CB sN11707b 4.1 sN11641a 7.9 CB10097b 8.5 Ra2G PFM niam086niam032a 56.0 Ol12F11b 56.6 Bras041a 60.2 PFM Bras Na14F11a128.4 CB10572 niam096 sN11707a 0.0 sN11641b 10.8 CB10097a11.4 CB niam niam032b Ol12F11a 62.1 Bras041b68.3 Na12C Na14F11b CB10081 niam086 CB10572 A1 chromosomeC1 chromosome 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).

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) Number of individuals Estimated chromosome number

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 CB sN CB nia-m096 Ra2G CZ0b nia-m032 nia-m Bras Na14F11 A1 chromosome % 5.0% 10.0% 15.0% 20.0% 25.0% C1 chromosome CB10081 sN CB nia-M096* 32.5 nia-M086* 55.2 Bras Na12C CB CZ3b C1 chromosome CB10081 sN CB10587*30.6 nia nia Bras041* 60.4 Na12C08* 78.9 CB CZ3b % 5.0% 10.0% 15.0% 20.0% 25.0% b

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 CB sN CB nia-m nia-m Bras Na12C CB CZ3b CB sN CB nia-m096 Ra2G CZ0b nia-m032 nia-m Bras Na14F % 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.