L compartementation of phenolics biosynthetic pathways in different rapeseed tissues. HR, hypocotyl and radicle; IC, inner cotyledon; OC, outer cotyledon; and SE, seed coat and endosperm. doi:10.1371/journal.pone.0048006.gLaser 370-86-5 MicrodissectionThe basic work flow of LMD and its application to plant tissue has been reported [15,77]. Mature rapeseed was embedded vertically in Jung tissue freezing medium (Leica Microsystems GmbH, Nussloch, Germany), and immediately frozen in liquid nitrogen. Serial cryosections (60 mm thickness) were prepared at ?24uC using a cryostat microtome (Leica CM1850, Bensheim, Germany) and directly mounted on PET-Membrane FrameSlides (MicroDissect GmbH, Herborn, Germany). LMD was performed on the Leica LMD 6000 laser microdissection system (Leica Microsystems GmbH, Wetzlar, Germany) equipped with a nitrogen solid state diode laser of a short pulse duration (355 nm). The cutting settings were as MNS follows: 206magnification, laser intensity of 128 (the strongest), laser moving speed of 1 (the slowest). The cut materials were collected in the cap of 0.5 ml centrifuge tubes by gravity and then transferred to an HPLC vial. The pictures were taken by a microscope-integrated camera HVD20P (Hitachi, Tokyo, Japan). Rapeseed was dissected into four parts, HR, IC, OC, and SE (Figure 1), and weights, including the supporting PET membrane of the frame slide, which was unavoidably cut along with the plant tissue, are listed in Table 1.in 
200 ml 20 (v/v) MeCN for NG analysis. The DEAE Sephadex cartridges were further eluted by 1 ml H2O twice and 500 ml 0.02 M 2-(N-morpholino)ethanesulfonic acid (MES) buffer (pH 5.2). Sulfatase (30 ml solution) (Sigma, Steinheim, Germany) was prepared as described in [80] and loaded onto the cartridge. The cartridges were capped, incubated at ambient temperature overnight, and eluted with 500 ml H2O for desulfated glucosinolate analysis.Identification and Quantification of GlucosinolatesDesulfated glucosinolates were identified with HPLC-DAD/MS by comparing their mass spectrometric data and retention times with those of references [81]. The compounds were quantified based on an internal standard with DAD. HPLC was conducted on an Agilent series HP1100 (binary pump G1312A, autosampler G1367A, diode array detector G1315A; Agilent Technologies, Waldbronn, Germany). Chromatographic separation was performed on 
a LiChrospher RP18 column (5 mm, 25064.6 mm, Merck, Darmstadt, Germany) with a guard column (5 mm, 464 mm) using a linear binary gradient of H2O (solvent A) containing 0.2 (v/v) formic acid (FA) and MeCN (solvent B), with a flow rate of 1.0 ml min21 at 25uC as follows: 0 min: 1.5 B, 1 min: 1.5 B, 6 min: 5 B, 8 min: 7 B, 18 min: 21 B, 23 min: 29 B, 23.1 min: 100 B, 24 min: 100 B, 24.1 min: 1.5 B, and 28 min: 1.5 B. The injection volume was 50 ml. The absorption of HPLC eluate was monitored by DAD at 229 nm.Sample PreparationGenerally, each sample was separated into glucosinolate fraction and non-glucosinolate (NG) fraction for further analysis through the procedure adapted from the literature [78]. The four dissected tissue groups (HR, IC, OC, and SE) were extracted separately in an ultrasonic bath for 10 min with 1 ml 80 (v/v) MeOH, which contains 10 mM sinalbin as an internal standard for glucosinolates and 10 mM cinnamic acid choline ester (synthesized according to [79]) as an internal standard for sinapine. The weak anion exchange DEAE Sephadex cartridges (Sigma, Steinheim, Germany).L compartementation of phenolics biosynthetic pathways in different rapeseed tissues. HR, hypocotyl and radicle; IC, inner cotyledon; OC, outer cotyledon; and SE, seed coat and endosperm. doi:10.1371/journal.pone.0048006.gLaser MicrodissectionThe basic work flow of LMD and its application to plant tissue has been reported [15,77]. Mature rapeseed was embedded vertically in Jung tissue freezing medium (Leica Microsystems GmbH, Nussloch, Germany), and immediately frozen in liquid nitrogen. Serial cryosections (60 mm thickness) were prepared at ?24uC using a cryostat microtome (Leica CM1850, Bensheim, Germany) and directly mounted on PET-Membrane FrameSlides (MicroDissect GmbH, Herborn, Germany). LMD was performed on the Leica LMD 6000 laser microdissection system (Leica Microsystems GmbH, Wetzlar, Germany) equipped with a nitrogen solid state diode laser of a short pulse duration (355 nm). The cutting settings were as follows: 206magnification, laser intensity of 128 (the strongest), laser moving speed of 1 (the slowest). The cut materials were collected in the cap of 0.5 ml centrifuge tubes by gravity and then transferred to an HPLC vial. The pictures were taken by a microscope-integrated camera HVD20P (Hitachi, Tokyo, Japan). Rapeseed was dissected into four parts, HR, IC, OC, and SE (Figure 1), and weights, including the supporting PET membrane of the frame slide, which was unavoidably cut along with the plant tissue, are listed in Table 1.in 200 ml 20 (v/v) MeCN for NG analysis. The DEAE Sephadex cartridges were further eluted by 1 ml H2O twice and 500 ml 0.02 M 2-(N-morpholino)ethanesulfonic acid (MES) buffer (pH 5.2). Sulfatase (30 ml solution) (Sigma, Steinheim, Germany) was prepared as described in [80] and loaded onto the cartridge. The cartridges were capped, incubated at ambient temperature overnight, and eluted with 500 ml H2O for desulfated glucosinolate analysis.Identification and Quantification of GlucosinolatesDesulfated glucosinolates were identified with HPLC-DAD/MS by comparing their mass spectrometric data and retention times with those of references [81]. The compounds were quantified based on an internal standard with DAD. HPLC was conducted on an Agilent series HP1100 (binary pump G1312A, autosampler G1367A, diode array detector G1315A; Agilent Technologies, Waldbronn, Germany). Chromatographic separation was performed on a LiChrospher RP18 column (5 mm, 25064.6 mm, Merck, Darmstadt, Germany) with a guard column (5 mm, 464 mm) using a linear binary gradient of H2O (solvent A) containing 0.2 (v/v) formic acid (FA) and MeCN (solvent B), with a flow rate of 1.0 ml min21 at 25uC as follows: 0 min: 1.5 B, 1 min: 1.5 B, 6 min: 5 B, 8 min: 7 B, 18 min: 21 B, 23 min: 29 B, 23.1 min: 100 B, 24 min: 100 B, 24.1 min: 1.5 B, and 28 min: 1.5 B. The injection volume was 50 ml. The absorption of HPLC eluate was monitored by DAD at 229 nm.Sample PreparationGenerally, each sample was separated into glucosinolate fraction and non-glucosinolate (NG) fraction for further analysis through the procedure adapted from the literature [78]. The four dissected tissue groups (HR, IC, OC, and SE) were extracted separately in an ultrasonic bath for 10 min with 1 ml 80 (v/v) MeOH, which contains 10 mM sinalbin as an internal standard for glucosinolates and 10 mM cinnamic acid choline ester (synthesized according to [79]) as an internal standard for sinapine. The weak anion exchange DEAE Sephadex cartridges (Sigma, Steinheim, Germany).