1. CB100810.0 sN11707b 4.1 sN11641a 7.9 CB10097b 8.5 Ra2G09 32.6 PFM34149.6 niam086niam032a 56.0 Ol12F11b 56.6 Bras041a 60.2 PFM668 100.0 Bras067104.9 Na14F11a128.4 CB10572 niam096 sN11707a 0.0 sN11641b 10.8 CB10097a11.4 CB10587 35.2 niam096 37.2 niam032b Ol12F11a 62.1 Bras041b68.3 Na12C08 85.7 107.8 Na14F11b 134.5 CB10081 niam086 CB10572 A1 chromosomeC1 chromosome 0 10000 20000 30000 40000 50000 60000 0100002000030000400005000060000 Peak area of Ol12F11 C allele Peak area of Ol12F11 A allele Supporting Information Fig. S1: Homoeologous markers were used to assess the number of copies of chromosomes A1 and C1 in resynthesized Brassica napus. The markers are shown in red on the A1 and C1 linkage groups (left). The black regions indicate centromeres. An example of allele dosage is shown to the right with marker Ol12F11, where the C allele peak area was compared with the A peak area. Each dot represents a PCR repetition for F 1 -EMZ (blue), CD.S 0 (red) and UG.S 0 (purple, indicated by arrows).

2. Supporting information Fig. S2: Distribution of estimated chromosome number in individuals from the cross between F 1 -EMZ and cv ‘Darmor’ using flow cytometer. Individuals delimited in the grey area were kept for further analysis (F 1 xBn population). 0 10 20 30 40 50 303438424650545862 Number of individuals Estimated chromosome number

3. A1 20% A1 and C1 7% C1 16% non rearr. 57% CD.S 0 x Bn A1 15% A1 and C1 19% C1 20% non rearr. 46% Bn x CD.S 0 Male meiosis Female meiosis (Szadkowski et al. 2010) Supporting information Fig. S3: Comparison between male (Bn x CD.S 0 ) and female (CD.S 0 x Bn) meioses from an identical resynthesized B. napus plant. A similar rate of homoeologous recombination was found (81.5% vs 85.3% on A1, 94.7% vs 73.9 on C1 for Bn x CD.S 0 and CD.S 0 x Bn, respectively, χ square test); however less gametes from male meiosis carried rearrangements as shown in (a) (43.3% vs 54.6% for Bn x CD.S 0 and CD.S 0 x Bn, respectively, p<0.05, χ square test). (b) Rearrangement rates were reduced on C1 for five markers (Star next to marker name). The occurrence of multiple breakpoints per plant was also reduced in male meiosis (on average 0.34 breakpoints per plant vs 0.50 for A1 and 0.31 vs 0.56 for C1 for Bn x CD.S 0 and CD.S 0 x Bn, respectively, p<0.05 χ square test, data not shown). a A1 chromosome CB100810.0 sN11707 3.7 CB10097 8.7 nia-m096 Ra2G09 33.7 CZ0b699112 49.2 nia-m032 nia-m086 56.1 Bras067104.0 Na14F11 A1 chromosome 0.0 3.7 8.7 33.7 49.2 56.1 104.0 0.0 8.7 33.7 49.2 56.1 104.0 0 20 40 60 80 100 120 140 0.0% 5.0% 10.0% 15.0% 20.0% 25.0% C1 chromosome CB10081 sN116417.7 CB1058730.6 nia-M096* 32.5 nia-M086* 55.2 Bras041 60.4 Na12C08 78.9 CB10572 99.0 CZ3b697214 C1 chromosome CB10081 sN116417.7 CB10587*30.6 nia- 32.5 nia- 55.2 Bras041* 60.4 Na12C08* 78.9 CB10572 99.0 CZ3b697214 7.7 30.6 32.5 55.2 60.4 78.9 99.0 0.0% 5.0% 10.0% 15.0% 20.0% 25.0% 0 20 40 60 80 100 120 b

4. A1 chromosome 0% 5% 10% 15% 20% 25% A1 chromosome 82% of genotyping types75% of genotyping types CD.S 0 xBn 0% 5% 10% 15% 20% 25% C1 chromosome CB10081 0.0 sN11641 7.7 CB1058730.6 nia-m096 32.5 nia-m086 55.2 Bras041 60.4 Na12C08 78.9 CB10572 99.0 CZ3b697214106.4 CB100810.0 sN11707 3.7 CB10097 8.7 nia-m096 Ra2G09 33.7 CZ0b699112 49.2 nia-m032 nia-m086 56.1 Bras067104.0 Na14F11 127.6 76% of genotyping types78% of genotyping types UG.S 0 xBn CD.S 0 xBn Supporting Information Fig. 4: The most frequent rearrangement types following a first round of meiosis in different resynthesized Brassica napus. For rearranged A1 chromosomes (left) or C1 chromosomes (right) found in the UG.S 0 xBn (purple bars) or CD.S 0 xBn population (red bars), the respective frequency (%) was represented for each recombined chromatid type that was found two or more times in the population.