45S rDNA methylation states of the two pair chromosomes of 65 cells at different stages.

<p><b>Type I:</b> In the two pairs of chromosomes, the 45S rDNA of one pair were unmethylated and the other were methylated. <b>Type II:</b> In the two pairs of chromosomes, the 45S rDNA of one pair were methylated in telomeric region and the other were methylated. <b>Type III:</b> In the two pairs of chromosomes, the 45S rDNA of one pair were methylated in telomeric region. One of the other pair was unmethylated and the other was methylated. <b>Type IV:</b> In the two pairs of chromosomes, the 45S rDNA of one pair were methylated in telomeric region and the other were unmethylated.</p

FISH analysis of <i>J. curcas</i> from different sources using 45S rDNA as a probe.

<p><b>A:</b> Hainan; <b>B:</b> Guizhou; <b>C:</b> Guangxi; <b>D:</b> GOF70-1; <b>E:</b> GOF38-2; <b>F:</b> 17#. All chromosomes were counterstained with DAPI; all scale bars = 5 µm. The yellow arrows indicated the stronger signals and the white arrows indicated the weaker signals.</p

Summary of 45S rDNA FISH Signals and DNA methylation.

<p>Summary of 45S rDNA FISH Signals and DNA methylation.</p

FISH and karyogram analysis of <i>J. curcas</i> prometaphase chromosomes.

<p><b>A:</b> FISH image showing 45S rDNA probe signals on <i>J. curcas</i> metaphase chromosomes. <b>B:</b> Numbered <i>J. curcas</i> metaphase chromosomes from A. <b>C:</b> Karyogram of <i>J. curcas</i> somatic metaphase chromosomes. Scale bars = 5 µm.</p

Distribution of the 5-MeC foci (green fluorescence) and 45S rDNA loci (red fluorescence) on metaphase chromosomes of <i>J. curcas</i>.

<p><b>A:</b> In the two pairs of chromosomes, the 45S rDNA of one pair were methylated in telomeric region and the other were methylated. <b>(Type II)</b>. <b>B:</b> In the two pairs of chromosomes, the 45S rDNA of one pair were methylated in telomeric region. One of the other pair was unmethylated and the other was methylated. <b>(Type III)</b>. <b>C:</b> In the two pairs of chromosomes, the45S rDNA of one pair were methylated in telomeric region and the other were unmethylated. <b>(Type IV)</b>. All chromosomes were counterstained with DAPI. Scale bars = 5 µm. The yellow arrows indicated the stronger signals of 45S rDNA and the white arrows indicated the weaker signals of 45S rDNA.</p

FISH analysis of <i>J. curcas</i> chromosomes using 45S rDNA as a probe at different stages of mitosis.

<p><b>A–B:</b> Interphase; <b>C–E:</b> Prophase; <b>F–G:</b> Prometaphase; <b>H:</b> Metaphase; <b>I:</b> Anaphase. <b>J:</b> Prophase; <b>K:</b> The FISH signals of image j; <b>L:</b> The chromosome of image j dyed by Gimesa. All chromosomes were counterstained with DAPI in image A–K; all scale bars = 5 µm. The yellow arrows indicated the stronger signals and the white arrows indicated the weaker signals.</p

Distribution of the 5-MeC foci (green fluorescence) and 45S rDNA loci (red fluorescence) on interphase and prometaphase chromosomes <i>J. curcas</i>.

<p><b>A: interphase; B–C:</b> prophase; All chromosomes were counterstained with DAPI. Scale bars = 5 µm. The yellow arrows indicated the stronger signals of 45S rDNA and the white arrows indicated the weaker signals of 45S rDNA.</p

Morphometric data for <i>Jatropha curcas</i> chromosomes.

<p>Data represents the mean ± SD of five replicates from different cells.</p><p>L: long arm length.</p><p>S: short arm length.</p><p>TL: absolute chromosome length.</p><p>RL (relative chromosome length) = 100 × TL/Total chromosome absolute length;</p><p>Arm ratio (r = L/S), length ratio between the long and short arms.</p><p>On the basis of centromere position, the arm ratio (r) was used to classify the chromosomes according to Levan et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084284#pone.0084284-Levan1" target="_blank">[48]</a> into m, metacentric (r = 1.05−1.69); sm, submetacentric (r = 1.70−2.99); st, subtelocentric (r = 3.00−6.99); and t, telocentric (r = 7.00−39.00).</p

Additional file 1: Table S1. of GNS4, a novel allele of DWARF11, regulates grain number and grain size in a high-yield rice variety

Primers used in this study. (PDF 37 kb

Mutation of the <i>Light-Induced Yellow Leaf 1</i> Gene, Which Encodes a Geranylgeranyl Reductase, Affects Chlorophyll Biosynthesis and Light Sensitivity in Rice

<div><p>Chlorophylls (Chls) are crucial for capturing light energy for photosynthesis. Although several genes responsible for Chl biosynthesis were characterized in rice (<i>Oryza sativa</i>), the genetic properties of the hydrogenating enzyme involved in the final step of Chl synthesis remain unknown. In this study, we characterized a rice <i>light-induced yellow leaf 1-1</i> (<i>lyl1-1</i>) mutant that is hypersensitive to high-light and defective in the Chl synthesis. Light-shading experiment suggested that the yellowing of <i>lyl1-1</i> is light-induced. Map-based cloning of <i>LYL1</i> revealed that it encodes a geranylgeranyl reductase. The mutation of <i>LYL1</i> led to the majority of Chl molecules are conjugated with an unsaturated geranylgeraniol side chain. <i>LYL1</i> is the firstly defined gene involved in the reduction step from Chl-geranylgeranylated (Chl_GG) and geranylgeranyl pyrophosphate (GGPP) to Chl-phytol (Chl_Phy) and phytyl pyrophosphate (PPP) in rice. <i>LYL1</i> can be induced by light and suppressed by darkness which is consistent with its potential biological functions. Additionally, the <i>lyl1-1</i> mutant suffered from severe photooxidative damage and displayed a drastic reduction in the levels of α-tocopherol and photosynthetic proteins. We concluded that <i>LYL1</i> also plays an important role in response to high-light in rice.</p></div