Supplementary Tables Table S1. Summary of markers

Supplementary Tables Table S1. Summary of markers in the growth-related QTL regions of C. farreri. LG

Marker

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3

dm10051 df29353 mf34637 f36957 df19122 m106896 df19611 dm28438 df12539 mf96507 dm27311 m82543 f50242 dm33637 dm23547 m124552 m101355 dm25825 df22025 df12165 df31092 dm1403 df35041 f107490 df16474

Position (cM)

LOD

Scaffold name

Length (bp)

Gene annotation

E value

59.45 59.59 59.69 59.82 59.90 59.98 60.32 60.34 61.10 61.15 61.89 64.24 65.08 65.60 65.87 66.54 68.26 34.86 35.86 36.01 36.42 37.4 37.77 38.11 38.3

2.13 2.20 2.20 2.16 2.17 2.21 2.32 2.42 2.51 2.50 2.50 2.45 2.10 2.23 2.31 2.22 2.22 2.25 2.21 2.16 2.54 2.79 2.59 2.52 2.42

scaffold1320728

565

endonuclease-reverse transcriptase

2.00E-07

scaffold1272909

464

hypothetical protein BRAFLDRAFT_121010

4.00E-07

scaffold74435

11,349

Putative transposon-derived protein ZK1236.4

1.00E-08

scaffold1422843

1,103

Gamma-glutamylcyclotransferase

4.00E-05

scaffold256317

2,200

Uncharacterized histidine-rich protein DDB_G0274557

1.00E-04

scaffold427388

6,278

Calmodulin

2.00E-25

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

df20361 df32466 dm31113 df373 f73742 df34508 f79188 df30945 df32061 df1304 df23527 f68558 df5395 m21582 mf24481 dm32217 df35295 f54711 mf67269 dm17312 mf91198 dm31756 m15773 m29115 m84812 dm10549 m109934 m15833 m45497 m10667

38.54 38.85 39.11 39.15 39.37 39.43 39.77 39.81 39.98 40.05 40.1 40.12 40.15 40.17 40.3 40.31 40.33 40.5 40.94 41.08 41.1 41.16 41.17 41.2 41.21 41.22 41.23 41.24 41.25 41.27

2.38 2.52 2.61 2.61 2.64 2.66 2.63 2.56 2.55 2.56 2.72 2.93 2.99 2.98 2.97 2.78 2.63 2.66 2.58 3.26 3.28 3.17 3.18 3.18 3.19 3.19 3.19 3.19 3.19 3.20

scaffold320542

7510

hypothetical protein Y39B6A.1

4.00E-12

Scaffold1408867

1,965

prophet of pit-like transcription factor

1.00E-35

scaffold1445618 scaffold200485

1,557 4,934

Homeobox protein XENK-2 Thioredoxin domain-containing protein 16

1.00E-51 5.00E-12

scaffold1374883 scaffold426677 scaffold44707

754 20,514 644

Uncharacterized protein C20orf26 homolog Putative homeobox protein Meis3-like 1 Putative uncharacterized protein ENSP00000383309

5.00E-20 3.00E-07 5.00E-10

scaffold1435312

1,292

Proteasome activator complex subunit 4

1.00E-13

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

dm5251 m102012 dm19900 dm15827 dm2009 dm24465 dm10532 mf38089 dm28913 dm16626 dm20549 dm14182 m122610 dm27550 m66732 mf85827 dm14807 m19159 m114454 dm7095 dm17216 dm4245 dm22195 dm35745 m122995 dm3534 dm2484 dm23897 dm7530 dm25984

41.28 41.29 41.31 41.36 41.42 41.47 41.49 41.57 41.6 41.61 41.63 41.65 41.75 41.82 41.97 42.62 43.15 43.19 43.29 43.34 43.35 43.36 43.38 43.4 43.41 43.47 43.48 43.49 43.67 43.68

3.20 3.20 3.20 3.21 3.47 3.53 3.30 3.23 3.23 3.23 3.23 3.23 3.23 3.23 3.23 3.17 3.35 3.51 3.51 3.52 3.52 3.52 3.52 3.52 3.52 3.52 3.52 3.52 3.53 3.52

scaffold177666 scaffold19346

9,343 1,543

Coagulation factor V Acid trehalase-like protein 1

1.00E-05 4.00E-10

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

m2349 dm7034 m55167 dm34964 f53523 df32988 dm32414 dm17351 df14330 m91314 dm8647 dm6422 m68992 dm9901 m74301 f17843 m119628 dm19756 dm25598 dm30625 dm35428 dm25566 dm33930 dm6973 dm7474 dm21147 m48146 df29617 dm18664 m54253

43.75 44.07 44.62 45.2 46.09 46.49 47.11 47.46 47.47 47.89 48.01 48.2 48.38 48.44 48.7 48.72 48.83 48.93 49.33 49.93 51.22 51.79 52.07 52.14 53.11 53.37 53.61 53.99 54.1 54.16

3.52 3.51 3.65 3.45 3.13 3.13 3.25 3.34 3.37 3.23 3.16 3.35 3.53 3.55 3.68 3.76 3.69 3.59 3.48 3.41 3.35 2.77 2.69 2.89 2.72 2.55 2.49 2.45 2.42 2.45

scaffold417721

4,360

Acid trehalase-like protein 1

4.00E-14

scaffold1455365 scaffold1440555

2,204 1,406

Solute carrier family 46 member 3 Poly [ADP-ribose] polymerase 1

3.00E-28 2.00E-14

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

dm9752 dm28988 m53802 df23316 dm17643 dm21379 m32758 m92420 df19261 df29295 df21743 df25793 df15013 f108589 dm17734 f35141 df7316 df9244 dm22517 mf21185 df32796 dm15675 dm15029 dm22320 dm25622 m49962 m92616 dm25876 m108631

54.26 54.32 54.49 56.01 56.5 56.7 56.82 57.07 57.38 57.4 57.44 57.57 57.7 57.79 57.81 57.83 58.04 58.13 58.54 58.7 59.25 60.72 60.74 60.94 60.97 61.26 61.27 61.4 61.59

2.54 2.62 2.62 2.71 2.70 2.63 2.62 2.61 2.60 2.83 2.99 2.77 2.59 2.59 2.59 2.58 2.52 2.43 2.76 2.26 3.33 2.72 2.58 2.57 2.55 2.53 2.50 2.49 2.43

scaffold262249

4,234

scaffold1300671

518

Retrovirus-related Pol polyprotein from transposon 297

4.00E-82

Myosin-I heavy chain

8.00E-38

Table S2. Summary of 27 sex-related markers in C. farreri. LG 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

Marker df5716 f130598 f24948 df624 df12252 df14782 f93422 f83709 f124909 df29018 df18745 df24116 df25477 df7620 f52564 df10409 df12488 f121322 df9717 f56575 f130246 f60478 df29898 f77824 df23546 df11926 f49902

Position (cM) 32.05 33.77 33.94 33.96 33.99 34.01 34.6 34.61 34.63 34.64 34.65 34.73 34.74 34.75 34.76 34.77 34.78 34.93 34.94 34.96 34.99 35.54 35.58 35.63 35.76 35.78 36.07

LOD 15.68 17.18 15.96 17.01 18.67 17.88 16.79 17.2 20.39 17.75 18.16 17.02 18.99 18.16 17.72 17.57 17 20.39 19.56 20.18 18.17 17.08 17.02 17.49 17.79 17.36 14.77

Scaffold name

Length(bp)

Gene annotation

E value

scaffold1254680

434

NFX1-type zinc finger-containing protein 1

2.00E-36

scaffold1313899

548

hypothetical protein BRAFLDRAFT_223334

6.00E-06

scaffold1446481 scaffold236631 scaffold344960

1589 4454 3213

Ephrin type-B receptor 3 Synaptobrevin Endoglucanase E-4

1.00E-34 1.00E-10 2.00E-11

scaffold1446035

1572

DNA-directed RNA polymerase. mitochondrial

1.00E-10