QTL-seq identifies cooked grain elongation QTLs near soluble starch synthase and starch branching enzymes in rice (Oryza sativa L.)


Supplementary Fig. S1 Box plots of average raw grain length (A.) and cooked grain length (B.) among 178 F2 lines. The positions of the grain lengths in Pathum Thani1 (PTT1) and Basmati are presented with their names. S1 

Supplementary Table




  


Supplementary Table S4 List of predicted candidate genes in 1-Mb intervals of the qGE6.2.1 and qGE6.2.2 regions.

  Phenotypic data analyses of grain elongation ratio for 178 F 2 individuals.Supplementary TableS2Forty selected F 2 lines used to generate high GE bulk and low GE bulk.Plants with high grain elongation ratio and low grain elongation ratio.The letters A and a represent Basmati's and PTT1's marker alleles, respectively. 


	6 6793120 LOC_Os06g12520 hypothetical protein 6 7047258 LOC_Os06g12876 expressed protein 6 7231572 LOC_Os06g13200 proton-dependent oligopeptide transport, putative, expressed 6 7519619 LOC_Os06g13590 PE-PGRS family protein, putative, expressed 6 16264254 LOC_Os06g28590 bg55, putative, expressed 6 16732924 LOC_Os06g29310 ulp1 protease family protein, putative, expressed
	Trait PTT1 Basmati GE 1.50 2.26 Low GE bulk Mean Max Min Skewness Kurtosis F2 Population 1.76 2.37 1.35 0.46 3.8 High GE bulk Line number Average GE 6 6794150 LOC_Os06g12530 CS domain containing protein, putative, expressed 6 6796598 LOC_Os06g12539 expressed protein 6 6801945 LOC_Os06g12550 expressed protein 6 6809574 LOC_Os06g12560 zinc finger, C3HC4 type, domain containing protein, expressed 6 6814708 LOC_Os06g12570 expressed protein 6 6816402 LOC_Os06g12580 pro-resilin precursor, putative, expressed 6 6822979 LOC_Os06g12590 protein kinase, putative, expressed 6 6842811 LOC_Os06g12600 kinase, pfkB family, putative, expressed 6 6866393 LOC_Os06g12610 auxin efflux carrier component, putative, expressed 6 6878753 LOC_Os06g12620 expressed protein 6 6892489 LOC_Os06g12630 glutathione S-transferase, N-terminal domain containing protein, 6 6905844 LOC_Os06g12649 expressed protein 6 6915783 LOC_Os06g12660 NHL repeat-containing protein, putative, expressed 6 6923215 LOC_Os06g12680 RING-H2 finger protein, putative, expressed 6 6928341 LOC_Os06g12690 DCN1-like protein 2, putative, expressed 6 6937045 LOC_Os06g12700 conserved hypothetical protein 6 6950487 LOC_Os06g12730 expressed protein 6 6953695 LOC_Os06g12740 expressed protein 6 6963552 LOC_Os06g12760 hypothetical protein 6 6980031 LOC_Os06g12780 OsDegp10 -Putative Deg protease homologue, expressed 6 6990939 LOC_Os06g12790 ras-related protein, putative, expressed 6 6995343 LOC_Os06g12800 expressed protein 6 7000436 LOC_Os06g12810 proteins of unknown function domain containing protein, expressed 6 7005872 LOC_Os06g12820 proteins of unknown function domain containing protein, expressed 6 7019819 LOC_Os06g12830 expressed protein 6 7025603 LOC_Os06g12840 expressed protein 6 7031413 LOC_Os06g12850 expressed protein 6 7037048 LOC_Os06g12860 proteins of unknown function domain containing protein, putative, 6 7043611 LOC_Os06g12870 leaf senescence related protein, putative, expressed 6 7053689 LOC_Os06g12882 S phase cyclin A-associated protein in the ER, putative, expressed 6 7059669 LOC_Os06g12890 expressed protein 6 7067117 LOC_Os06g12910 XPA-binding protein 2, putative, expressed 6 7072753 LOC_Os06g12920 hypothetical protein 6 7076782 LOC_Os06g12930 expressed protein 6 7079677 LOC_Os06g12940 expressed protein 6 7085090 LOC_Os06g12950 expressed protein 6 7093925 LOC_Os06g12960 expressed protein 6 7102791 LOC_Os06g12980 cyclin, putative, expressed 6 7118829 LOC_Os06g12990 tRNA methyltransferase, putative, expressed 6 7121120 LOC_Os06g13000 ankyrin repeat domain-containing protein, chloroplast precursor, 6 7128352 LOC_Os06g13020 DNA polymerase lambda, putative, expressed 6 7133789 LOC_Os06g13030 OsLIM -LIM domain protein, putative actin-binding protein and transcription factor, expressed 6 7144204 LOC_Os06g13040 glycosyl hydrolases family 16, putative, expressed 6 7148961 LOC_Os06g13050 peroxidase family protein, expressed 6 7159988 LOC_Os06g13060 heat shock protein DnaJ, putative, expressed 6 7169830 LOC_Os06g13070 hhH-GPD superfamily base excision DNA repair protein, putative, 6 7181648 LOC_Os06g13080 spotted leaf 11, putative, expressed 6 7186601 LOC_Os06g13090 armadillo/beta-catenin repeat family protein, putative, expressed 6 7188393 LOC_Os06g13100 CREG1 precursor, putative, expressed 6 7201591 LOC_Os06g13120 expressed protein 6 7205227 LOC_Os06g13130 expressed protein 6 7209516 LOC_Os06g13140 WD domain, G-beta repeat domain containing protein, expressed 6 7216473 LOC_Os06g13150 hypothetical protein 6 7218853 LOC_Os06g13160 viral-response family protein, expressed 6 7221749 LOC_Os06g13170 expressed protein 6 7224942 LOC_Os06g13180 metalloendoproteinase 1 precursor, putative, expressed 6 7230154 LOC_Os06g13190 expressed protein 6 7247729 LOC_Os06g13210 peptide transporter PTR2, putative, expressed 6 7256821 LOC_Os06g13215 growth regulator related protein, putative, expressed 6 7260407 LOC_Os06g13220 expressed protein 6 7267160 LOC_Os06g13230 expressed protein 6 7278365 LOC_Os06g13240 BURP domain containing protein, expressed 6 7293011 LOC_Os06g13250 hypothetical protein 6 7306306 LOC_Os06g13280 O-methyltransferase, putative, expressed 6 7318599 LOC_Os06g13310 SAM dependent carboxyl methyltransferase, putative, expressed 6 7325614 LOC_Os06g13320 protein kinase, putative, expressed 6 7333278 LOC_Os06g13330 expressed protein 6 7338076 LOC_Os06g13340 expressed protein 6 7341809 LOC_Os06g13350 SAM dependent carboxyl methyltransferase, putative, expressed 6 7367791 LOC_Os06g13380 expressed protein 6 7369137 LOC_Os06g13390 SAM dependent carboxyl methyltransferase, putative, expressed 6 7376286 LOC_Os06g13410 OsSCP33 -Putative Serine Carboxypeptidase homologue, expressed 6 7378698 LOC_Os06g13420 OsSCP34 -Putative Serine Carboxypeptidase homologue, expressed 6 7397012 LOC_Os06g13440 expressed protein 6 7401127 LOC_Os06g13450 cystathionine beta-lyase, putative, expressed 6 7406037 LOC_Os06g13460 SAM dependent carboxyl methyltransferase family protein, putative, 6 7417633 LOC_Os06g13470 SAM dependent carboxyl methyltransferase, putative, expressed 6 7423689 LOC_Os06g13480 expressed protein 6 7429730 LOC_Os06g13490 SAM dependent carboxyl methyltransferase domain containing protein, 6 7455885 LOC_Os06g13510 SAM dependent carboxyl methyltransferase family protein, putative 6 7459467 LOC_Os06g13520 SAM dependent carboxyl methyltransferase domain containing protein, 6 7468750 LOC_Os06g13530 benzoate carboxyl methyltransferase, putative, expressed 6 7474908 LOC_Os06g13550 SAM dependent carboxyl methyltransferase family protein, putative, 6 7480067 LOC_Os06g13560 SAM dependent carboxyl methyltransferase, putative, expressed 6 7488066 LOC_Os06g13570 expressed protein 6 7498331 LOC_Os06g13580 expressed protein 6 7530834 LOC_Os06g13600 HEAT repeat family protein, putative, expressed 6 7540774 LOC_Os06g13610 expressed protein 6 7544706 LOC_Os06g13620 expressed protein 6 7555463 LOC_Os06g13640 expressed protein 6 7564755 LOC_Os06g13650 alpha-mannosidase 2, putative, expressed 6 7574978 LOC_Os06g13660 alanyl-tRNA synthetase, putative, expressed 6 7584780 LOC_Os06g13670 E2F family transcription factor protein, putative, expressed 6 7591912 LOC_Os06g13680 B12D protein, putative, expressed 6 7595183 LOC_Os06g13690 expressed protein 6 7596393 LOC_Os06g13700 hypothetical protein 6 7600956 LOC_Os06g13710 glycosyltransferase, putative, expressed 6 7602364 LOC_Os06g13720 dehydrogenase E1 component domain containing protein, expressed 6 7607108 LOC_Os06g13730 glutamate receptor precursor, putative, expressed 6 7619834 LOC_Os06g13750 expressed protein 6 7629547 LOC_Os06g13760 glycosyl transferase 8 domain containing protein, putative, expressed 6 7642070 LOC_Os06g13780 expressed protein 6 7647852 LOC_Os06g13800 expressed protein 6 7648922 LOC_Os06g13810 pyrophosphate--fructose 6-phosphate 1-phosphotransferase subunit beta, putative, expressed 6 7661691 LOC_Os06g13820 dynamin, putative, expressed qGE6.2.1 Chr Start Stop Gene Name Putative Function qGE6.2.2 Chr Start Stop Gene Name Putative Function 6 16052471 LOC_Os06g28250 expressed protein 6 16058398 LOC_Os06g28260 expressed protein 6 16070798 LOC_Os06g28300 zinc knuckle family protein, expressed 6 16168793 LOC_Os06g28420 expressed protein 6 16195179 LOC_Os06g28470 expressed protein 6 16198162 LOC_Os06g28480 polygalacturonase inhibitor 1 precursor, putative, expressed 6 16217263 LOC_Os06g28520 expressed protein 6 16224024 LOC_Os06g28524 expressed protein 6 16245674 LOC_Os06g28550 nmrA-like family domain containing protein, expressed 6 16251104 LOC_Os06g28560 expressed protein 6 16276332 LOC_Os06g28600 expressed protein 6 16302034 LOC_Os06g28630 expressed protein 6 16329395 LOC_Os06g28670 polygalacturonase, putative, expressed 6 16335038 LOC_Os06g28680 expressed protein 6 16339515 LOC_Os06g28690 expressed protein 6 16352388 LOC_Os06g28720 expressed protein 6 16353727 LOC_Os06g28730 expressed protein 6 16363079 LOC_Os06g28740 expressed protein 6 16381270 LOC_Os06g28760 hypothetical protein 6 16385565 LOC_Os06g28770 expressed protein 6 16400699 LOC_Os06g28820 cycloartenol synthase, putative, expressed 6 16440845 LOC_Os06g28840 expressed protein 6 16481194 LOC_Os06g28890 expressed protein 6 16502251 LOC_Os06g28940 hypothetical protein 6 16504514 LOC_Os06g28950 expressed protein 6 16506995 LOC_Os06g28960 expressed protein 6 16509328 LOC_Os06g28970 bolA, putative, expressed 6 16534747 LOC_Os06g29010 expressed protein 6 16579007 LOC_Os06g29080 expressed protein 6 16588693 LOC_Os06g29100 expressed protein 6 16593797 LOC_Os06g29110 MLO domain containing protein, putative, expressed 6 16604790 LOC_Os06g29120 STE_PAK_Ste20_STLK.5 -STE kinases include homologs to sterile 7, sterile 11 and sterile 20 from yeast, expressed 6 16649544 LOC_Os06g29180 erythronate-4-phosphate dehydrogenase domain containing protein, expressed 6 16658542 LOC_Os06g29190 expressed protein 6 16676478 LOC_Os06g29220 erythronate-4-phosphate dehydrogenase domain containing protein, expressed 6 16687151 LOC_Os06g29240 expressed protein 6 16693757 LOC_Os06g29250 expressed protein 6 16719384 LOC_Os06g29290 pentatricopeptide, putative, expressed 6 16774133 LOC_Os06g29350 myosin, putative, expressed 6 16785962 LOC_Os06g29360 expressed protein 6 16791220 LOC_Os06g29370 expressed protein 6 16793634 LOC_Os06g29380 phospholipid-transporting ATPase, putative, expressed 6 16810191 LOC_Os06g29390 expressed protein 6 16825601 LOC_Os06g29400 surp module family protein, putative, expressed 6 16852004 LOC_Os06g29430 cytidine and deoxycytidylate deaminase zinc-binding region family protein, expressed 6 16862021 LOC_Os06g29440 expressed protein 6 16877329 LOC_Os06g29450 expressed protein 6 16879347 LOC_Os06g29460 expressed protein 6 16896515 LOC_Os06g29470 peroxidase precursor, putative, expressed 6 16910985 LOC_Os06g29490 expressed protein 6 16927219 LOC_Os06g29540 expressed protein 6 16933182 LOC_Os06g29560 expressed protein 6 16960716 LOC_Os06g29590 expressed protein 6 16983848 LOC_Os06g29620 hypothetical protein 6 17003628 LOC_Os06g29650 CDP-diacylglycerol--inositol 3-phosphatidyltransferase 1, putative, expressed 6 17020710 LOC_Os06g29670 expressed protein 6 17029405 LOC_Os06g29679 expressed protein 6 17035080 LOC_Os06g29690 dynein light chain type 1 domain containing protein, expressed 6 17044170 LOC_Os06g29700 OsFBD11 -F-box and FBD domain containing protein, expressed 6 17054545 LOC_Os06g29710 OsFBD12 -F-box and FBD domain containing protein, expressed 6 17066919 LOC_Os06g29730 RALFL28 -Rapid ALkalinization Factor RALF family protein precursor, expressed 6 17077761 LOC_Os06g29740 OsFBX197 -F-box domain containing protein, expressed Supplementary Table S7 Grain elongation ratios and marker genotypes for Wx, SSI, SSIIa, SBEIII and SBEIIa among 170 F2 plants A A A A A 2.09 A H H H A 1.78 H H H H B 1.65 H B H H H 1.63 H H H H A 1.78 H H H H B 1.88 A H H B A 1.75 A H H H B 1.79 A A B H H 1.65 B B B B A 1.76 B B B B H 2.00 H H H H B 1.99 Supplementary Table S6 No. SSIIa SBEIII SBEIIa GE ratio Aa AA Aa 2.37 5 Aa Aa aa 2.30 89 Aa Aa Aa 2.29 95 AA Aa AA 2.29 Aa AA AA 2.24 73 AA Aa Aa 2.15 Aa Aa aa 2.11 AA Aa aa 2.08 71 Aa Aa aa 2.06 35 AA Aa Aa 2.04 AA Aa AA 2.04 Aa Aa Aa 2.01 AA AA Aa 2.00 AA Aa Aa 2.00 Aa Aa AA 1.99 52 AA Aa Aa 1.98 98 AA Aa AA 1.96 8 AA Aa AA 1.95 79 Aa Aa Aa 1.95 37 Aa Aa aa 1.93 18 Aa Aa Aa 1.64 Aa Aa Aa 1.63 Aa Aa Aa 1.63 aa aa Aa 1.62 aa aa aa 1.62 Aa Aa Aa 1.62 40 aa aa Aa 1.61 83 aa aa aa 1.61 19 Aa aa aa 1.60 aa aa aa 1.59 Aa aa aa 1.57 aa aa Aa 1.56 22 aa Aa aa 1.55 aa aa aa 1.55 6 aa aa AA 1.47 Aa Aa aa 1.44 Aa aa aa 1.39 25 aa aa aa 1.39 aa aa Aa 1.39 56 aa aa Aa 1.35 Sample Name Wx SSI SSIIa SBEIII SBEIIa H H H A A 1.60 H H A A H 1.73 Phenotype H H H A H 1.70 H H H A H 1.82 (GE ratio) 1 B B B B A A H H H A 2.06 B B B H H 1.90 1.87 2 H H H H H A H B H H 2.15 H H H H H 1.61 1.78 4 H H H B A H H A H H 1.91 B H H H H 1.83 1.78 5 H H H H A H H H B B 1.87 H H A A B 1.49 2.30 6 A A A A B A A A A A 1.70 A A A A H 1.90 1.47 7 B B B H H H H B B H 1.88 B B B B H 1.66 1.89 8 B B B H B H H H H H 1.95 A H H B B 2.24 1.95 10 B B B H H A A H H H 1.66 H H H H H 2.01 1.81 11 H H H H H A A A A A 1.51 B B B B H 1.92 1.67 12 B B H H A H H A A A 1.61 H H H H H 1.57 1.96 13 H H H H B H H A A A 1.77 B B B B H 1.76 1.83 14 H H H H H H H B H A 1.83 B H H H H 1.63 1.86 15 B B B B H H H B B B 1.86 A A H H H 1.58 1.69 16 H B B H A B B B B H 1.78 A A A H A 1.51 1.39 17 B B H A B A H H H H 2.29 A A A A A 1.55 1.77 18 H H H H H H H A A A 1.61 H H H H H 1.69 1.83 19 H H H A A A H A A H 1.76 H A H H H 1.92 1.60 21 H H H H A B B H H H 1.83 H H B B H 1.45 1.80 22 A A A H A A A A A A 1.74 A B B B H 1.67 1.55 23 H B H B B H A A A H 1.50 A H H H H 1.62 1.85 25 H H A A A A A B H B 2.29 H H H A A 1.73 1.39 26 H H H B B H B H H A 1.63 H H H H H 1.76 1.63 27 A A A H H H H A A A 1.73 B B B B B 1.93 1.91 28 H H H B H B B B H B 1.96 A A A A A 1.59 1.80 31 H H A A H A A H H A 1.86 A A A A H 1.56 1.66 32 A A H H A 100 A A H A A 1.39 A A A A H 1.84 1.78 33 H H B B H 101 A H H H A 2.11 B B B B H 1.84 1.65 34 A A A A B 102 A A A H H 1.72 H H H H A 1.89 1.99 35 B B B H H 103 B B H H B 1.72 H H H H B 1.75 2.04 36 H H H H A 104 H B H H B 1.66 A H A A H 1.73 1.73 37 H H H H A 105 H H H H H 1.74 A H H H H 1.64 1.93 38 H H H A A 106 B H H A A 1.72 H H A A A 1.62 1.42 39 H A A A A 108 A A A A H 1.39 A A A A H 1.62 1.41 40 B H A A H 110 H H H H B 1.74 H H H H A 1.88 1.61 41 H H H H H 111 H H H H H 1.87 H H B H A 2.08 1.70 42 B B B B H 113 H H H H B 1.82 B H H H H 1.94 1.79 43 A A A A A 114 H H H H H 1.83 A A H H A 1.87 1.76 44 H A H H H 115 A A H B H 1.72 H H H H H 1.88 1.53 45 H H H H A 117 H B B B H 1.88 A H H H A 1.44 1.79 46 B B H H H 118 B B H B H 2.37 A H H H A 1.94 1.82 47 A A H A H 119 B B H A B 1.68 A H H H H 1.89 1.70 48 A H H H B 120 H H H A A 1.57 B B H H A 1.89 1.66 49 A A A A A 121 H H H H A 1.77 A A H H A 1.80 1.90 50 H H H H H 122 A A B H A 1.68 B B B B A 1.76 1.55 51 H H H H H 124 H B H H B 1.87 B B H H A 1.65 1.62 52 H H B H H 125 A H B B H 1.65 A A H H H 1.65 1.98 54 H B B B H 126 B B B H B 2.04 H H H H A 1.67 1.91 55 H H H H A 127 H H H H H 1.62 H H B H B 1.85 1.82 56 A A A A H 129 A A H H H 1.66 B H H H H 1.73 1.35 57 H B B B A 59 B B H H H 60 A H H H H 1.86 132 H H H H A 1.82 1.51 131 A A A A A 1.71 1.71 130 B B B H H 2.00 H H H H H 1.63

5497369 LOC_Os06g10590 expressed protein 6 5499342 LOC_Os06g10600 homeobox and START domains containing protein, putative, expressed 6 5522553 LOC_Os06g10610 expressed protein 6 5523780 LOC_Os06g10620 transcription elongation factor SPT5 homolog 1, putative, expressed 6 5555007 LOC_Os06g10650 tyrosine phosphatase family protein, putative, expressed 6 5559909 LOC_Os06g10660 lysM domain-containing GPI-anchored protein 1 precursor, putative, 6 5569910 LOC_Os06g10670 aspartic proteinase nepenthesin-1 precursor, putative, expressed 6 5572599 LOC_Os06g10680 expressed protein 6 5575867 LOC_Os06g10690 PHD-finger domain containing protein, putative, expressed 6 5586611 LOC_Os06g10700 expressed protein 6 5588196 LOC_Os06g10710 expressed protein 6 5597520 LOC_Os06g10720 expressed protein 6 5601748 LOC_Os06g10730 expressed protein 6 5613999 LOC_Os06g10750 integral membrane protein DUF6 containing protein, expressed 6 5619105 LOC_Os06g10760 emp24/gp25L/p24 family protein, putative, expressed 6 5621926 LOC_Os06g10770 peptidase, putative, expressed 6 5629416 LOC_Os06g10780 AP2 domain containing protein, expressed 6 5633354 LOC_Os06g10790 lectin-like receptor kinase, putative, expressed 6 5636936 LOC_Os06g10800 zinc finger family protein, putative, expressed 6 5638272 LOC_Os06g10810 phosphate carrier protein, mitochondrial precursor, putative, expressed 6 5642245 LOC_Os06g10820 helix-loop-helix DNA-binding domain containing protein, expressed 6 5653538 LOC_Os06g10840 expressed protein 6 5657850 LOC_Os06g10850 lipase, putative, expressed 6 5663968 LOC_Os06g10860 glucosyltransferase, putative, expressed 6 5677080 LOC_Os06g10880 bZIP transcription factor, putative, expressed 6 5688535 LOC_Os06g10890 sterol carrier protein-2, putative, expressed 

12931779 LOC_Os06g22290 legume lectins beta domain containing protein, expressed 6 12962817 LOC_Os06g22330 expressed protein 6 12967302 LOC_Os06g22340 cytochrome P450, putative, expressed 6 12973921 LOC_Os06g22350 expressed protein 6 12983166 LOC_Os06g22360 hypothetical protein 6 12988184 LOC_Os06g22370 expressed protein 6 12990974 LOC_Os06g22380 expressed protein 6 13003028 LOC_Os06g22390 expressed protein 6 13009938 LOC_Os06g22394 expressed protein 6 13019641 LOC_Os06g22400 expressed protein 6 13029814 LOC_Os06g22410 expressed protein 6 13031173 LOC_Os06g22420 ZOS6-04 -C2H2 zinc finger protein, expressed 6 13041900 LOC_Os06g22440 SAM dependent carboxyl methyltransferase, putative, expressed 6 13052769 LOC_Os06g22450 expressed protein 6 13055162 LOC_Os06g22460 disease resistance protein RPM1, putative, expressed 6 13061315 LOC_Os06g22470 hypothetical protein 6 13070021 LOC_Os06g22490 sphingolipid C4-hydroxylase SUR2, putative, expressed 6 13094272 LOC_Os06g22530 hypothetical protein 6 13097662 LOC_Os06g22540 expressed protein 6 13101544 LOC_Os06g22550 transducin family protein, putative, expressed 6 13117696 LOC_Os06g22560 formyl transferase, putative, expressed 6 13143806 LOC_Os06g22600 aluminum-activated malate transporter, putative, expressed 6 13148277 LOC_Os06g22610 heat shock factor protein HSF8, putative, expressed 6 13152632 LOC_Os06g22620 hypothetical protein 6 13161181 LOC_Os06g22640 expressed protein 

Supplementary
Siwaret Arikit, Samart Wanchana, Srisawat Khanthong, Chatree Saensuk, Tripop Thianthavon, Apichart Vanavichit, Theerayut Toojinda
QTL-seq identifies cooked grain elongation QTLs near soluble starch synthase and starch branching enzymes in rice (Oryza sativa L.)