The kinetics of expression of various MAP-encoding genes in wild-type and <i>bot1-1</i> plants during AR induction.

<p>RNA was extracted from 3–4 biological replicas at the indicated time points and expression analysis was performed by the nanostring method. Scaling of gene expression signals was performed by subtracting the mean of the log₂ signals. An agglomerative hierarchical algorithm was applied with the “ward” method parameter on both the genes and the samples and a “heatmap” was illustrated by “Heatplus” R-package.</p

GFP expressed under the <i>MOR1</i> promoter is upregulated in response to IBA in the root and accumulates in LR and AR primordium.

<p>(A-D) <i>MOR1</i>_<i>pro</i>:<i>GFP</i> seedlings were grown on MS medium for 6 days. Half were then transferred to plates containing MS and 10 μ M IBA for 16h, after which a comparative examination by confocal microscopy was performed. (E-F) In another experiment, etiolated hypocotyls were excised (E) or excised and incubated in MS and 10 μ M IBA for 2d (F). (G) Fluorescence was measured in 3 plants from three independent transgenic lines (total of 9), asterisks show statistically significant differences as measured by Scheffe analysis p<0.05. Scale bars in A-F are 200 μ m.</p

Statistical analysis of the expression of several MAPs during AR induction in wild-type and <i>bot1-1</i> plants.

<p>Hypocotyls (5-6mm in length) were excised from etiolated seedlings and incubated in MS with 1% sucrose and 10 μ M IBA. RNA was extracted at the indicated time periods and expression of the various transcripts was analyzed in 3–4 biological replicates by the nanostring method. Light and dark green asterisks show statistically significant differences of expression in Col+IBA in relation to <i>bot1-1</i>+IBA or Col respectively, as determined by Scheffe analysis p<0.05. Col = wild type <i>A</i>. <i>thaliana</i> Columbia.</p

Expression of GFP under the <i>MOR1</i>_prom during AR induction.

<p>Etiolated hypocotyls were cut and induced to form AR by 10 μ M IBA. GFP fluorescence was followed before induction (A), and 1, 2, and 3 days post induction (B—E). (G). A hypocotyl that was incubated in MS without IBA for 3 days. The different primordium stages as in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143828#pone.0143828.ref008" target="_blank">8</a>] are shown by arrows. Scale bars in A, E, F are 50 μ M and in B -D are 20 μ M.</p

AR induction is hampered in <i>KATANIN</i> mutant plants.

<p>Hypocotyls (5-6mm in length) were excised from etiolated seedlings and incubated in MS with 1% sucrose and 10 μ M IBA for 3 days or 6 days. A-H representative images, scale bar = 500 μ m. I. Quantitative analysis of hypocotyls without roots (no), with emerged roots (root) or with AR primordium (prim). Asterisks show significant difference from control wild-type plants as determined by Scheffe analysis p<0.05. Scale Bar = 500 μ m.</p

Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity

<div><p>Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.</p></div

Gene ontology (GO) categorization of genes induced in ON buds.

<p>BG, background; Ref, reference; FDR, false discovery rate.</p

Distribution of SNP substitutions within and between ‘Nana’ and ‘Black’ accessions.

<p>The frequency of nucleotide substitutions was counted in ‘Nana’ (green) and ‘Black’ (blue). Where ‘Nana’ was homozygous for one allele and ‘Black’ was homozygous for another, it was counted as a between-accession SNP (turquoise).</p

Gene ontology (GO) categorization of genes induced in OFF buds.

<p>BG, background; Ref, reference; FDR, false discovery rate.</p

Bud morphology in ON- and OFF-crop trees.

<p>Buds were collected from ON- and OFF-crop trees in mid-July (A) and during the indicated months (B), fixed, dissected, dyed and photographed. Bud width and length were measured following photography (B). Mean values of 50 buds ± SE. Stars denote a significant difference between ON and OFF buds during the same time point (P<0.02).</p