Clustalw alignment of protein (94.57%) 

Supplementary Table

 S1


  




  




  




  




  




  




  




  




  


. Observations on anatomical characters in root tips of IR 20 and Nootripathu

  
		Number	Number of	Length of	Width of	Root	Number	Root
	Genotypes	of cells in divisional zone	cells in elongation zone	cells in elongation zone (µm)	cells in elongation zone (µm)	cap length (µm)	of cells per root cap	thickness (µm)
		(100µm	(100µm					
		scale)	scale)					
	IR20	385 b	188.75 b	30.1 b	20.2 b	215.0 a	173.7 b	265 b
	Nootripathu	502.5 a	207.5 a	38.0 a	23.4 a	177.5 b	291.3 a	390 a
	*Measurements were made in roots of 5 days old seedlings; Each observation is an average of
	6 independent measurements.					

Supplementary Table 2. 
Co-localization analysis of DE Proteins against QTLs for root growth related traits in rice

  
							(2006) Price et al Courtois et al al (2002a)
	LOCs LOC_Os03g27450 D1 Spot ID LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os03g27450 D1 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os11g11730 D2 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os01g54700 D3 LOC_Os06g47150 D6 LOC_Os06g47150 D6 LOC_Os06g47150 D6 LOC_Os06g47150 D6 LOC_Os06g47150 D6 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os01g56790 D7 LOC_Os02g03100 D8 LOC_Os02g03100 D8 LOC_Os02g03100 D8 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16734 D9 LOC_Os04g16824 D10 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os01g08510 D11 LOC_Os11g12040 D13 LOC_Os01g08510 D11 LOC_Os11g12040 D13 LOC_Os01g08510 D11 LOC_Os10g36190 D14 LOC_Os01g08510 D11 LOC_Os02g37420 D15 LOC_Os01g08510 D11 LOC_Os02g37420 D15 LOC_Os01g08510 D11 LOC_Os02g37420 D15 LOC_Os05g10830 D12 LOC_Os02g37420 D15 LOC_Os05g10830 D12 LOC_Os02g37420 D15 LOC_Os05g10830 D12 LOC_Os02g37420 D15 LOC_Os05g10830 D12 LOC_Os02g37420 D15 LOC_Os05g10830 D12 LOC_Os02g37420 D15 LOC_Os05g10830 D12 LOC_Os02g37420 D15 LOC_Os11g12040 D13 LOC_Os02g37420 D15 LOC_Os01g56790 D7 LOC_Os04g16824 D10 LOC_Os11g12040 D13 LOC_Os02g37420 D15	Protein Name Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Putative ADP-ribosylation factor Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Cell wall adhesion Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Retrotransposon protein Auxin response factor Auxin response factor Auxin response factor Auxin response factor Auxin response factor Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Expressed protein Oxidoreductase, aldo/keto reductase family protein Oxidoreductase, aldo/keto reductase family protein Oxidoreductase, aldo/keto reductase family protein Maturase K Maturase K Maturase K Maturase K Maturase K Maturase K Maturase K Maturase K Maturase K Chloroplast 30S ribosomal protein S3 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 MAR-binding filament-like protein 1 Disease resistance protein RPM1 MAR-binding filament-like protein 1 Disease resistance protein RPM1 MAR-binding filament-like protein 1 PPR repeat domain containing protein MAR-binding filament-like protein 1 Ras-related protein MAR-binding filament-like protein 1 Ras-related protein MAR-binding filament-like protein 1 Ras-related protein Proteophosphoglycan ppg4 Ras-related protein Proteophosphoglycan ppg4 Ras-related protein Proteophosphoglycan ppg4 Ras-related protein Proteophosphoglycan ppg4 Ras-related protein Proteophosphoglycan ppg4 Ras-related protein Proteophosphoglycan ppg4 Ras-related protein Disease resistance protein RPM1 Ras-related protein Expressed protein Chloroplast 30S ribosomal protein S3 Disease resistance protein RPM1 Ras-related protein	Trait name Maximum root length Root penetration index Root fresh weight Root fresh weight Lateral root length Deep root weight Deep root ratio Penetrated root number Penetrated root number Root penetration index Root penetration index Root to shoot ratio Maximum root length Deep root weight per tiller Root growth rate in depth Root dry weight Root dry weight Deep root weight Maximum root length Deep root ratio Deep root ratio Maximum root length Root thickness Root dry weight Root thickness Deep root weight Deep root weight per tiller Maximum root length Root thickness Deep root ratio Deep root ratio Root thickness Root fresh weight Root thickness Root dry weight Maximum root length Root thickness Maximum root length Root branching index Deep root weight Deep root weight per tiller Root thickness Maximum root length Deep root weight per tiller Deep root to shoot ratio Deep root ratio Deep root ratio Root thickness Root fresh weight Root thickness Penetrated root length Penetrated root thickness Root dry weight Root dry weight in the 30-60cm layer Deep root to shoot ratio Root number Root dry weight Root to shoot ratio Deep root weight per tiller Maximum root length Deep root ratio Maximum root length Root dry weight in the 30-Deep root to shoot ratio Root number Root growth rate in depth Root dry weight Root dry weight Root to shoot ratio Root dry weight Deep root weight per tiller Deep root weight Maximum root length Maximum root length Deep root ratio Deep root ratio Maximum root length Deep root ratio Deep root ratio Maximum root length Deep root weight Root thickness Root dry weight in the 60-Root number 90cm layer Deep root ratio Maximum root length Root dry weight Root thickness Maximum root length Root thickness Root thickness Penetrated root number Lateral root length Root thickness Deep root ratio Root thickness Deep root weight per tiller Penetrated root number Root volume Root penetration index Deep root to shoot ratio Penetrated root number Maximum root length Penetrated root number Maximum root length 60cm layer Deep root weight per tiller Root penetration index	Chromo some 3 A123616 Left locus 3 A123616 3 RM60 3 RM60 3 RG409A 3 PC20M11 3 PC20M11 3 PC73M13 3 PC73M13 3 PC73M13 3 PC73M13 3 RM231 11 R2918 11 C477 11 RM332 11 C794 11 C794 11 R642 11 R642 11 RM286 11 RM286 11 RM286 11 OSR1 1 RZ19 1 RZ19 1 R2417 1 R2417 1 R2417 1 R2417 1 RG957 1 RG957 1 ME10_14 1 C955 1 C904 6 CDO544 6 P0547F09 6 P0547F09 6 P0547F09 6 RM454 1 R2417 1 R2417 1 R2417 1 RG690 1 RG690 1 RG690 1 RG957 1 RG957 1 ME10_14 1 C955 1 C904 2 PC33M9 2 R1483 2 R1483 4 RM261 4 RM261 4 RG190 4 C820 4 C820 4 PC11M12 4 RG190 4 RM335 4 RM335 4 RM261 4 RG190 11 RM332 4 C820 11 C794 4 C820 11 C794 4 PC11M12 11 R642 4 RG190 11 R642 4 RM335 11 RM286 4 RM335 11 RM286 1 RG400 11 RM286 1 RG400 11 OSR1 1 RG246 10 RM258 1 RM428 2 RM3762 1 RM7383 2 RG157 1 RM7383 2 RG157 5 R2232 2 RG171 5 RG313 2 A18438 5 ME5_13 2 A18438 5 ME5_13 2 C499 5 RZ556A 2 C499 5 RZ556A 2 PC33M8 11 R2918 2 PC33M8 1 R2417 4 RM261 11 C477 2 PC33M8	Start Position 15335608 RZ474 Right locus 15335608 RZ474 105852 C814B 105852 C814B 3495798 T17 5729669 PC20M12 5729669 PC20M12 5729669 PC3M5 5729669 PC3M5 5729669 PC3M5 5729669 PC3M5 2453085 G51 2449321 C794 5460751 EM17_10 2840213 RM167 3033385 RG118 3033385 RG118 2015713 RZ141 2015713 RZ141 383711 RM332 383711 RM332 383711 RM332 201993 RM202 30870169 RG690 30870169 RG690 31427184 RM212 31427184 RM212 31427184 RM212 31427184 RM212 31227089 C813 31227089 C813 31367453 CDO345 7476866 C813 13902370 C742 26409713 RG653 28370801 OSJNBA0 069C14 28370801 OSJNBA0 069C14 28370801 OSJNBA0 069C14 23380386 RM412 31427184 RM212 31427184 RM212 31427184 RM212 32310761 RZ730 32310761 RZ730 32310761 RZ730 31227089 C813 31227089 C813 31367453 CDO345 7476866 C813 13902370 C742 744663 PC79M6 744663 RG437 744663 RG437 6574396 RZ69 6574396 RZ69 8610617 RG908 6898105 C933 6898105 C933 3571596 PC28M1 8610617 C734A 688353 RM307 688353 RM307 6574396 RZ69 8610617 RG908 2840213 RM167 6898105 C933 3033385 RG118 6898105 C933 3033385 RG118 3571596 PC28M1 2015713 RZ141 8610617 C734A 2015713 RZ141 688353 RM307 383711 RM332 688353 RM307 383711 RM332 4058510 R1194 383711 RM332 4058510 RG532 201993 RM202 3509004 K5 18014265 RG134 2606364 RM490 22456471 RM526 3483439 RM243 19865083 RZ318 3483439 RM23 19865083 RZ318 4107103 R569 17484665 G45 2781980 E1328 22595831 G39 2781980 G387 22595831 G39 2781980 G387 20878430 PC11M1 2091558 RG403 20878430 PC11M1 2091558 RG403 20878430 PC21M1 2449321 C794 20878430 PC21M1 31427184 RM212 6574396 RZ69 5460751 EM17_10 20878430 PC21M1	Stop Position	Reference MacMillan et al (2006) Price et al (2000) Li et al (2005) Li et al (2005) Zheng et al (2003) Kamoshita et al (2002b) Kamoshita et al (2002b) Ali et al (2000) Ali et al (2000) Ali et al (2000) Ali et al (2000) Li et al (2005) Xu et al (2004) Kamoshita et al (2002a) Yue et al (2006) Xu et al (2004) Xu et al (2004) MacMillan et al (2006) Price et al (1999) Yue et al (2006) Yue et al (2006) Li et al (2005) Yadav et al (1997) Yadav et al (1997) Kamoshita et al (2002a) Kamoshita et al (2002a) Price et al (1999) Price et al (2002c) Kamoshita et al (2002a) Kamoshita et al (2002a) Kamoshita et al (2002a) Li et al (2005) Li et al (2005) Yadav et al (1997) MacMillan et al (2006) MacMillan et al (2006) Price et al (2002c) Horii et al (2006) Kamoshita et al (2002a) Kamoshita et al (2002a) Price et al (2002c) Courtois et al (2003) Courtois et al (2003) Yadav et al (1997) Kamoshita et al (2002a) Kamoshita et al (2002a) Kamoshita et al (2002a) Li et al (2005) Li et al (2005) Ali et al (2000) Zhang et al (2001a) Zhang et al (2001a) Courtois et al (2003) Courtois et al (2003) Hemamalini et al (2000) Xu et al (2004) Xu et al (2004) Kamoshita et al (2002b) Price et al (2002c) Yue et al (2006) Yue et al (2006) Courtois et al (2003) Yue et al Hemamalini et (2006) al (2000) Xu et al (2004) Xu et al (2004) Xu et al (2004) Xu et al (2004) MacMillan et Kamoshita et al (2006) al (2002b) Price et al Price et al (1999) (2002c) Yue et al Yue et al (2006) (2006) Yue et al Yue et al (2006) (2006) Yue et al Kamoshita et (2006) al (2002a) Li et al (2005) MacMillan et Courtois et al al (2006) (2003) Zheng et al Yue et al (2000) (2006) Yue et al Hemamalini et (2006) al (2000) Horii et al Hemamalini et (2006) al (2000) Horii et al Price et al (2006) (2000) Price et al MacMillan et (2002c) al (2006) Zheng et al Price et al (2003) (2002c) Kamoshita et Ali et al al (2002a) (2000) Kamoshita et Ali et al al (2002a) (2000) Hemamalini et Ali et al al (2000) (2000) Yadav et al Ali et al (1997) (2000) Xu et al (2004) Ali et al Yue et al (1999) (2003) Kamoshita et (2000)

Supplementary Information


OsARD4 encoding an acireductone dioxygenase