3.94 ± 0.50 (95% CI) Correlative inhibition index (slope)

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1 Supplementl Tle S. Selected rchitecturl prmeters of phy nd phyphy grown under. Vlues re mens ± SE, except for predicted primry rosette rnches where the vlues re the men with the ssocited 9% confidence intervl, nd the correltive inhiition vlue which is regression slope s descried in the text. phy phyphy Primry rosette leves. ± ±. Time to nthesis (dys). ±.. ±. Primry rosette rnches.9 ±.9.7 ±.9 Primry rosette uds. ±.. ±. Rosette rnch n secondry rnches. ±.. ±. Rosette rnch n secondry leves. ±..9 ±. Culine rnch n secondry rnches. ±..9 ±. Culine rnch n secondry leves.9 ±.. ±. Predicted primry rosette rnches t 7.7 rnches (phyphy verge).9 ±. (9% CI) Culine rnch n+ length. ±.9. ± 7.9 Culine rnch n+ length 9. ± ± 9. Culine rnch n+ length. ±..7 ±. Culine rnch n+ length.9 ±..7 ±.9 Culine rnch n length.7 ±.9. ± 7. Min shoot length 7.9 ±.. ±. Rosette rnch n length 79. ±.. ±.7 Rosette rnch n- length. ±.. ±.9 Rosette rnch n- length 9. ±.. ± 9. Rosette rnch n- length 77. ±.9.7 ±. Rosette rnch n- length 9. ± 9.7 Rosette rnch n- length.97 ±.9 Correltive inhiition index (slope). 9.

2 Supplementl Tle S. Sequence of primers used for QPCR. mrn Forwrd primer Reverse primer trget RC GTCCTCCCGCTC TTGTGCTGGGTCTCTTGG RC TCGGGCGCTTGG CCGGGTCTCTTCTCTC DRM TGTTGTGGCTGGCCTC TTGGGTTCCGGGCTCCT T TTTCCTCTTCCCGTCCCTG TGCTCTTCCTTGTGTCTCCTC PCN GGTTTTCTCTGCCGGTGCT TGTCCTCGGGCTGGG th- CTCCGGGCTTGCTTTCC CCCTTCCCTTGTCTTGCTC CLV GTTCGGCTTTCCCCGCG TCTCCTTTGCTCCCCCTT WUS CCGCTTCTCGGGTTTTCT GC TCTGTGCCTTGGCTTC CCCCT RR TCTTGGGGGCTGGTTTC TGCTTCGCTCTCTCTTGTGCT CYC; TCTCCGGCGCGC GGCTTGGTTCTTCGCTTCTT CYCD; CCTTTCGGGCGTGC TGTTCCCCGCCTTCTCCTC CYCD; TTGTCCCTTTGCCCTCTT TTGGTCTGTCCGTGC CLV CTTCTTGCTGGCTCTTTGG CTCCTCTTCTCGTCCCTTTC STM GGCTCGTCCCTGCTTGT CCTTGTTTTCTGTTTCTGGTCC From guilr- Mrtínez, J.., Poz-Crrión, C., nd Cus, P. (7) ridopsis RNCHED cts s n integrtor of rnching signls within xillry uds. Plnt Cell 9: -7 From Müller, R., orghi, L., Kwitkowsk, D., Lufs, P., nd Simon, R. () Dynmic nd Compenstory Responses of ridopsis Shoot nd Florl Meristems to CLV Signling. Plnt Cell : 9

3 time (dys) Dys to nthesis PHY phy rc rc rcrc xr- mx mx rc rc rcrc Supplementl Figure S. Time to nthesis of vrious ridopsis genotypes with or without functionl phy (left pnel of ech grph) or under high nd (shded right pnel of ech grph). sterisks indicte significnt difference etween genotypes or light tretments t α =.. Dt re mens ± SE. For nlyses compring lines with or without functionl phy, n = (phymx) to 7 (), verge n =. For high nd, n = (rc) to 7 (), verge n = 7.

4 PHY =.x +.9 r =.9 phy =.x -.9 r =. phy rc rc PHY =.x +. r =.9 phy =.x -.7 r =.9 PHY =.x +.79 r =.97 phy =.x +.9 r =.97 PHY =.9x +. r =.7 phy =.9x +. r =.9 Primry rosette rnches rcrc PHY =.7x +. r =.9 phy =.x +.9 r =. xr- mx mx PHY = -.x +. r =. phy =.x +. r =.9 PHY =.9x +. r =.99 phy =.x +. r =. PHY =.9x +.7 r =.9 phy =.9x +. r =.9 rc rc rcrc High R:FR =.7x +. r =. Low R:FR =.x +. r =.99 High R:FR =.x +.7 r =.79 Low R:FR =.9x -. r =. High R:FR = -.x +. r =. Low R:FR = -.x +. High R:FR =.7x +. r =.99 Low R:FR =.x -. r =.99 Primry rosette leves Primry rosette rnches 9% confidence intervl of regression t phy men lef numer =. ±.7 9% confidence intervl of phy men lef numer =.7 ±. PHY =. x +.9, r = difference in men rosette lef numer PHY vs. phy oserved PHY men PHY clculted PHY t oserved phy men phy phy men lef numer Primry rosette leves phy =. x -.9, r =. Method description ) PHY nd phy (or high nd ) dt were seprted into su-clsses sed on lef numer nd the mens for ech pplicle rnching prmeter were regressed ginst lef numer to revel the correltion. ) The stndrd errors of the intercept nd slope of the regression from () were used to generte the respective 9% confidence intervls. ) The regression eqution of PHY (or high R:FR) from () ws used to clculte the vlue of the rnching prmeter t the oserved phy (or ) men lef numer. The 9% confidence intervl ssocited with the clculted vlue were derived using the vlues otined in (). ) The 9% confidence intervl of the clculted rnching prmeter vlue for PHY (or ) from () ws compred to the 9% confidence intervl of the oserved men phy (or ) men rnching prmeter vlue. Exmple (PHY vs phy rosette rnches) PHY =. x +.9, r =.9 phy =. x -.9, r =. (not used for clcultion) PHY =. x +.9. Slope lower limit =., upper limit =.. Intercept lower limit =.9, upper limit =.9. Oserved men phy rosette lef numer = 7.9. PHY c = =.. 9% confidence limits for clculted PHY men rnch numer ( c ) =. ± (. -((. 7.9) +.9)) =. ±.7 PHY c =. ±.7 phy =.7 ±. The 9% confidence intervls do not overlp, therefore the stndrdized rnch numers re significntly different. Supplementl Figure S. ) Regressions of primry rosette rnch numers versus primry rosette lef numers of vrious ridopsis genotypes with or without functionl phy (top two rows) or under high nd (shded lower row). ) Exmple () of the method used to generte stndrdized rnch (ud) numers nd errors employing regression to clculte PHY or rnch (ud) numers t the sme men lef numer s phy or. Error rs re 9% confidence intervls.

5 PHY m =.x +. r =.9 phy m =.9x +. r =.9 phy rc rc PHY m =.x +. r =.97 phy m =.7x +. r =.97 PHY m =.9x +. r =. phy m =.x +.7 r =. PHY m =.97x +. r =. phy m =.x -. r =. Primry rosette uds rcrc PHY m =.9x +. r =.97 phy m =.9x -. r =.9 xr- mx mx PHY m =.x +.7 r =.9 phy m =.9x +. r =.97 PHY m =.x -.7 r =.9 phy m =.x +.7 r =. PHY m =.9x +. r =. phy m =.x +. r =.9 rc rc rcrc High R:FR m =.x -. r =. High R:FR m =.x -. r =.97 Low R:FR m =.9x +.7 r =. High R:FR m =.9x +.7 r =. Low R:FR m =.x -. High R:FR m =.x +. r =. Low R:FR m =.x -. r =.99 Low R:FR m =.9x -. r =.9 Primry rosette leves Supplementl Figure S. Regressions of primry rosette ud numers versus primry rosette lef numers of vrious ridopsis genotypes with or without functionl phy (top two rows) or under high nd (shded lower row).

6 Rosette rnch n secondry rnches PHY phy numer of leves numer of rnches Rosette rnch n secondry leves rc rc rcrc xr- mx mx rc rc Supplementl Figure S. Secondry rnching prmeters of primry rosette rnch n (uppermost rosette rnch) of vrious ridopsis genotypes t ten DP with or without functionl phy (left pnel of ech grph) or under high nd (shded right pnel of ech grph). Sttisticl comprisons for secondry rosette rnch numers () nd secondry rosette lef numers () were mde within ech genotype sufficient (PHY), or deficient (phy) for phy, or within ech genotype grown under high versus. sterisks indicte significnt difference etween genotypes or light tretments t α =.. Dt re mens ± SE. For nlyses compring lines with or without functionl phy, n = (phymx) to 7 (), verge n =. For high nd, n = (rc) to 7 (), verge n = 7. rcrc

7 7 Culine rnch n secondry rnches PHY phy numer of leves numer of rnches 7 Culine rnch n secondry leves rc rc rcrc xr- mx mx rc rc rcrc Supplementl Figure S. Secondry rnching prmeters of primry culine rnch n (lowest culine rnch) of vrious ridopsis genotypes t ten DP with or without functionl phy (left pnel of ech grph) or under high nd (shded right pnel of ech grph). Sttisticl comprisons for secondry culine rnch numers () nd secondry culine lef numers () were mde within ech genotype sufficient (PHY), or deficient (phy) for phy, or within ech genotype grown under high versus. sterisks indicte significnt difference etween genotypes or light tretments t α =.. Dt re mens ± SE. For nlyses compring lines with or without functionl phy, n = (phymx) to 7 (), verge n =. For high nd, n = (rc) to 7 (), verge n = 7.

8 length (mm) phy phy phyphy rc rc length (mm) rc phyrc rc phyrc rcrc phyrcrc rc rc rcrc rcrc length (mm) xr- phyxr- mx phymx mx phymx Supplementl Figure S. Min shoot height (longest r), lengths of culine rnches (to left of longest r, with lowest rnch to immedite left of longest r) nd lengths of rosette rnches (to right of longest r) of vrious ridopsis genotypes t ten DP grown under with or without functionl phy (left pnels) or under high nd (shded right pnels). sterisks indicte significnt height difference etween genotypes or light tretments t α =.. Dt re mens ± SE. For nlyses compring lines with or without functionl phy, n = (phymx) to 7 (), verge n =. For high nd, n = (rc) to 7 (), verge n = 7.

9 ud n ud n- RC RC ' ' DRM ' '..... T c TH- ' ' PCN trget trnscripts - S trnscripts..... CLV CYC; ' ' WUS CYCD; ' ' RR CYCD; ' ' STM ' CLV phy phy phy phy phy phy phy phy ' phy phy phy phy phy phy phy phy phy phy phy phy phy phy phy phy Supplementl Figure S7. undnce of vrious mrns in unelongted primry rosette ud n [uppermost ud] nd ud n- [ud immeditely elow ud n] of, phy, phy nd phyphy grown under (left pnel of ech grph) or grown under high nd (shded right pnel of ech grph). Results re the mens of QPCR nlysis of iologicl replictes ± SE of the men. rs with different letters re significntly different t α =..

10 RC RC DRM T PCN TH- CLV WUS RR CYC; CYCD; CYCD; STM CLV r =. q =.9 r =. q =. r =. q =. r =.7 q =. r =. q =.7 r =. q =. r =. q =.7 r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. STM r =. q =. r =. q =.7 r =. q =. r =.9 q =. r =.7 q =. r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. CYCD; r =.9 q =. r =. q =. r =. q =.9 r =.7 q =. r =. q =. r =. q =. r =.7 q =. r =. q =. r =. q =.9 r =. q =. r =. q =. CYCD; r =. q =. r =. q =. r =.9 q =. r =. q =.7 r =.7 q =. r =. q =. r =. q =.7 r =. q =. r =. q =. r =. q =. CYC; r =. q =. r =. q =. r =. q =.9 r =. q =.9 r =. q =.9 r =. q =. r =.7 q =. r =.9 q =. r =. q = RR. WUS trget trnscripts - S trnscripts.. r =. q =. r =.77 q =. r =.7 q =. r =.9 q =. r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. r =. q =. r =.9 q =. r =. q =. r =. q =. r =. q =..... trget trnscripts - S trnscripts r =. q =. CLV.. r =. q =.9 r =.7 q =. r =. q =. r =. q =. r =.7 q =. r =.9 q =. TH- r =. q =.7 r =. q =. r =. q =.7 r =.9 q =. r =. q =. PCN r =. q =. r =. q =. r =. q =. r =. q = T... r =.9 q =. r =. q =. r =. q =. r =. q =. DRM r =. q =. r =. q =. RC Supplementl Figure S. Correltion mtrix of the undnce of ech mesured mrn species regressed ginst ll others. Significnt correltion t q =. is indicted y squre mgent symols.

11 DRM T PCN WUS TH- CLV RR rosette rnch length (mm) r =. p =. r =. p =.7 r =.7 p =. r =.7 p =. r =.9 p =. r =. p =.7 r =.7 p =. correltive inhiition (slope) ud n- ud n r =.7 p =.7 r =. p =.7 - r =. p =. r =. p =. r =. p =.7 r =. p =. r =. p =. r =.9 p =. r =.7 p =. r =.9 p =. r =.7 p =.9 r =. p =..... r =. p =.9 r =. p =..... trget trnscripts - S trnscripts Supplementl Figure S9. Correltion nlysis of the mrn undnce of selected genes regressed ginst rosette rnch lengths (ud n [uppermost ud] nd ud n- [ud immeditely elow ud n] dt regressed together) nd correltive inhiition (ud n nd n- dt regressed seprtely). Significnt correltion t α =. is indicted y green tringulr symols. Significnt correltion t α =. is indicted y squre mgent symols.

12 .... photon flux density (µmol m - s - )..... High R:FR Low R:FR wvelength (nm) Supplementl Figure S. Spectr of light sources used in the experiments. Spectrum of light source used for comprisons of vrious genotypes with nd without functionl phy (). Spectrum of light sources used for high nd low R:FR comprisons ().

Supplementary material

Supplementary material 10.1071/FP11237_AC CSIRO 2012 Accessory Puliction: Functionl Plnt Biology 2012, 39(5), 379 393. Supplementry mteril Tle S1. Effect of wter regime nd genotype on different growth prmeters: spike dry mtter