1. Supplementary Figure S7 QTL for silique width in CTF 2 linkage groups A1, A3 and A4 by MQM. Marker names are on the right of the linkage group bar and the positions in centiMorgans (cM) are on the left. The adjacent graphs show the logarithm of odds (LOD) profile for each linkage group. On the X-axis of the graph are the markers and on the Y-axis the corresponding LOD scores. The dotted line drawn parallel to the X-axis on each graph is the LOD threshold. The position of QTL (one LOD interval) is indicated by bars. The two LOD intervals on either side of the peak are represented by whiskers Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene, a homologue of CLAVATA3 in Arabidopsis Theoretical and Applied Genetics Satish Kumar Yadava 1, Kumar Paritosh 1, Priya Panjabi-Massand 1,2, Vibha Gupta 1, Atika Chandra 1,4, Y S Sodhi 1, Akshay K Pradhan 1,2, Deepak Pental 1,2* Address: 1 Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi – 110021. India. 2 Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi – 110021. India. 3 Present address: Department of Botany, University of Delhi, Delhi – 110007. India. 4 Present address: Department of Botany, Maitreyi College, University of Delhi, New Delhi – 110021. India. *Corresponding author dpental@gmail.com Telephone: 91-011-24112609 Fax: 91-011-24116392

2. At4g37510 0.0 cnu_m504a 0.3 nia_m113a 0.5 nia_m110a 0.6 nia_m109a 4.3 At4g35530.1 6.5 At5g60620 9.0 At4g34700.2 11.9 cnu_m143a cnu_m142a 13.1 cnu_m139a 15.1 nia_m096a 19.6 BrGMS783 23.4 BrGMS403 24.0 At4g29660 26.5 At4g29735 28.6 At4g17540 30.0 nia_m085a 38.9 At4g24160 39.6 At4g23860 39.7 nia_m032a cnu_m238a 39.8 cnu_m561a 40.6 BrGMS456 41.9 At1g59740 46.6 At3g19900 47.3 cnu_m462a 47.5 BrGMS7 47.9 cnu_m480a 48.0 BrGMS471 48.3 At1g61620 48.6 At3g51610.1 48.8 BrGMS3083.1 48.9 cnu_m068a 49.3 cnu_m132a 49.4 BrGMS132.2 50.4 At3g17900 55.7 At3g16760 58.4 cnu_m461a 60.1 At3g15190 62.8 cnu_m214a 63.1 At3g12260.3 63.6 At3g11150 67.0 BrGMS226 68.7 At3g07950 69.7 CTF2-Sw1 012345 A1-CTF2 cnu_m421a 0.0 nia_m023a 8.5 BrGMS480 14.2 BrGMS474 14.9 At5g15650 23.6 BrGMS3213 23.9 BrGMS3216 At5g15650 24.4 At5g16650 25.8 At5g16330.1 26.4 At5g17160 26.9 At5g18480 28.7 At5g20130 At5g20060 30.3 At5g56300 34.1 BrGMS126 34.8 BrGMS1502 35.1 At2g33620.1 37.1 At2g33040.1 37.2 At2g30350.2 37.3 BrGMS3072 At2g31750 37.4 BrGMS2971 37.8 At2g36305 38.3 BrGMS8 39.7 cnu_m288a 40.4 BrGMS3444 41.0 BrGMS3124 42.1 BrGMS3125 42.2 BrGMS3126 42.4 At2g43945.1 43.2 At2g44065 43.9 BrGMS74 44.5 BrGMS2980 44.8 At2g45790 45.0 At2g46390.1 At1g14620 45.2 At2g42880 46.4 At2g28520 48.0 BrGMS3120 51.2 cnu_m098a 59.0 At3g04950 62.7 BrGMS312 63.0 BrGMS3209 63.3 BrGMS3274 71.8 At3g12260.1 72.2 cnu_m477a 74.6 cnu_m479a 77.1 BrGMS3083.2 At3g24315 81.0 BrGMS3081 cnu_m320a 81.1 BrGMS3082 BrGMS3080 81.2 At3g21400 81.7 cnu_m073a 82.6 At5g35320 85.1 At3g51100 87.6 cnu_m409a BrGMS134 89.1 nia_m024a 93.7 cnu_m521a 96.9 cnu_m492a 97.0 At4g34700.1 At2g39010 110.1 At4g35905 At4g35530.2 111.7 BrGMS3098 nia_m013a nia_m072a.2 BrGMS3099 112.2 CTF2-Sw3 012345 A3-CTF2 BrGMS867 0.0 At2g44610.1 2.5 At2g42610 4.9 BrGMS2904 6.4 BrGMS82 8.2 At2g39760 9.8 At2g40740 11.4 At2g40890 11.5 cnu_m524a 13.0 cnu_m256a 13.2 At2g38880 14.5 BrGMS678 17.8 At2g35770 21.2 At2g35990 21.7 At2g33620.2 At2g33710 24.0 At2g33040.2 25.5 At2g30350.1 29.9 At2g29530.1 30.3 At2g29540 31.9 At2g29580 32.0 BrGMS336 32.6 BrGMS729 32.9 cnu_m246a 33.7 At2g27170 34.3 tet-o 35.3 nia_m072a.1 42.1 At5g40200 43.1 At2g44860 44.1 At5g40740 45.0 At5g40390 At5g40950 At5g40300 45.1 At5g39220 45.2 At2g21120.1 45.3 At2g22000 45.7 At5g37600.1 At5g57655 47.4 BrGMS223 48.1 At5g37360 48.4 nia_m076a.2 51.2 BrGMS247 62.6 cnu_m436a 68.3 cnu_m566a 69.0 BrGMS2125 69.1 cnu_m123a 69.2 CTF2-Sw4 012345678 A4-CTF2 Supplementary Figure S7 QTL for silique width in CTF 2 linkage groups A1, A3 and A4 by MQM. Marker names are on the right of the linkage group bar and the positions in centiMorgans (cM) are on the left. The adjacent graphs show the logarithm of odds (LOD) profile for each linkage group. On the X-axis of the graph are the markers and on the Y-axis the corresponding LOD scores. The dotted line drawn parallel to the X-axis on each graph is the LOD threshold. The position of QTL (one LOD interval) is indicated by bars. The two LOD intervals on either side of the peak are represented by whiskers