S_Table 2. Genes related to each trait searched through QTL analysis.

(A) Height
LG Gene name Functional annotation
1 AT5G54280 myosin 2
AT5G54270 light-harvesting chlorophyll B-binding protein 3
Potri.001G407200 no_info
AT5G54260 DNA repair and meiosis protein (Mre11)
Potri.001G407401 no_info
Potri.001G407500 no_info
Potri.001G407650 no_info
AT5G54250 cyclic nucleotide-gated cation channel 4
AT4G27360 Dynein light chain type 1 family protein
Potri.001G408001 no_info
Potri.001G408100 no_info
AT5G54110 membrane-associated mannitol-induced
Potri.001G408300 no_info
Potri.001G408400 no_info
Potri.001G408500 no_info
Potri.001G408700 no_info
AT3G20630 ubiquitin-specific protease 14
Potri.001G408900 no_info
Potri.001G408950 no_info
AT4G27330 sporocyteless (SPL)
AT4G27320 Adenine nucleotide alpha hydrolases-like superfamily protein
Potri.001G409300 no_info
Potri.001G414600 no_info
Potri.001G414677 no_info
AT4G27310 B-box type zinc finger family protein
9 AT1G49570 Peroxidase superfamily protein
AT3G19090 RNA-binding protein
AT4G37180 Homeodomain-like superfamily protein
AT4G37180 Homeodomain-like superfamily protein
AT1G49520 SWIB complex BAF60b domain-containing protein
AT2G15820 endonucleases
AT4G33950 Protein kinase superfamily protein
AT4G33960 no_info
AT3G50440 methyl esterase 10
9 Potri.009G107350 no_info
AT3G50440 methyl esterase 10
AT3G19000 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
AT3G19000 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
AT2G15860 no_info
17 AT5G37475 Translation initiation factor eIF3 subunit
AT1G68270 AMP-dependent synthetase and ligase family protein
Potri.017G138401 no_info
AT1G68270 AMP-dependent synthetase and ligase family protein
AT3G54230 suppressor of abi3-5
AT1G69990 Leucine-rich repeat protein kinase family protein
AT3G03190 glutathione S-transferase F11
Potri.017G139000 no_info
AT5G37180 sucrose synthase 5
Potri.017G139300 no_info
AT1G65900 no_info
AT1G65910 NAC domain containing protein 28
AT1G65920 Regulator of chromosome condensation (RCC1) family with FYVE zinc finger domain
Potri.017G139650 no_info
AT5G17290 autophagy protein Apg5 family
AT3G03210 (1 of 48) PF13839 - GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase)
Potri.017G139900 no_info
AT3G03220 expansin A13
Potri.017G140066 no_info
Potri.017G140132 no_info
AT1G65810 P-loop containing nucleoside triphosphate hydrolases superfamily protein
AT1G65810 P-loop containing nucleoside triphosphate hydrolases superfamily protein
AT1G65810 P-loop containing nucleoside triphosphate hydrolases superfamily protein
Potri.017G140400 no_info
AT1G65810 P-loop containing nucleoside triphosphate hydrolases superfamily protein
AT1G65810 P-loop containing nucleoside triphosphate hydrolases superfamily protein
Potri.017G140700 no_info
AT4G02230 Ribosomal protein L19e family protein
AT1G65820 microsomal glutathione s-transferase, putative
AT5G37020 auxin response factor 8
(B) Diameter at root collar
1 Potri.001G392050 no_info
AT2G42590 general regulatory factor 9
Potri.001G392300 no_info
AT4G18596 Pollen Ole e 1 allergen and extensin family protein
AT1G78870 ubiquitin-conjugating enzyme 35
Potri.001G392601 no_info
AT3G14960 Galactosyltransferase family protein
AT3G14980 Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger protein
Potri.001G393000 no_info
Potri.001G393001 no_info
Potri.001G393101 no_info
Potri.001G393200 no_info
AT1G53270 ABC-2 type transporter family protein
AT3G15000 cobalt ion binding
AT1G53250 (1 of 2) PF07460 - NUMOD3 motif (2 copies) (NUMOD3)
AT3G14440 nine-cis-epoxycarotenoid dioxygenase 3
AT1G31660 (1 of 1) PTHR12821 - BYSTIN
12 Potri.012G101100 no_info
Potri.012G101200 no_info
Potri.012G101301 no_info
AT5G63530 farnesylated protein 3
Potri.012G101500 no_info
AT5G50720 HVA22 homologue E
AT5G50610 (1 of 11) PF14364 - Domain of unknown function (DUF4408) (DUF4408)
AT5G50600 hydroxysteroid dehydrogenase 1
AT5G50600 hydroxysteroid dehydrogenase 1
Potri.012G102100 no_info
Potri.012G102200 no_info
AT3G06600 no_info
Potri.012G102400 no_info
AT3G48710 DEK domain-containing chromatin associated protein
AT5G50760 SAUR-like auxin-responsive protein family
AT4G24970 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase family protein
AT4G24972 tapetum determinant 1
12 Potri.012G103000 no_info
AT4G24990 Ubiquitin family protein
AT5G50790 Nodulin MtN3 family protein
Potri.012G103300 no_info
AT5G50810 translocase inner membrane subunit 8
Potri.012G103500 no_info
AT5G50830 no_info
AT3G48770 DNA binding;ATP binding
AT5G50860 Protein kinase superfamily protein
AT5G50870 ubiquitin-conjugating enzyme 27
Potri.012G104200 no_info
AT4G25040 Uncharacterised protein family (UPF0497)
AT5G50900 ARM repeat superfamily protein
AT3G48780 serine palmitoyltransferase 1
AT1G70170 matrix metalloproteinase
AT5G23680 Sterile alpha motif (SAM) domain-containing protein
AT5G50915 basic helix-loop-helix (bHLH) DNA-binding superfamily protein
AT3G48830 polynucleotide adenylyltransferase family protein / RNA recognition motif (RRM)-containing protein
Potri.012G105100 no_info
AT4G25050 acyl carrier protein 4
AT5G23700 (1 of 3) PTHR31762SF4 - EXPRESSED PROTEIN
(C) Recovery of defoliator damage
9 AT3G52070 no_info
AT3G21640 FKBP-type peptidyl-prolyl cis-trans isomerase family protein
AT3G27310 plant UBX domain-containing protein 1
AT3G52080 cation/hydrogen exchanger 28
AT3G08020 PHD finger family protein
AT3G08010 RNA binding
AT3G08020 PHD finger family protein
AT3G08020 PHD finger family protein
AT3G08010 RNA binding
AT3G63510 FMN-linked oxidoreductases superfamily protein
AT5G47940 no_info
AT3G60830 actin-related protein 7
Potri.009G060300 no_info
AT3G07970 Pectin lyase-like superfamily protein
AT3G63520 carotenoid cleavage dioxygenase 1
Potri.009G060600 no_info
AT5G05170 Cellulose synthase family protein
Potri.009G060901 no_info
Potri.009G061000 no_info
AT3G08040 MATE efflux family protein
AT3G08490 no_info
AT3G08500 myb domain protein 83
AT5G13450 delta subunit of Mt ATP synthase
AT4G26900 HIS HF
AT3G52105 no_info
AT3G52110 no_info
AT3G63530 RING/U-box superfamily protein
AT5G13490 ADP/ATP carrier 2
Potri.009G062300 no_info
Potri.009G062400 no_info
AT3G63540 Mog1/PsbP/DUF1795-like photosystem II reaction center PsbP family protein
AT3G08505 zinc finger (CCCH-type/C3HC4-type RING finger) family protein
Potri.009G062700 no_info
Potri.009G062901 no_info
Potri.009G063200 no_info
Potri.009G063300 no_info
9 AT4G37990 elicitor-activated gene 3-2
AT1G03495 HXXXD-type acyl-transferase family protein
AT2G41905 no_info
AT3G12650 no_info
AT3G12640 RNA binding (RRM/RBD/RNP motifs) family protein
AT3G12630 A20/AN1-like zinc finger family protein
AT2G03870 Small nuclear ribonucleoprotein family protein
Potri.009G064100 no_info
AT3G52115 gamma response gene 1
AT3G12610 Leucine-rich repeat (LRR) family protein
AT5G26880 AGAMOUS-like 26
AT3G52120 SWAP (Suppressor-of-White-APricot)/surp domain-containing protein / D111/G-patch domain-containing protein
Potri.009G064700 no_info
Potri.009G064800 no_info
Potri.009G064900 no_info
Potri.009G064950 no_info
AT3G20120 cytochrome P450, family 705, subfamily A, polypeptide 21
Potri.009G065100 no_info
Potri.009G065201 no_info
AT3G52140 tetratricopeptide repeat (TPR)-containing protein
AT5G48030 gametophytic factor 2