LG2

9L0.0

3G2.0

7K3.9

14K7.5

(bottom-up)

LG3

2O0.0

5F0.7

6N3.0

8a4.8

(bottom-up)

LG4

4G0.0

6F1.5

7G3.3

6O5.2

(bottom-up)

LG5

5J0.0

2I1.8

6I4.3

(bottom-up)

LG6LG7

LG8 LG9

19b0.0

9b3.1

5h8.7

(bottom-up)

LG2

18b0.0

24b3.1

9k8.7

13012.1

(bottom-up)

LG3 LG4 LG5

cMcM

cMcM

cM

cM

cMcM

cM cM cM cM

12a0.0

4b1.710C1.9

3L3.2

10b3.9

(bottom-up)

3J0.0

4D1.2

7N2.913J3.4

4O5.9

(bottom-up)

13a0.0

6J0.9

9N2.012N2.1

(bottom-up)

5b0.0

9O2.1

11J2.7

10O3.3

(bottom-up)

16b0.0

4D2.1

10F4.310C4.7

(bottom-up)

7F0.0

11J2.1

15F3.4

(bottom-up)

7N0.0

6J0.8

9K2.4

(bottom-up)

13O0.0

4O2.8

9N7.6

(bottom-up)

LG6 LG7cM cM

(a)

(b)Suppl. Fig. 1

No. of ovules/

plant used for

clearing

Apomictic Embryo

sacs

(48 individuals)

Sexual

Embryo sacs

(38 individuals)

Facultative

individuals

Total no. of

plants

10-20 10 (80-90%) 10 (80-90%) 105 191

25-35 18 (90-100%) 20 (90-100%)

More than 40 7 (100%)

25-35 13 (100%)

10-15 8 (90-100%)

Suppl. Table 1 Classification of F2 individuals of Cenchrus ciliaris based on their mode of reproduction as observed after ovule clearing

Parents F1progeny

F2 (progeny)

IG-96-443 (♀) Sexual pollen acceptor

IG-96-3108 (♂)Apomictic pollen donor

Apomictic Sexual

1 2 3 1 2 3

MM 00 M0 00 00 00 MM M0 M0

00 mm m0 mm m0 m0 00 00 00

*Supposing the M allele is from the first parent and the m allele from the second, then the two situations are possible:1) The m allele is the null allele: MM x 00 -> F1: M0 -> F2: MM, M0, 00 2) The M allele is the null allele: 00 x mm -> F1: m0 -> F2: 00, m0, mm

Suppl. Table 2 Pattern of segregation of markers used for JoinMap analysis

AFLP Sequence

ID

Annotation Score e value P value Identities Positives Strand

18GOs08g25650|12008.t02332|unspliced-genomic hypothetical protein

202 (36.4 bits)

0.083 0.079 78/113 (69%) 78/113 (69%) Minus / Plus

19GOs01g38170|12001.t03355|unspliced-genomic retrotransposon protein putative unclassified

138 (26.8 bits)

5.5 0.996 94/156 (60%) 94/156 (60%) Plus / Plus

20GOs01g53250|12001.t04747|unspliced-genomic NADPH reductase TAH18 putative expressed

152 (28.9 bits)

1.3 0.73 56/79 (70%) 56/79 (70%) Minus / Plus

23GOs04g10740|12004.t00905|unspliced-genomic expressed protein

144 (27.7 bits)

3 0.95 62/96 (64%) 62/96 (64%) Minus / Plus

3EOs03g60550|12003.t05293|unspliced-genomic NEDD8-activating enzyme E1 regulatory subunit putative expressed

400 (66.1 bits)

5.00E-17 5.00E-17 96/113 (84%) 96/113 (84%) Minus / Plus

23EOs08g38720|12008.t03607|unspliced-genomic cytochrome c oxidase assembly protein COX15 putative expressed

145 (27.8 bits)

2.7 0.93 59/83 (71%) 59/83 (71%) Minus / Plus

24EOs07g27910|12007.t02483|unspliced-genomic retrotransposon protein putative Ty1-copia subclass

296 (50.5 bits)

5.50E-08 5.50E-08 68/79 (86%) 68/79 (86%) Plus / Plus

25EOs05g40770|12005.t03616|unspliced-genomic protein kinase putative expressed

145 (27.8 bits)

2.7 0.93 95/158 (60%) 95/158 (60%) Minus / Plus

30EOs05g29110|12005.t02560|unspliced-genomic retrotransposon protein putative unclassified

159 (29.9 bits)

0.63 0.47 63/99 (63%) 63/99 (63%) Minus / Plus

31EOs06g48940|12006.t04580|unspliced-genomic ARA1 putative expressed

140 (27.1 bits)

4.6 0.99 66/103 (64%) 66/103 (64%) Plus / Plus

32EOs02g18330|12002.t01626|unspliced-genomic retrotransposon protein putative Ty1-copia subclass

146 (28.0 bits)

2.4 0.91 58/85 (68%) 58/85 (68%) Minus / Plus

34EOs10g34110|12010.t02713|unspliced-genomic hypothetical protein

172 (31.9 bits)

0.15 0.14 70/101 (69%) 70/101 (69%) Plus / Plus

2bOs11g07922|12011.t00683|unspliced-genomic retinol dehydrogenase 12 putative expressed

366 (61.0 bits)

2.20E-10 2.20E-10 86/102 (84%) 86/102 (84%) Plus / Plus

8b None

Suppl. Table 3 Annotation of 42 and 5 AFLP fragments associated with apomictic and sexual modes of reproduction based on BLAST analysis

21bOs03g35326|12003.t03022|unspliced-genomic retrotransposon protein putative unclassified

140 (27.1 bits)

4.5 0.99 30/31 (96%) 30/31 (96%) Minus / Plus

22bOs05g19220|12005.t01688|unspliced-genomic retrotransposon protein putative Ty3-gypsy subclass

143 (27.5 bits)

3.4 0.97 53/76 (69%) 53/76 (69%) Plus / Plus

7aOs05g11080|12005.t00940|unspliced-genomic transposon protein putative CACTA En/Spm sub-class

195 (35.3 bits)

0.015 0.015 117/195 (60%) 117/195 (60%) Minus / Plus

9aOs02g29464|12002.t02640|unspliced-genomic DNA repair protein RAD50 putative expressed

164 (30.7 bits)

0.39 0.32 106/175 (60%) 106/175 (60%) Minus / Plus

10aOs05g11080|12005.t00940|unspliced-genomic transposon protein putative CACTA En/Spm sub-class

194 (35.2 bits)

0.017 0.017 120/205 (58%) 120/205 (58%) Plus / Plus

12a Os05g11080 unspliced-genomic transposon protein195

(35.3 bits)0.015 0.015 117/195 (60%) 117/195 (60%) Minus / Plus

11a Os05g11080 unspliced-genomic transposon protein195

(35.3 bits)0.015 0.015 117/195 (60%) 117/195 (60%) Minus / Plus

21a None

22a Os11g05210 unspliced-genomic retrotransposon protein151

(28.7 bits)1.5 0.77 71/113 (62%) 71/113 (62%) Plus / Plus

23a Os02g51430 unspliced-genomic SEC6215

(38.3 bits)0.0019 0.0019 63/85 (74%) 63/85 (74%) Minus / Plus

2H Os07g10256 unspliced-genomic mitosis protein dim1418

(68.8 bits)9.80E-13 9.80E-13 194/296 (65%) 194/296 (65%) Minus / Plus

6H Os11g29730 unspliced-genomic retrotransposon protein421

(69.2 bits)7.90E-13 7.90E-13 171/263 (65%) 171/263 (65%) Minus / Plus

9H Os07g10256 unspliced-genomic mitosis protein dim1456

(74.5 bits)1.80E-14 1.80E-14 198/309 (64%) 198/309 (64%) Plus / Plus

13H None

4HS Os12g13640 unspliced-genomic HGA6531

(85.7 bits)8.50E-18 8.50E-18 233/342 (68%) 233/342 (68%) Plus / Plus

10HS Os05g16480 unspliced-genomic retrotransposon protein232

(40.9 bits)0.00029 0.00029 136/218 (62%) 136/218 (62%) Plus / Plus

3F Os04g41470 unspliced-genomic protein ariadne-1482

(78.4 bits)1.50E-15 1.50E-15 114/136 (83%) 114/136 (83%) Plus / Plus

13FOs05g50120 unspliced-genomic OsMPK21-1 - putative MAPK based

660 (105.1 bits) 1.20E-23 1.20E-23 146/162 (90%) 146/162 (90%) Plus / Plus

9FSOs08g14109 unspliced-genomic retrotransposon protein Ty1-copia subclass

143 (27.5 bits)

3.4 0.97 85/145 (58%) 85/145 (58%) Plus / Plus

7DOs02g23840 unspliced-genomic retrotransposon protein Ty3-gypsy subclass

152 (28.9 bits)

1.3 0.73 60/85 (70%) 60/85 (70%) Minus / Plus

23D Os05g07020 unspliced-genomic hypothetical protein140

(27.1 bits)4.5 0.99 48/67 (71%) 48/67 (71%) Minus / Plus

24D Os12g01390 unspliced-genomic clathrin heavy chain138

(26.8 bits)5.8c0.997 62/93 (66%) Minus / Plus

*11AFLP sequence did not showed any similarity with rice