Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Traita: DOM SNPb: QTLc: qDOM_1_1 Bind: 1.07 S1_206738618 Genee Gene Functionf Zm00001d031988 Transmembrane 9 superfamily member 9 Zm00001d031989 hypothetical protein Zm00001d031990 Protein FATTY ACID EXPORT 1 chloroplastic Zm00001d031991 hypothetical protein Zm00001d031992 iddp1 - indeterminate domain p1 Zm00001d031993 Rhamnogalacturonate lyase family protein Zm00001d031994 hypothetical protein Zm00001d031995 dihydroneopterin aldolase Zm00001d031996 WD repeat-containing protein DWA2 Zm00001d031997 NAD(P)-binding Rossmann-fold superfamily protein Zm00001d032000 hypothetical protein Zm00001d032003 hypothetical protein Zm00001d032004 hypothetical protein Zm00001d032005 hypothetical protein Zm00001d032007 Zinc finger CCCH domain-containing protein 4 Zm00001d032008 NEP1-interacting protein-like 1 Zm00001d032009 Protein TIFY 6B, partial Zm00001d032010 26S proteasome non-ATPase regulatory subunit 3 homolog A Zm00001d032011 Stigma-specific STIG1-like protein 4 Zm00001d032012 hypothetical protein Zm00001d032013 hypothetical protein Zm00001d032015 Aquaporin SIP1-1, partial Zm00001d032016 hypothetical protein Zm00001d032019 acpt1 - acyl carrier protein1) Zm00001d032022 Beta-galactosidase Zm00001d032023 hypothetical protein Zm00001d032024 myb38 - myb transcription factor38 Zm00001d032025 Casein kinase II subunit alpha-4 chloroplastic Zm00001d032026 RNA-binding (RRM/RBD/RNP motifs) family protein Zm00001d032027 THAUMATIN-LIKE PROTEIN 1 Zm00001d032028 ARO1-like protein 1 Zm00001d032029 HEC/Ndc80p family protein Zm00001d032030 Chaperone protein dnaJ 11 chloroplastic Zm00001d032031 ER lumen protein retaining receptor family protein Zm00001d032032 myb167 - MYB-transcription factor 167 Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d032035 cytochrome P450 family 706 subfamily A polypeptide 5 Zm00001d032036 putative carboxylesterase 8 Zm00001d032040 srs1 - SHI/STY (SRS)-transcription factor 1

Traita : DOM SNPb: QTLc : qDOM_3_1 Bind : 3.05 S3_135508643 Genee Gene Functionf Zm00001d041727 40S ribosomal protein S29 Zm00001d041728 hypothetical protein Zm00001d041729 hypothetical protein Zm00001d041730 hypothetical protein Zm00001d041731 hypothetical protein Zm00001d041732 hypothetical protein Zm00001d041733 Peroxisomal membrane 22 kDa Zm00001d041734 hypothetical protein Zm00001d041735 hypothetical protein Zm00001d041738 late embryogenesis abundant protein Zm00001d041741 Cytochrome P450 71D7 Zm00001d041742 hypothetical protein Zm00001d041743 hypothetical protein Zm00001d041744 Protein cornichon homolog 1 Zm00001d041745 hypothetical protein Zm00001d041747 hypothetical protein Zm00001d041748 Ureide permease 5 Zm00001d041750 Glycine-rich RNA-binding protein 3 mitochondrial Zm00001d041751 hypothetical protein Zm00001d041752 ARF guanine-nucleotide exchange factor GNL2 Zm00001d041753 SSXT protein Zm00001d041755 hypothetical protein Zm00001d041756 60S ribosomal protein L6-3 Zm00001d041758 Translation initiation factor eIF-2B alpha subunit Zm00001d041759 Transducin/WD40 repeat-like superfamily protein Zm00001d041760 40S ribosomal protein S9-2 Zm00001d041762 Putative pentatricopeptide repeat- containing protein Zm00001d041763 UDP-glucose:p-hydroxymandelonitrile- O-glucosyltransferase Zm00001d041766 Transcription initiation factor TFIID subunit 8 Zm00001d041767 alf4 - Alfin-like-transcription factor 4 Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d041768 NEP-interacting protein 1 Zm00001d041769 Serine carboxypeptidase-like 20 Zm00001d041770 hypothetical protein Traita: DOM SNPb: S5_21577347, QTLc: qDOM_5_1 Bind: 5.09 S5_21577373 Genee Gene Functionf Zm00001d013812 Polyadenylate-binding protein RBP45C Zm00001d013814 Pentatricopeptide repeat-containing protein Zm00001d013815 Condensin-2 complex subunit H2 Zm00001d013816 DTW domain containing protein Zm00001d013817 Protein FATTY ACID EXPORT 5 Zm00001d013818 Tryptophan N-monooxygenase 2 Zm00001d013819 Galactose mutarotase-like superfamily protein Zm00001d013820 hypothetical protein Zm00001d013821 hypothetical protein Zm00001d013822 Putative disease resistance RPP13-like protein 1 Zm00001d013823 putative L-gulonolactone oxidase 6 Zm00001d013824 F-box domain containing protein expressed Zm00001d013825 F-box domain containing protein expressed Zm00001d013827 mybr99 - MYB-related-transcription factor 99 Zm00001d013828 Switch 2 Zm00001d013829 embryo defective 2016 Zm00001d013830 cytochrome P450 family 76 subfamily C polypeptide 7 Zm00001d013832 hypothetical protein Zm00001d013834 AAA-ATPase Zm00001d013836 Protein kinase superfamily protein Zm00001d013838 Tetratricopeptide repeat (TPR)-like superfamily protein Zm00001d013839 Cytochrome b5 isoform E Zm00001d013840 Ypt/Rab-GAP domain of gyp1p superfamily protein Zm00001d013841 hypothetical protein Zm00001d013842 Heat shock 70 kDa protein Zm00001d013844 methionine γ-lyase Zm00001d013845 E2F transcription factor-like E2FE Zm00001d013847 fringe-related protein Zm00001d013849 thx19 - Trihelix-transcription factor 19 Traita: DOM SNPb: S8_81881327 QTLc: qDOM_8_1 Bind: 8.03 Genee Gene Functionf Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d009813 Nucleotide/sugar transporter family protein Zm00001d009814 Putative leucine-rich repeat receptor-like protein kinase family protein Zm00001d009815 Cactin Zm00001d009816 hypothetical protein Zm00001d009820 hypothetical protein Zm00001d009821 Serine/arginine-rich-splicing factor SR34 Zm00001d009823 lbd35 - LBD-transcription factor 35 Zm00001d009824 OSJNBa0059D20.8-like protein Zm00001d009825 hypothetical protein Zm00001d009826 hypothetical protein Zm00001d009827 Cold-regulated 413 inner membrane protein 2 chloroplastic Zm00001d009828 Heat shock 70 kDa protein 14, partial Zm00001d009829 hypothetical protein Zm00001d009830 hypothetical protein Traita: DOM SNPb: QTLc: qDOM_8_2 Bind: 8.03 S8_100951060, S8_101210332 Genee Gene Functionf Zm00001d010155 Di-glucose binding with Kinesin motor domain-like protein, partial Zm00001d010157 glucose-1-phosphate adenylyltransferase Zm00001d010158 hypothetical protein Zm00001d010159 Actin-1 Zm00001d010161 Radical SAM superfamily protein Zm00001d010162 Histone deacetylase 8 Zm00001d010163 hypothetical protein Zm00001d010166 hypothetical protein Zm00001d010168 bzip116 - bZIP-transcription factor 116 Zm00001d010169 Cysteine-rich receptor-like protein kinase 40 Zm00001d010170 hypothetical protein Zm00001d010171 Soluble inorganic pyrophosphatase 1 Zm00001d010172 fructose-1,6-bisphosphatase Zm00001d010173 Polypyrimidine tract-binding protein homolog 3 Zm00001d010174 Protein LIKE COV 2 Zm00001d010175 ereb113 - AP2-EREBP-transcription factor 113 Zm00001d010176 hypothetical protein Zm00001d010177 Retrotransposon-like protein Zm00001d010178 Protein kinase superfamily protein Zm00001d010179 Putative subtilase family protein Zm00001d010180 (3R)-3-hydroxybutanoyl-[acyl-carrier- protein] hydratase Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d010181 hypothetical protein Zm00001d010182 Cyclin-A1-1 Zm00001d010183 hypothetical protein Zm00001d010184 hypothetical protein Zm00001d010185 hypothetical protein Zm00001d010189 DUF1682 family protein Zm00001d010190 glutamate-oxaloacetate transaminase5 Zm00001d010191 hypothetical protein Zm00001d010192 hagtf34 - GNAT-transcription factor 34 Zm00001d010195 Protein NRT1/ PTR FAMILY 5.10 Zm00001d010196 Asparagine synthetase [glutamine- hydrolyzing] 3 Zm00001d010197 amidophosphoribosyl transferase Zm00001d010198 Zm00001d010199 hypothetical protein Zm00001d010200 2'-deoxyadenosine kinase Zm00001d010201 myb25 - MYB-transcription factor 25 Zm00001d010202 Phosphoribosylanthranilate transferase, mRNA Zm00001d010203 hypothetical protein Zm00001d010204 alpha/beta-Hydrolases superfamily protein Zm00001d010205 Putative patellin family protein Traita: NDF SNPb: QTLc: qNDF_1_1 Bind: 1.08 S1_249307680 Genee Gene Functionf Zm00001d033157 Pleckstrin homology (PH) domain- containing protein Zm00001d033158 jmj22 - JUMONJI-transcription factor 22 Zm00001d033159 DEK domain-containing chromatin associated protein Zm00001d033160 Transposon protein Zm00001d033164 Leucine-rich repeat protein kinase family protein Zm00001d033165 hypothetical protein Zm00001d033166 gras16 - GRAS-transcription factor 16 Zm00001d033167 ACT domain-containing protein ACR4 Zm00001d033168 hypothetical protein Zm00001d033169 Adenine nucleotide alpha hydrolase-like superfamily protein Zm00001d033170 putative E3 ubiquitin-protein ligase RHB1A Zm00001d033171 Thioredoxin superfamily protein, partial Zm00001d033172 Regulator of chromosome condensation (RCC1) family protein Zm00001d033174 gap1 - Golgi associated protein homolog Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d033175 Pentatricopeptide repeat (PPR) superfamily protein Zm00001d033176 hypothetical protein Zm00001d033177 hypothetical protein Zm00001d033180 brd1 - brassinosteroid-deficient dwarf1 Zm00001d033181 fructokinase-like 2, chloroplastic Zm00001d033186 Mitochondrial import receptor subunit TOM5-like protein Zm00001d033187 glycerophosphoryl diester phosphodiesterase, periplasmic Zm00001d033188 UDP-glucose 6-dehydrogenase Zm00001d033189 hypothetical protein Zm00001d033190 hypothetical protein Zm00001d033191 hypothetical protein Zm00001d033192 Os03g0604500-like protein Zm00001d033194 Subtilisin-like protease Zm00001d033195 hypothetical protein Zm00001d033196 Gibberellin-regulated protein 1 Zm00001d033200 Gibberellin-regulated protein 1 Zm00001d033201 hypothetical protein Traita: NDF SNPb: S3_5989084 QTLc: qNDF_3_1 Bind: 3.02 Genee Gene Functionf Zm00001d039439 bzr2 - BZR-transcription factor 2 Zm00001d039440 hypothetical protein Zm00001d039441 hypothetical protein Zm00001d039444 UNE1 Zm00001d039446 dpold3a - DNA polymerase delta subunit 3a Zm00001d039448 Transducin/WD40 repeat-like superfamily protein Zm00001d039449 Putative pentatricopeptide repeat- containing protein Zm00001d039450 4'-phosphopantothenoylcysteine decarboxylase Zm00001d039451 Ribonuclease III family protein Zm00001d039452 DEAD-box ATP-dependent RNA helicase 20 Zm00001d039454 Ectonucleotide pyrophosphatase/phosphodiesterase 1 Zm00001d039455 PRA1 family protein F2 Zm00001d039456 RAP Zm00001d039458 Transducin family protein / WD-40 repeat family protein, partial Zm00001d039459 bhlh70 - bHLH-transcription factor 70 Zm00001d039460 Translation initiation factor SUI1 family protein Zm00001d039461 Harpin-induced protein Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d039462 hypothetical protein Zm00001d039464 hypothetical protein Zm00001d039465 Protein kinase superfamily protein Zm00001d039466 hypothetical protein Zm00001d039467 Protein indeterminate-domain 11 Zm00001d039468 dehydroascorbate reductase Zm00001d039470 EPIDERMAL PATTERNING FACTOR-like protein 3 Zm00001d039471 IQ-domain 6 Zm00001d039472 hypothetical protein Zm00001d039474 AUGMIN subunit 4 Zm00001d039475 mybr22 - MYB-related-transcription factor 22 Zm00001d039477 RNA methyltransferase family protein Zm00001d039480 hypothetical protein Zm00001d039481 F-box/LRR-repeat protein Zm00001d039482 dof7 - C2C2-Dof-transcription factor 7 Zm00001d039483 26S proteasome non-ATPase regulatory subunit 8 homolog A Zm00001d039486 hypothetical protein Zm00001d039487 acs1 - 1-aminocyclopropane-1- carboxylate synthase1 Zm00001d039488 Pollen-specific protein SF21 Zm00001d039489 cytomatrix protein-related Zm00001d039491 hggt3 - homogentisate geranylgeranyltransferase3 Zm00001d039492 myb-like transcription factor family protein Zm00001d039493 2-isopropylmalate synthase Zm00001d039494 SIT4 phosphatase-associated family protein Zm00001d039495 Zinc finger CCCH domain-containing protein 23 Traita: NDF SNPb: QTLc: qNDF_3_2 Bind: 3.05 S3_129967052, S3_129967086 Traita: NDF SNPb: QTLc: qNDF_3_3 Bind: 3.05 S3_129967052, S3_129967086 Genee Gene Functionf Zm00001d041577 hypothetical protein ZEAMMB73_Zm00001d041577 Zm00001d041578 gl6 - glossy6 Zm00001d041579 Zm00001d041580 myb118 - MYB-transcription factor 118 Zm00001d041581 Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d041582 zinc knuckle (CCHC-type) family protein Zm00001d041583 hypothetical protein Zm00001d041584 NB-ARC domain containing protein expressed Zm00001d041585 Zm00001d041586 hypothetical protein Zm00001d041587 mads55 - MADS-transcription factor 55 Zm00001d041588 hypothetical protein Zm00001d041589 Ankyrin repeat family protein Zm00001d041590 rte2 - rotten ear2 Zm00001d041591 hypothetical protein Zm00001d041592 modifier of snc1 Zm00001d041593 cts5 - citrate synthase5 Zm00001d041594 Membrane magnesium transporter Zm00001d041595 Translation elongation factor EF1B/ribosomal protein S6 family protein Zm00001d041596 gpat6 - glycerol-3-phosphate acyltransferase6 Zm00001d041597 Prefoldin subunit 3 Zm00001d041598 hypothetical protein Zm00001d041609 DNA-directed RNA polymerase subunit Zm00001d041611 hypothetical protein Zm00001d041612 Late embryogenesis abundant protein (LEA) family protein Zm00001d041613 guanylyl cyclase 1 Zm00001d041614 uncharacterized Zm00001d041621 uncharacterized Zm00001d041626 AP-3 complex subunit delta Zm00001d041627 Chaperone protein dnaJ 15 Zm00001d041632 Trafficking protein particle complex II- specific subunit 130-like protein Zm00001d041634 hypothetical protein Zm00001d041635 F-box family protein Zm00001d041636 Reverse transcriptase Zm00001d041637 allantoinase Zm00001d041638 Adenine nucleotide alpha hydrolase-like superfamily protein Zm00001d041639 c3h44 - C3H-transcription factor 344 Traita: NDF, ADF SNPb:S3_156634869 QTLc: qNDF_3_4, Bind: 3.05 qADF_3_1 Genee Gene Functionf Zm00001d042244 hak5 - potassium high-affinity transporter5 Zm00001d042245 hypothetical protein Zm00001d042246 nactf80 - NAC-transcription factor 80 Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d042247 5,10-methylenetetrahydrofolate reductase Zm00001d042248 putative anion transporter 3 chloroplastic Zm00001d042250 NAD(P)-binding Rossmann-fold superfamily protein Zm00001d042253 fatty acid α-dioxygenas Zm00001d042254 hypotheticala protein Zm00001d042255 aldolase like Zm00001d042257 Photosynthetic NDH subunit of subcomplex B 5 chloroplastic Zm00001d042258 RING finger protein Zm00001d042259 Prefoldin chaperone subunit family protein Zm00001d042260 Chloroplastic quinone-oxidoreductase Zm00001d042262 Retrovirus-related Pol polyprotein LINE- 1 Zm00001d042263 bhlh175 - bHLH-transcription factor 175 Zm00001d042264 aspartate kinase Zm00001d042265 hypothetical protein Zm00001d042266 eukaryotic initiation factor 3 gamma subunit family protein Zm00001d042267 (arftf10 - ARF-transcription factor 10 Zm00001d042268 crn1 - coryne1 Zm00001d042269 DNAJ heat shock N-terminal domain- containing protein Zm00001d042270 Heavy metal transport/detoxification superfamily protein Zm00001d042271 thx30 - Trihelix-transcription factor 30 Zm00001d042272 Histone-lysine N-methyltransferase H3 lysine-9 specific SUVH4 Zm00001d042273 Zm00001d042274 Sec14p-like phosphatidylinositol transfer family protein Zm00001d042275 Phosphatidylinositol transfer protein CSR1 Zm00001d042276 xylogalacturonan β-1,3- xylosyltransferase Zm00001d042277 Proline iminopeptidase Zm00001d042278 phytanoyl-CoA dioxygenase 2 Zm00001d042279 xylogalacturonan β-1,3- xylosyltransferase Zm00001d042280 Zm00001d042281 xylogalacturonan β-1,3- xylosyltransferase Zm00001d042282 transaldolase Zm00001d042283 hypothetical protein Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d042284 RING/U-box superfamily protein Traita: NDF SNPb: QTLc: qNDF_3_5 Bind: 3.05 S3_164968574 Genee Gene Functionf Zm00001d042427 Ribosomal protein S24/S35 mitochondrial Zm00001d042430 hypothetical protein Zm00001d042432 dcl104 - dicer-like 104 Zm00001d042433 Histone deacetylase HDT1 Zm00001d042434 Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family Zm00001d042435 hypothetical protein Zm00001d042436 mterf11 - mTERF domain protein11) Zm00001d042437 E3 ubiquitin-protein ligase RGLG1 Zm00001d042438 Proline transporter 2 Zm00001d042441 mgt9 - magnesium transporter9 Zm00001d042443 BTB/POZ and TAZ domain-containing protein 2 Zm00001d042444 Ypt/Rab-GAP domain of gyp1p superfamily protein Zm00001d042445 te1 - terminal ear1 Zm00001d042447 jmj18 - JUMONJI-transcription factor 18 Zm00001d042449 BCL-2 binding anthanogene-1 Zm00001d042450 Tetratricopeptide repeat (TPR)- containing protein Zm00001d042451 Vacuolar protein sorting-associated protein 53 A Zm00001d042452 glucosylceramide synthase Traita: NDF SNPb: QTLc: qNDF_5_1 Bind: 5.09 S5_215845523 Genee Gene Functionf Zm00001d018437 Desiccation-associated protein Zm00001d018438 Ypt/Rab-GAP domain of gyp1p superfamily protein Zm00001d018439 diphthine—ammonia ligase Zm00001d018440 uncharacterized Zm00001d018441 P-loop containing nucleoside triphosphate hydrolase superfamily protein Zm00001d018442 Zm00001d018443 Ankyrin repeat family protein Zm00001d018444 Transducin/WD40 repeat-like superfamily protein Zm00001d018445 phos3 - phosphate transporter3 Zm00001d018446 Zm00001d018447 Octicosapeptide/Phox/Bem1p family protein Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d018448 hypothetical protein Zm00001d018449 hypothetical protein Zm00001d018450 Trimeric LpxA-like enzyme Zm00001d018451 F-box protein PP2-B10 Zm00001d018452 Zm00001d018453 Zm00001d018454 glutathione reductase Zm00001d018455 very-long-chain 3-ketoacyl-CoA synthase Zm00001d018456 Proteasome subunit beta type-1 Zm00001d018457 (mannosyl)9-(N-acetylglucosaminyl)2- diphosphodolichol glucosyltransferas Zm00001d018458 hypothetical protein Zm00001d018459 hypothetical protein Zm00001d018460 lug2 - leunig-related2 Zm00001d018461 Thioredoxin Zm00001d018462 uncharacterized Zm00001d018463 Leukotriene A-4 hydrolase-like protein Zm00001d018464 hypothetical protein Zm00001d018465 mybr51 - MYB-related-transcription factor 51 Zm00001d018466 RNA-binding (RRM/RBD/RNP motifs) family protein Zm00001d018467 YCF37-like protein Zm00001d018468 fdh1 - formaldehyde dehydrogenase homolog1 Zm00001d018469 Diphthamide biosynthesis protein 1 Zm00001d018470 Carboxyl-terminal-processing peptidase 2 chloroplastic Zm00001d018471 Nucleic acid-binding OB-fold-like protein Zm00001d018472 Receptor-like serine/threonine-protein kinase ALE2 Zm00001d018473 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein Zm00001d018474 TGL1 Zm00001d018475 CLIP-associated protein Zm00001d018476 Zm00001d018477 Phosphatidylinositol N- acetyglucosaminlytransferase subunit P- related Zm00001d018478 Tubulin-folding cofactor A Zm00001d018479 NADH:ubiquinone oxidoreductase (H+- transporting) Zm00001d018480 Zm00001d018481 myo2 - myosin2 Zm00001d018482 Homeodomain Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d018483 hypothetical protein Zm00001d018484 Actin-related protein 2/3 complex subunit 1A Zm00001d018485 putative voltage-gated potassium channel subunit beta Zm00001d018486 Zm00001d018487 3-ketoacyl-CoA thiolase Zm00001d018488 cyp13 - cytochrome P450 13 Zm00001d018489 Tumor-related protein Zm00001d018490 Pentatricopeptide repeat-containing protein mitochondrial Zm00001d018491 hypothetical protein Zm00001d018492 Zm00001d018493 Protein MID1-COMPLEMENTING ACTIVITY 1, partial Zm00001d018494 putative protein S-acyltransferase 15 Zm00001d018495 Thioredoxin-like 3-2 chloroplastic Zm00001d018496 Pumilio homolog 4 Zm00001d018497 P-loop NTPase domain-containing protein LPA1 homolog 1 Zm00001d018498 Cysteine proteinases superfamily protein Zm00001d018499 Protein kinase superfamily protein Zm00001d018500 ABC transporter G family member 24 Zm00001d018501 Zim17-type zinc finger protein Zm00001d018502 Protein kinase superfamily protein Zm00001d018503 Serine/threonine-protein phosphatase Zm00001d018504 hypothetical protein Zm00001d018505 deoxyhypusine hydroxylase Zm00001d018506 deoxyhypusine hydroxylase Zm00001d018507 Bet1-like SNARE 1-1 Zm00001d018508 DNA-binding protein Zm00001d018509 hypothetical protein Zm00001d018510 hypothetical protein Zm00001d018511 putative E3 ubiquitin-protein ligase RHB1A Zm00001d018512 Ubiquitin carboxyl-terminal hydrolase 2 Zm00001d018513 RING/U-box superfamily protein Zm00001d018514 Protein BTR1 Zm00001d018515 AT-hook motif nuclear-localized protein 9 Zm00001d018516 putative DEAD-box ATP-dependent RNA helicase 48 Zm00001d018517 methionine adenosyltransferase Traita: NDF SNPb: S7_15277504 QTLc: qNDF_7_1 Bind: 7.02 Traita: NDF, ADF SNPb: S7_15277626 QTLc: qNDF_7_1, Bind: 7.02 qADF_7_1 Genee Gene Functionf Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d019062 mha3 - membrane H(+)-ATPase3 Zm00001d019063 calcium-binding EF hand family protein Zm00001d019064 Subtilisin-like protease SBT4.4 Zm00001d019065 Subtilisin-like protease SBT4.4 Zm00001d019066 Subtilisin-like protease SBT4.4 Zm00001d019067 hypothetical protein Zm00001d019068 Actin cross-linking protein Zm00001d019069 hypothetical protein Zm00001d019070 hypothetical protein Zm00001d019071 hydroxymethylglutaryl-CoA reductase Zm00001d019072 hypothetical protein Zm00001d019073 hypothetical protein Zm00001d019074 1,2-dihydroxy-5-(methylthio)pent-1-en- 3-one:oxygen oxidoreductase (formate- forming) Zm00001d019075 RNAligase Zm00001d019076 SAC3 family protein B Zm00001d019077 Glycine cleavage system H protein 2 mitochondrial Zm00001d019078 AAA-ATPase ASD mitochondrial Zm00001d019079 RNA-binding (RRM/RBD/RNP motifs) family protein Zm00001d019081 apx4 - ascorbate peroxidase4 Zm00001d019082 hypothetical protein Zm00001d019083 hypothetical protein Zm00001d019084 RNA-binding (RRM/RBD/RNP motifs) family protein Zm00001d019086 RNA-binding (RRM/RBD/RNP motifs) family protein Zm00001d019087 proline-rich family protein Zm00001d019089 glucose dehydrogenase Zm00001d019090 DDT domain-containing protein DDR4 Zm00001d019091 Vesicle-associated membrane protein 722 Zm00001d019092 CLE family OsCLE701 protein, partial Zm00001d019093 Small GTP-binding protein Zm00001d019094 Hydroxyproline O-galactosyltransferase GALT4, partial Zm00001d019096 ereb153 - AP2-EREBP-transcription factor 153 Zm00001d019098 ereb166 - AP2-EREBP-transcription factor 166 Traita: ADF SNPb: QTLc: qADF_3_1 Bind: 3.05 S3_156814126, S3_156814134,

Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Traita: ADF SNPb: QTLc: qADF_3_2 Bind: 3.05 S3_164968534 Genee Gene Functionf Zm00001d021720 hypothetical protein Zm00001d021721 vpp8 - vacuolar proton pump8 Zm00001d021724 F-box domain containing protein Zm00001d021725 hypothetical protein Zm00001d021726 G-type lectin S-receptor-like serine/threonine-protein kinase B120 Zm00001d021727 G-type lectin S-receptor-like serine/threonine-protein kinase B120 Zm00001d021728 hypothetical protein Zm00001d021729 kik1 - kinase interacting kinase1 Zm00001d021730 USP family protein Zm00001d021731 α-xylosyltransferase Zm00001d021732 α-xylosyltransferase Zm00001d021733 Pentatricopeptide repeat-containing protein chloroplastic Zm00001d021734 Pentatricopeptide repeat-containing protein chloroplastic Zm00001d021736 α-xylosyltransferase Zm00001d021737 pk3 - S-domain class receptor-like kinase3 Zm00001d021738 hypothetical protein Zm00001d021739 PLAC8 family protein Zm00001d021740 hypothetical protein Zm00001d021741 Eukaryotic translation initiation factor 4G Zm00001d021744 hypothetical protein Zm00001d021745 CYCD6 Zm00001d021746 Octicosapeptide/Phox/Bem1p family protein Zm00001d021747 Equilibrative nucleotide transporter 2 Zm00001d021748 bhlh90 - bHLH-transcription factor 90 Zm00001d021751 GC-rich sequence DNA-binding factor- like protein Zm00001d021752 Equilibrative nucleotide transporter 2 Zm00001d021753 Equilibrative nucleotide transporter 2 Zm00001d021754 Lysine-specific demethylase JMJ25 Zm00001d021755 cyanidin 5,3-O-glycosyltransferase Zm00001d021756 putative protein phosphatase 2C 33 Zm00001d021757 cyanidin 5,3-O-glycosyltransferase Zm00001d021758 ADF/NAD(P)-binding oxidoreductase family protein Zm00001d021759 RNA-binding (RRM/RBD/RNP motifs) family protein Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d021760 Pyrophosphate-energized vacuolar membrane proton pump 1 Zm00001d021761 myb105 - MYB-transcription factor 105 Zm00001d021762 inositol 1,4-bisphosphate 1-phosphatase Zm00001d021763 psb29 - photosystem II subunit29 Zm00001d021764 Protein THYLAKOID FORMATION 1 chloroplastic Zm00001d021765 hypothetical protein Zm00001d021766 Sec20 family protein Zm00001d021767 hypothetical protein Zm00001d021768 hypothetical protein Zm00001d021770 isocitrate dehydrogenase Zm00001d021772 hypothetical protein Zm00001d021773 hypothetical protein Zm00001d021774 Membrane lipoprotein lipid attachment site-containing protein-like Zm00001d021775 Sugar carrier protein C Zm00001d021776 Zm00001d021777 ARM repeat superfamily protein Zm00001d021778 hypothetical protein Zm00001d021779 F-box protein SKIP27 Zm00001d021780 Zm00001d021781 Organic cation/carnitine transporter 3 Traita: ADF SNPb: S5_94015884 QTLc: qADF_5_1 Bind: 5.04 Genee Gene Functionf Zm00001d015525 Zinc finger protein 2 Zm00001d015526 Proteasome subunit beta type Zm00001d015527 Phytosulfokine receptor Zm00001d015529 diphosphate:fructose-6-phosphate 1- phosphotransferase Zm00001d015531 nitric oxide synthase Zm00001d015532 hypothetical protein Zm00001d015533 hypothetical protein Zm00001d015534 Ypt/Rab-GAP domain of gyp1p superfamily protein Zm00001d015536 hypothetical protein Zm00001d015538 hypothetical protein Zm00001d015544 Ureide permease 5 Zm00001d015545 hypothetical protein Zm00001d015546 hypothetical protein Zm00001d015548 hypothetical protein Zm00001d015549 knox6 - knotted related homeobox6 Traita: ADF SNPb: QTLc: qADF_6_1 Bind: 6.04 S6_114380959, S6_114380960 Genee Gene Functionf Zm00001d037239 glycine-rich protein Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population Zm00001d037240 dhar4 - glutathione dehydroascorbate reductase4 Zm00001d037241 Methionine aminopeptidase 1D chloroplastic/mitochondrial Zm00001d037242 Urea-proton symporter DUR3 Zm00001d037243 hypothetical protein Zm00001d037244 RING-H2 finger protein ATL46 Zm00001d037245 Putative RING zinc finger domain superfamily protein Zm00001d037246 Defective in cullin neddylation protein Zm00001d037247 Protease Do-like 9 Zm00001d037248 Putative DUF231 domain containing family protein Zm00001d037249 Putative DUF231 domain containing family protein Zm00001d037250 Putative DUF231 domain containing family protein Zm00001d037251 hypothetical protein Zm00001d037252 limtf12 - LIM-transcription factor 12 Zm00001d037254 Putative pentatricopeptide repeat family protein Zm00001d037255 hypothetical protein Zm00001d037257 Chaperone protein dnaJ 16 Zm00001d037258 ROS1 protein Zm00001d037260 Pentatricopeptide repeat-containing protein Zm00001d037261 Pyridoxamine 5'-phosphate oxidase family protein Zm00001d037263 TMV response protein Zm00001d037264 S-adenosyl-L-methionine-dependent methyltransferase superfamily protein Zm00001d037265 O-fucosyltransferase family protein Zm00001d037266 hypothetical protein Zm00001d037267 Alpha-L RNA-binding motif/Ribosomal protein S4 family protein Zm00001d037268 F12M16.11 Zm00001d037270 hypothetical protein Zm00001d037271 ARM repeat superfamily protein Zm00001d037272 Alpha-mannosidase 2 a: DOM:Digestibility of the organic matter; NDF: neutral detergent fibre; ADF: acid detergent fibre. b: The number before the underscores indicates the chromosome and the number after the underscores indicates the marker position. c. The number before the underscores indicates the chromosome and the number after the underscores indicates the QTL within the chromosome. d: A bin is the interval that includes all loci from the leftmost or top Core Marker to the next Core Marker. The genetic maps are divided into 100 segments of Suplementary Table S1: Complete list of candidate genes for QTLs found for forage digestibility traits in a MAGIC population approximately 20 centiMorgans designated with the chromosome number followed by a two-digit decimal. e: Name of the gene in B73 Reference Genome version 4