Table S1 Number of segregating AFLP fragments by primer combination for each of both crosses (F1-2856 and F1-2872) for the species Picea glauca. Primer combinations Total number of polymorphic fragmentsa Primer combinations Total number of polymorphic fragments EcoRI primer Cross F1-2856 Cross F1-2872 EcoRI primer MseI primer Cross F1-2856 Cross F1-2872 13 7 24 13 13 11 10 11 7 15 11 7 29 15 11 5 10 8 15 14 19 11 8 9 9 - 9 23 16 18 9 7 10 8 13 6 9 5 17 10 13 24 13 12 AAG CAA CAT CTA CTC CTG CTT CAG CAT CGC CTA CTC CTG CTT CCAA CCAC CCAG CCAT CCCA CCCG CCCT CCGA CCGC CCGG CCGT CCTA CCTC CCTG CCTT 6 10 11 9 22 3 26 18 12 13 7 24 21 12 12 10 14 14 9 10 11 16 11 11 19 22 - 10 6 25 21 25 19 25 17 17 14 11 17 17 23 16 29 34 MseI primer CAA CAG CTG CCAC CCAG CCAT CCCG CCGA CCGC CCGG CCGT CCTA CCTC CCTG CAA ACT CAC CAG CAT CCT CGC CGT CTC CTG CTT CCAG CCCG CCCT CCGA CCGG CCGT CCTA CCTC CCTG “-”, not tested. ACA ACG Table S2 DNA amplification conditions from 35 SSR primer pairs previously developed from various Picea species. Amplification SSR primer conditions pair PCR programa Referenceb Tm MgCl2 (mM) PGL13 paGB3 SpAC1B8 EAC1D10 UAPgAG150(A) UAPsTG25 SpAG2 pgGB5 paGB8 EAC1G05 EAC6F05 EATC2C01 EAC7F10 EAC6E09 EAC7H07 SpAC03 PAAC17 PAAC19 SpAC1H8 SpAGD1 SpAGH1 PAAC3 SpAC1F7 SpAGC1 SpL3AG1A4 SpAGG3 EAC6B01 EATC1D02A pgGB7 EAC7F08 NACG07 EATC1E03 EAC1F04 UAPgCA91 PGL15 a 42 45 47 48 50 50 50 50 50 52 52 53 53 53 53 53 53 53 55 55 55 55 55 55 55 57 57 57 57 58 TD58 TD58 TD58 60 MicroTD 3.0 5.0 3.5 5.0 2.5 2.5 3.5 5.0 5.0 3.0 3.0 2.5 2.5 2.5 2.5 3.5 5.0 5.0 2.5 2.5 3.5 3.0 5.0 5.0 5.0 2.5 3.0 3.0 5.0 2.5 2.5 2.5 3.5 2.0 1.5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 2 2 2 3 4 4 7 1 6 3 3 1 7 7 6 6 5 6 6 6 1 2 2 1 1 1 2 1 1 1 1 6 5 7 6 6 5 6 3 4 PCR programs as follows: (1) 4 min at 95°C for initial denaturation, 37 cycles of 45 s at 94°C, 45 s at annealing temperature and 45 s at 72°C, followed by 10 min at 72°C; (2) 5 min at 95°C, then 12 cycles of 45 s at 94°C, 45 s at 58°C (temperature decreasing by 0.5°C per cycle until 52°C) and 45 s at 72°C, followed by a second round of 27 cycles of 30 s at 94°C, 30 s at 52°C and 45 s at 72°C, followed by 10 min at 72°C; (3) 5 min at 94°C, then 33 cycles of 30 s at 94°C, 30 s at 60°C and 30 s at 72°C, followed by 5 min at 72°C; (4) 3 min at 94°C, then 2 cycles of 30 s at 94°C, 30 s at 60°C and 30 s at 72°C, followed by 25 cycles of 15 s at 94°C, 15 s at 54°C and 15 s at 72°C, followed by 3 min at 72°C. b 1= Pfeiffer et al. (1997); 2= Scotti et al. (2000); 3= Hodgetts et al. (2001); 4= Rajora et al. (2001); 5= Scotti et al. (2002a); 6= Scotti et al. (2002b); 7= Besnard et al. (2003). Table S3 Number of markers genotyped for each of two crosses in Picea glauca. Type of marker Cross F1-2856 Cross F1-2872 Segregation 1:1 or 1:1:1:1 Segregation 3:1 or 1:2:1 Total Segregation 1:1Segregation or 3:1 or 1:1:1:1 1:2:1 Total Shared markers AFLPs (% msda) 575 (7) 82 (6) 657 (13) 456 (8) 91 (3) 547 (11) 64 SSRs (% msda) 31b (1) 4 (0) 35 (1) 31c (0) 4 (0) 35 (0) 28 ESTPs (% msda) 46d (0) 4 (0) 50 (0) 40d (0) 3 (1) 43 (1) 35 Total (% msda) 652 (8) 90 (6) 742 (14) 527 (8) 98 (4) 625 (12) 127 % markers with distorted segregation, significant at P ≤ 0.01 / number of tests (Bonferroni correction). Including 15 dominant SSR markers. c Including 14 dominant SSR markers. d Including 1 dominant ESTP marker. a b Table S4 Primer sequences of Picea glauca used to amplify orthologous markers mapped in both Pseudotsuga menziesii and Pinus taeda. Marker GenBank accession# Forward primer Reverse primer Length of observed PCR products b (bp) estPg 137G09 - CTACCATGAGCAGCTTTCTGTG CCTCAGTACTCGTCTCCCTCAT 519 estPg 143D03 - GTCAACTCGGGCTATGCTAATC GCCCTCTGCTATGGCTACTG 766 or 783 estPg 152A04 - CGATAACATGCAACCAGGTG ACGAAGCATTCACGGGTAAC 634 estPg 200A01 - GCTCACTTGAAGCTCTCTGAAC GCAGAGACGGGAGAGCAGTA 420 estPg 6C12F - GGATCCAGTGTGATGCTCCT ATTGCGATGGCAGACTAACC 1057c a DNA amplification was carried out by an initial denaturation of 4 min at 95 °C, then 40 cycles of 30 s at 95 °C, 30 s at 60 °C and 1 min at 72 °C, followed by 10 min at 72 °C. b Including intronic regions. c Not taking into account the primer pair length.