Average percentage (%) of individual chromosome contributing to aneuploids in the seven diploid <i>Malus</i> crosses.

a<p>The percentage was calculated based on the summary data in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029449#pone-0029449-t002" target="_blank">Table 2</a>; Six aneuploid seedlings with cytotype of 2<i>n</i>−1 were found in the seven crosses, and among them two seedlings were affected by the LG02 (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029449#pone-0029449-t002" target="_blank">Table 2</a>), thus the percentage of LG02 was approximately estimated 33.333% as contributors to 2<i>n</i>−1 cytotype.</p

Schematic Summary of the Features of Gametic Combinations for Apple Polyploidization in Diploid <i>Malus</i>.

<p>Ova have two cytotypes, <i>n</i> and 2<i>n</i> ova; spermatozoa have a range but classified-into three cytotypes, <i>n</i>, 2<i>n</i>, and aneuploid spermatozoa for apple polyploidization. ‘<i>n</i>−1’ and ‘<i>n</i>+1’ refers to two aneuploid spermatozoa for aneuploidization. Diploid <i>Malus</i> exhibited a unique gametic combinational pattern, ova preserving euploidy exclusively, while spermatozoa presenting both euploidy and aneuploidy, for polyploidization. Molecular features showed that non-reduced gametes were genetically heterozygous, indicating first-division restitution was the exclusive mode for apple polyploidization. Figure depicts only three basic chromosomes with different colours in the legend to elucidate the basic chromosome number in the apples is odd.</p

Percentage (%) of cytotypes in the seven F₁ diploid <i>Malus</i> populations^a and statistical comparisons^b.

a<p>Actual population numbers are presented in parentheses.</p>b<p>Analysis of Deviance table was constructed to determine the effects due to cytotypes, crosses and type of cross in a generalized linear model (<i>N</i> = 28). Coverage intervals (CI) were calculated using an equivalent Bayesian model (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029449#s4" target="_blank">Methods</a>).</p>c<p>y = number of chromosomes (linkage groups) greater or fewer than the diploid number 2<i>n</i> = 34.</p

Genetic summary of cytotype distribution and the contribution of individual linkage group (LG) to aneuploid cytotypes.

a<p>Based on analysis of all aneuploid seedlings in the study, summed over the crosses.</p>b<p>In column “2<i>n</i>−1”, data represents absence of linkage group, for all other aneu-cytotypes, data represents one duplicate linkage group. For example, of the 16 individual “2<i>n</i>+10” seedlings, 11 had a duplicate copy of LG02.</p

Table_1_Down-Regulation of PpBGAL10 and PpBGAL16 Delays Fruit Softening in Peach by Reducing Polygalacturonase and Pectin Methylesterase Activity.DOCX

<p>β-galactosidases are cell wall hydrolases that play an important role in fruit softening. However, PpBGALs mechanism impacting on ethylene-dependent peach fruit softening was still unclear. In this study, we found that PpBGAL4, -6, -8, -10, -16, and -17 may be required for ethylene-dependent peach softening and PpBGAL10, -16 may make a main contribution to it among 17 PpBGALs. Utilization of virus-induced gene silencing (VIGS) showed that fruits were firmer than those of the control at 4 and 6 days after harvest (DAH) when PpBGAL10 and PpBGAL16 expression was down-regulated. Suppression of PpBGAL10 and PpBGAL16 expression also reduced PpPG21 and PpPME3 transcription, and polygalacturonase (PG) and pectinmethylesterases (PME) activity. Overall, total cell wall material and protopectin slowly declined, water-soluble pectin slowly increased, and cellulose and hemicellulose was altered significantly at 4 DAH, relative to control fruit. In addition, PpACO1 expression and ethylene production were also suppressed at 4 DAH because of inhibiting PpBGAL10 and PpBGAL16 expression. These results suggested that down-regulation of PpBGAL10 and PpBGAL16 expression delays peach fruit softening by decreasing PG and PME activity, which inhibits cell wall degradation and ethylene production.</p

Proteome Analyses Using iTRAQ Labeling Reveal Critical Mechanisms in Alternate Bearing <i>Malus prunifolia</i>

Alternate bearing (AB) trees, including <i>Malus prunifolia</i>, are characterized by alternating cycles of heavy (ON tree) and low (OFF tree) fruit loads. The mechanisms regulating the AB phenomenon have not been fully characterized. We completed an iTRAQ-based investigation of <i>M. prunifolia</i> to identify the proteome and metabolic differences between the leaves of ON and OFF trees. We identified 667 differentially expressed proteins, and they influenced multiple biochemical pathways, including photosynthesis, carbohydrate metabolism, glycolysis, protein processing, redox activities, and secondary metabolism. Bioinformatics analyses indicated photosynthesis was the most significant biological process affecting the AB. We observed that 47 photosynthetic proteins affecting photosystem I and II reaction centers, cytochrome b6/f complex, electron transport, and light-harvesting chlorophyll were less abundant in ON tree leaves than in OFF tree leaves. Additionally, physiological analyses validated the potential metabolic activities. Nitrogen and phosphorus contents were significantly higher in ON tree leaves, while potassium levels were lower. Starch content, ZR, GA₄₊₇ levels, and flower control gene expression levels (i.e., <i>MdFT1</i>, <i>MdLFY</i>, <i>MdAP1</i>, and <i>MdSPL9</i>) were lower in ON tree leaves than in OFF tree leaves, suggesting they affected the AB phenotype. Our findings help further investigate on the photosynthesis as well as other processes in AB. Those identified DEPs and important biological processes can be useful theoretical basis and provide new insights into the molecular mechanisms regulating AB in perennial woody plants

Additional file 8: of Transcriptome analysis reveals the effects of sugar metabolism and auxin and cytokinin signaling pathways on root growth and development of grafted apple

Gene-specific primers used for quantitative real-time PCR. (DOC 37 kb

Additional file 1: of Transcriptome analysis reveals the effects of sugar metabolism and auxin and cytokinin signaling pathways on root growth and development of grafted apple

Photosynthetic parameters of WT and MB grafted apple leaves. Comparison of photosynthetic parameters, including net photosynthetic rate (Pn), stomatal conductance (Gs) and intercellular CO2 concentration (Ci), in WT and MB leaves. Values are means ± SE (n = 10). Significant differences (*P < 0.05 and **P < 0.01) are based on Student’s t-tests. (DOC 111 kb

Additional file 1: of Comprehensive analysis of GASA family members in the Malus domestica genome: identification, characterization, and their expressions in response to apple flower induction

Alignment of GASA domains from AtGASA proteins. (a) Multiple alignments of the AtGASA protein sequences and their conserved GASA domains, red column represented their conserved twelve cysteines. (b) Sequence logo analysis of the conserved AtGASA domains. Each stack represented their amino acids. (TIFF 5642 kb

Additional file 3: of Transcriptome analysis reveals the effects of sugar metabolism and auxin and cytokinin signaling pathways on root growth and development of grafted apple

Selected genes related to sugar metabolism. (DOC 93 kb