14.00/0.00	14.00/0.00	ALBA	ALBA	N		
GCPM 124	(a)	SSR	F	1	9131199	NA	-	0.990/0.144	0.005/0.125	42.2/0.07	0.11/2.90	ALBA	TREMULA	Y		
ORPM 030_2	(b)	SSR	N	1	NF	-	-	1.000/0.755	1.000/0.755	0.00/0.29	0.00/0.29	ALBA	ALBA	N		
ASP 376	(e)	SSR	H	1	13305781	1	1	0.768/0.046	0.000/0.231	3.18/0.05	0.00/3.34	ALBA	TREMULA	Y		
PMGC 2852	(a)	SSR	H	1	14548235	1	1	0.009/0.000	ND	1.55/0.00	ND	NS	-	L		
ASP 302	(e)	SSR	H	1	30444460	NA	1	0.041/0.067	0.412/0.163	0.81/1.36	1.45/0.40	NS	ALBA	(Y)		
GCPM 1719	(a)	SSR	M	1	35488299	-	1	0.613/0.255	0.613/0.255	1.61/0.35	1.61/0.35	ALBA	ALBA	N		
GCPM 1274	(a)	SSR	H	1	45729652	NA	1	0.837/0.783	0.163/0.217	1.55/0.45	0.93/1.32	ALBA	NS	(Y)		
GCPM 1158	(a)	SSR	M	2	2786953	-	NA	0.484/0.925	0.484/0.925	0.53/6.86	0.53/6.86	TREMULA	TREMULA	N		
GCPM 1376	(a)	SSR	N	2	23223011	-	-	0.935/0.213	0.935/0.213	6.42/0.12	6.42/0.12	ALBA	ALBA	N		
GCPM 1133	(a)	SSR	H	3	4716200	NA	NA	0.006/0.735	ND	0.02/7.02	ND	TREMULA	-	(Y)		
ORPM 30_1	(b)	SSR	M	3	10738041	-	3	0.253/0.404	0.253/0.404	0.77/1.54	0.77/1.54	TREMULA	TREMULA	N		
GCPM 1887	(a)	SSR	M	3	11096030	-	3	0.000/0.000	0.000/0.000	0.00/0.00	0.00/0.00	NS	NS	N		
GCPM 1629	(a)	SSR	H	3	11310099	NA	3	0.211/0.682	0.042/0.000	0.62/5.02	1.24/0.00	TREMULA	NS	(Y)		
ORPM 203	(b)	SSR	N	3	12009761	-	-	0.955/0.454	0.955/0.454	6.50/0.25	6.50/0.25	ALBA	ALBA	N		
AQ	(d)	Indel	H	3	13317983	NA	3	ND	ND	-	-	-	-	N		
GCPM 1688	(a)	SSR	H	3	17574301	NA	NA	0.447/0.133	0.237/0.750	2.36/0.45	0.25/2.44	ALBA	TREMULA	Y		
GAD	(d)	Indel	F	4	6069536	4	-	ND	ND	-	-	-	-	L		
ORPM 127	(b)	SSR	F	4	6447111	4	-	0.983/0.556	0.000/0.133	11.18/0.24	0.00/3.31	ALBA	TREMULA	Y		
ORPM 220	(b)	SSR	F	4	NF	4	-	0.000/0.259	1.000/0.009	0.00/3.45	0.00/0.01	TREMULA	ALBA	Y		
GCPM 1809	(a)	SSR	N	4	9110826	-	-	1.000/0.418	1.000/0.418	0.00/0.18	0.00/0.18	ALBA	ALBA	N		
DE	(d)	Snapshot-SNP	F	4	17018435	NA	-	ND	ND	-	-	-	-	N		
GCPM 1255	(a)	SSR	F	5	1728177	5	-	0.000/1.000	1.000/0.000	0.00/0.00	0.00/0.00	TREMULA	ALBA	Y		
GCPM 1192	(a)	SSR	F	5	4083913	5	-	0.552/0.000	0.297/1.000	1.35/0.00	0.66/0.00	ALBA	TREMULA	Y		
PER1	(d)	Indel	F	5	5054897	5	-	ND	ND	-	-	-	-	L		
GCPM 1838	(a)	SSR	M	5	8802188	-	NA	0.813/0.234	0.813/0.234	2.63/0.19	2.63/0.19	ALBA	ALBA	N		
GCPM 20	(a)	SSR	N	5	23171353	-	-	0.913/0.981	0.913/0.981	0.71/3.49	0.71/3.49	TREMULA	TREMULA	N		
WPMS 15	(c)	SSR	F	5	25424511	NA	-	0.000/0.088	0.015/0.000	0.00/3.11	1.53/0.00	TREMULA	NS	(Y)		
GCPM 139	(a)	SSR	F	6	2280933	6	-	0.576/0.000	ND	2.13/0.00	ND	ALBA	-	(Y)		
GCPM 1831	(a)	SSR	H	6	3671072	6	6	0.000/0.167	0.016/0.029	0.00/3.21	0.77/1.43	TREMULA	NS	(Y)		
GCPM 1074	(a)	SSR	F	6	3989327	6	-	0.000/0.954	1.000/0.046	0.00/39.8	0.00/0.03	TREMULA	ALBA	Y		
ORPM 26	(b)	SSR	H	6	5786927	6	6	0.577/0.000	0.005/0.980	2.32/0.00	0.01/90.59	ALBA	TREMULA	Y		
ORPM 167	(b)	SSR	F	6	5820900	6	-	0.000/0.991	0.984/0.000	0.00/191.00	37.00/0.00	TREMULA	ALBA	Y		
AS1	(d)	Snapshot-SNP	F	6	6291114	6	-	ND	ND	-	-	-	-	L		
GCPM 1485	(a)	SSR	N	6	7166708	-	-	0.964/0.990	0.964/0.990	0.74/2.83	0.74/2.83	NS	NS	N		
PHE	(d)	Snapshot-SNP	F	6	10031860	6	-	ND	ND	-	-	-	-	L		
AP2	(d)	Snapshot-SNP	M	6	11403862	-	NA	ND	ND	-	-	-	-	N		
ASP 933	(e)	SSR	F	6	13019628	6	-	0.000/0.066	0.745/0.000	0.00/2.98	3.12/0.00	TREMULA	ALBA	Y		
ORPM 190	(b)	SSR	F	6	13717996	6	-	0.828/0.000	0.000/0.740	4.15/0.00	0.00/8.11	ALBA	TREMULA	Y		
GCPM 2034	(a)	SSR	H	6	22218920	6	6	0.000/0.923	ND	0.00/25.5	ND	TREMULA	-	(Y)		
ORPM 369	(b)	SSR	M	6	22796592	-	6	0.691/0.068	0.691/0.068	1.65/0.05	1.65/0.05	ALBA	ALBA	N		
ORPM 60	(b)	SSR	F	6	23655062	6	-	0.732/0.065	0.041/0.824	2.80/0.07	0.09/9.90	ALBA	TREMULA	Y		
GCPM 1065	(a)	SSR	F	6	24118972	6	-	0.005/0.260	ND	0.05/3.28	ND	TREMULA	-	(Y)		
ASP 322	(e)	SSR	H	6	25184584	6	6	0.000/0.566	0.240/0.000	0.00/5.17	1.73/0.00	TREMULA	ALBA	Y		
GCPM 1260	(a)	SSR	N	7	3438279	-	-	0.011/0.510	0.011/0.510	0.05/4.48	0.05/4.48	TREMULA	TREMULA	N		
WPMS 17	(c)	SSR	N	7	8695999	-	-	ND	ND	-	-	NS	NS	N		
GCPM 1416	(a)	SSR	N	7	9247483	-	-	0.969/0.978	0.969/0.978	0.94/1.36	0.94/1.36	NS	NS	N		
GCPM 1295	(a)	SSR	F	7	NF	NA	-	0.798/0.043	0.202/0.957	2.13/0.02	0.47/40.78	ALBA	TREMULA	Y		
ORPM 312	(b)	SSR	H	7	11625105	NA	NA	0.386/0.110	0.157/0.050	2.18/0.43	1.79/0.51	ALBA	TREMULA	Y		
GCPM 2062	(a)	SSR	F	8	5051202	8	-	0.637/0.000	0.047/0.222	2.57/0.00	0.40/2.29	ALBA	TREMULA	Y		
PHYB	(d)	Snapshot-SNP	F	8	6560536	8	-	ND	ND	-	-	-	-	L		
ORPM 374	(b)	SSR	F	8	6575398	8	-	0.000/0.000	0.000/0.000	0.00/0.00	0.00/0.00	NS	NS	L		
ORPM 376	(b)	SSR	H	8	6626259	8	NA	ND	ND	-	-	-	-	L		
ORPM 202	(b)	SSR	F	8	13152048	NA	-	0.954/0.69	0.000/0.010	3.25/0.35	0.00/2.98	ALBA	NS	(Y)		
ORPM 268	(b)	SSR	M	8	13427006	-	NA	0.295/0.000	0.295/0.000	1.81/0.00	1.81/0.00	ALBA	ALBA	N		
GCPM 1949	(a)	SSR	N	9	1444377	-	-	0.619/0.263	0.619/0.263	1.40/0.31	1.40/0.31	ALBA	ALBA	N		
ORPM 23	(b)	SSR	H	9	4156608	NA	NA	0.000/0.314	0.040/0.000	0.00/3.49	1.61/0.00	TREMULA	ALBA	Y		
ORPM 21	(b)	SSR	N	9	5179553	-	-	1.000/1.000	1.000/1.000	0.00/0.00	0.00/0.00	NS	NS	N		
THAU	(d)	Indel	H	9	10733809	NA	NA	0.308/0.000	ND	2.44/0.00	-	ALBA	-	(Y)		
GCPM 1250	(a)	SSR	F	10	1292471	5*	-	0.936/0.136	0.064/0.864	4.03/0.04	0.25/23.05	ALBA	TREMULA	Y		
GCPM 2020	(a)	SSR	H	10	8741853	NA	NA	0.247/0.000	0.000/0.585	1.73/0.00	0.00/5.41	ALBA	TREMULA	Y		
ORPM 344	(b)	SSR	F	10	14738629	10	-	0.000/0.343	0.758/0.259	0.00/3.73	2.27/0.25	TREMULA	ALBA	Y		
GCPM 1574	(a)	SSR	F	10	16527911	10	-	1.000/0.000	0.000/0.029	0.00/0.00	0.00/2.84	ALBA	TREMULA	Y		
ORPM 149	(b)	SSR	F	10	16581692	10	-	0.000/0.327	0.959/0.000	0.00/3.80	14.00/0.00	TREMULA	ALBA	Y		
GCPM 114	(a)	SSR	N	10	20637517	-	-	0.995/0.064	0.995/0.064	86.34/0.03	86.34/0.03	ALBA	ALBA	N		
GCPM 1037	(a)	SSR	N	11	several	-	-	0.814/0.630	0.814/0.630	1.45/0.56	1.45/0.56	ALBA	ALBA	N		
GCPM 154	(a)	SSR	F	12	8796415	12	-	0.000/0.028	ND	0.00/2.79	ND	TREMULA	-	(Y)		
WPMS 05	(c)	SSR	F	12	9208533	12	-	0.397/0.000	0.000/0.060	1.85/0.00	0.00/3.06	ALBA	TREMULA	Y		
GCPM 1186	(a)	SSR	H	12	13872323	NA	NA	0.000/0.725	ND	0.00/7.79	ND	TREMULA	-	(Y)		
PHYA	(d)	Snapshot-SNP	F	13	19556	NA	-	ND	ND	-	-	-	-	N		
ORPM 16	(b)	SSR	H	30 (13)	/282451/	NA	NA	0.563/0.217	0.438/0.783	1.31/0.28	0.76/3.54	ALBA	TREMULA	Y		
GCPM 1353	(a)	SSR	M	13	817443	-	NA	0.896/0.294	0.896/0.294	3.92/0.19	3.92/0.19	ALBA	ALBA	N		
GCPM 1292	(a)	SSR	F	14	8054865	14	-	1.000/0.000	0.000/1.000	0.00/0.00	0.00/0.00	ALBA	TREMULA	Y		
GCPM 1812	(a)	SSR	N	14	9862226	-	-	0.098/0.402	0.031/0.314	0.43/2.64	0.22/3.10	TREMULA	TREMULA	N		
EN	(d)	Snapshot-SNP	F	14	10523850	14	-	ND	ND	-	-	-	-	L		
GCPM 2014	(a)	SSR	N	14	13260233	-	-	1.000/1.000	1.000/1.000	0.00/0.00	0.00/0.00	NS	NS	N		
GCPM 1894	(a)	SSR	F	15	809286	15	-	0.000/0.980	0.818/0.000	0.00/97.00	3.86/0.00	TREMULA	ALBA	Y		
GCPM 1454	(a)	SSR	H	15	913028	15	15	0.000/0.281	0.309/0.531	0.00/3.72	0.72/1.82	TREMULA	TREMULA	L		
GCPM 1608	(a)	SSR	H	15	4979950	15	15	ND	0.346/0.000	ND	1.85/0.00	-	ALBA	(Y)		
ORPM 430	(b)	SSR	N	15	10362678	-	-	ND	ND	-	-	-	-	N		
ORPM 14	(b)	SSR	N	16	NF	-	-	0.959/0.943	0.959/0.943	1.14/0.82	1.14/0.82	NS	NS	N		
GCPM 1381	(a)	SSR	N	17	6100061	-	-	0.168/1.000	0.168/1.000	0.41/0.00	0.41/0.00	TREMULA	TREMULA	N		
ORPM 214	(b)	SSR	F	18	4583970	18	-	0.000/0.721	1.000/0.087	0.00/7.76	0.00/0.04	TREMULA	ALBA	Y		
GCPM 1577	(a)	SSR	H	18	6073880	18	18	0.005/0.971	0.321/0.000	0.01/63.36	1.79/0.00	TREMULA	ALBA	Y		
ORPM 28	(b)	SSR	M	18	11993222	-	18	0.375/0.923	0.375/0.923	0.46/9.14	0.46/9.14	TREMULA	TREMULA	N		
SOS2	(d)	Indel	N	18	13517223	-	-	ND	ND	-	-	-	-	N		
GCPM 162	(a)	SSR	H	18	14881684	NA	18	0.016/0.000	0.000/0.265	1.52/0.00	0.00/3.67	NS	TREMULA	(Y)		
Yin8	(f)	SSR	N	19	113246	-	-	ND	ND	ND	ND	-	-	N		
Yin2	(f)	SSR	F	19	863793	19	-	0.250/0.000	0.000/0.093	2.64/0.00	0.00/1.90	ALBA	TREMULA	Y		
ORPM 276	(b)	SSR	F	19	886814#	NA	-	ND	ND	-	-	-	-	N		
con3.1	(g)	SSR	M	19	NF	-	19	0.000/ND	0.000/ND	ND	ND	-	-	N		
con49.1	(g)	SSR	H	19	1291484#	19	19	0.000/ND	0.174/ND	ND	ND	-	-	L		
con49.2	(g)	SSR	H	19	1296123#	19	19	0.000/0.000	0.289/0.173	ND	0.73/1.43	-	NS	L		
con52.4	(g)	SSR	F	19	1342437	1*	-	0.000/ND	0.000/ND	ND	ND	-	-	N		
con58.1	(e)	SSR	H	19	1426114	19	19	0.000/ND	0.000/ND	ND	0.00/0.00	-	NS	L		
Yin1	(f)	SSR	F	19	2861202#	19	-	0.250/0.000	0.000/0.093	2.64/0.00	0.00/1.90	ALBA	TREMULA	Y		
con7.1	(g)	SSR	N	19	2977881	-	-	ND	ND	ND	ND	-	-	N		
ORPM 206	(b)	SSR	F	19	3629960	19	-	0.000/0.373	0.944/0.000	0.00/4.06	10.27/0.00	TREMULA	ALBA	Y		
																
																
LEGEND																
																
Heterozygosity																
X: did not amplify																
H: heterozygous for both parents																
F: heterozygous for the female parent (BET3) only																
M: heterozygous for the male parent (J1) only																
N: homozygous for both parents																
Position																
Marker positions and order following Populus trichocarpa Genome Assembly v2. For some markers, ambiguous locations on Genome Assembly v2 were resolved using the linkage mapping data.																
NF: not found in Populus trichocarpa Genome Assembly v2																
# Marker found in more than one chromosomal position in Populus trichocarpa Genome Assembly v2																
Linkage mapping																
NA: not assigned																
* Marker maps to a different chromosome in Populus trichocarpa Genome Assembly v2																
Allele frequency and odd ratio																
ND: no data																
Test result																
NS: assigment not significant																
Assignment																
Y: both alleles clearly assigned																
L: alleles assigned through linkage with other, clearly assigned loci																
(Y): one allele clearly assigned																
N: not assigned																
																
																
Primer sources																
(a) http://www.ornl.gov/sci/ipgc/ssr_resource.htm																
(b) Tuskan et al. 2004 Canadian Journal of Forest Research																
"(c) van der Schoot et al. 2000 Theor Appl Genet; and Smulders et al. 2001 Mol Ecol Notes"																
(d) Joseph & Lexer 2008 Mol Ecol Notes																
(e) de Carvalho et al. 2010 Mol Ecol																
(f) Yin et al. 2009 New Phytologist																
(g) Newly developed from scaffold 117, known to be homologous to chromosome XIX (see Supp. Table 2 for primer info)																
																
See Joseph and Lexer (2008), de Carvalho et al. (2010) and Lexer et al. (2010) for additional details of the markers.