scholarly journals Endogenous Auxin Content Contributes to Larger Size of Apple Fruit

2020 ◽  
Vol 11 ◽  
Author(s):  
Haidong Bu ◽  
Wenquan Yu ◽  
Hui Yuan ◽  
Pengtao Yue ◽  
Yun Wei ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Fruit Size ◽  
Apple Fruit ◽  
Auxin Signaling ◽  
Endogenous Auxin ◽  
Rna Seq ◽  
Synthetic Genes ◽  
Economic Trait ◽  
Bud Sport ◽  
Auxin Content

Fruit size is an important economic trait that is controlled by multiple genes. However, the regulatory mechanism for fruit size remains poorly understood. A bud sport variety of “Longfeng” (LF) apple (Malus domestica) was identified and named “Grand Longfeng” (GLF). The fruit size of GLF is larger than that of LF, and both varieties are diploid. We found that the cell size in GLF fruit was larger than that of LF. Then, we compared the fruit transcriptomes of the two varieties using RNA-Seq technology. A total of 1166 differentially expressed genes (DEGs) were detected between GLF and LF fruits. The KEGG analysis revealed that the phytohormone pathway was the most enriched, in which most of the DEGs were related to auxin signaling. Moreover, the endogenous auxin levels of GLF fruit were higher than those of LF. The expressions of auxin synthetic genes, including MdTAR1 and MdYUCCA6, were higher in GLF fruit than LF. Collectively, our findings suggest that auxin plays an important role in fruit size development.

scholarly journals Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12675
Author(s):  
Zhe Zhou ◽  
Yanmin Zhu ◽  
Hengtao Zhang ◽  
Ruiping Zhang ◽  
Qiming Gao ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Fruit Size ◽  
Size Variation ◽  
Apple Fruit ◽  
Rna Seq ◽  
Hormone Synthesis ◽  
Transcriptional Changes ◽  
Transgenic Apple

Background MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes. Methods To answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data. Results Overexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.

scholarly journals Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1268
Author(s):  
Shengchao Zhang ◽  
Sibtain Ahmad ◽  
Yuxia Zhang ◽  
Guohua Hua ◽  
Jianming Yi
Keyword(s):  
Mammary Gland ◽  
Crude Protein ◽  
Regulatory Mechanism ◽  
Differentially Expressed ◽  
Milk Replacer ◽  
Rna Seq ◽  
Fat Pad ◽  
Mammary Fat Pad ◽  
Non Coding Rnas ◽  
Gland Development

Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs’ quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.

A comparison of ‘Empire’ apple fruit size and anatomy in unthinned and hand-thinned trees

1995 ◽  
Vol 70 (3) ◽  
pp. 375-387 ◽  
Author(s):  
M. C. Goffinet ◽  
T. L. Robinson ◽  
A. N. Lakso
Keyword(s):  
Fruit Size ◽  
Apple Fruit

scholarly journals Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Riccardo Lorrai ◽  
Francesco Gandolfi ◽  
Alessandra Boccaccini ◽  
Veronica Ruta ◽  
Marco Possenti ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Hypocotyl Elongation ◽  
Auxin Signaling ◽  
Rna Seq ◽  
Genome Wide

DEVELOPMENTAL STUDIES OF THE APPLE FRUIT IN THE VARIETIES McINTOSH RED AND WAGENER: II. AN ANALYSIS OF DEVELOPMENT

1941 ◽  
Vol 19c (10) ◽  
pp. 371-382 ◽  
Author(s):  
Mary MacArthur ◽  
R. H. Wetmore
Keyword(s):  
Cell Division ◽  
Cell Size ◽  
Fruit Size ◽  
Apple Fruit ◽  
Vascular Bundles ◽  
Developmental Studies ◽  
Cell Enlargement ◽  
Ground Tissue ◽  
Fundamental Pattern

Growth in the various tissues of the fruit of a McIntosh Red and a Wagener tree, both self-pollinated, is compared. For several days succeeding pollination no increase in fruit size is apparent. Fertilization is followed by general cell division and cell enlargement. The period of cell division varies with the tissue and with the variety. Final cell size is reached first by the cells of those tissues near the centre of the apple. Impressed upon the fundamental pattern of growth is the localized activity of the primary vascular bundles, the cambia of which add cells to the ground tissue. Angulation in the Wagener is accentuated by this activity. With the exception of cells of the epidermis, final cell size is approximately equal in comparable regions of the two varieties. Differences in regional extent are due to differences in numbers of cells in that region.

Harvest date and fruit size affect postharvest softening of apple fruit

2002 ◽  
Vol 77 (3) ◽  
pp. 355-360 ◽  
Author(s):  
Jason W. Johnston ◽  
Errol W. Hewett ◽  
Maartem L. A. T. M. Hertog ◽  
F. Roger Harker
Keyword(s):  
Fruit Size ◽  
Apple Fruit ◽  
Harvest Date

scholarly journals RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 213
Author(s):  
Yu Xu ◽  
Junjie Zou ◽  
Hongyan Zheng ◽  
Miaoyun Xu ◽  
Xuefeng Zong ◽  
...  
Keyword(s):  
Cell Wall ◽  
Root Growth ◽  
Primary Root ◽  
Glutathione Metabolism ◽  
Auxin Signaling ◽  
Antioxidant Enzyme Activities ◽  
Rna Seq ◽  
Root Tips ◽  
Primary Roots ◽  
Quercetin Treatment

Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H2O2 and O2− levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots.

scholarly journals RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 820 ◽  
Author(s):  
Chao Zeng ◽  
Michiaki Hamada
Keyword(s):  
Alternative Splicing ◽  
Subcellular Localization ◽  
Cell Lines ◽  
Biological Diversity ◽  
Rna Binding ◽  
Regulatory Mechanism ◽  
Intron Retention ◽  
Rna Seq ◽  
Motif Analysis ◽  
Structurally Stable

Alternative splicing, a ubiquitous phenomenon in eukaryotes, is a regulatory mechanism for the biological diversity of individual genes. Most studies have focused on the effects of alternative splicing for protein synthesis. However, the transcriptome-wide influence of alternative splicing on RNA subcellular localization has rarely been studied. By analyzing RNA-seq data obtained from subcellular fractions across 13 human cell lines, we identified 8720 switching genes between the cytoplasm and the nucleus. Consistent with previous reports, intron retention was observed to be enriched in the nuclear transcript variants. Interestingly, we found that short and structurally stable introns were positively correlated with nuclear localization. Motif analysis reveals that fourteen RNA-binding protein (RBPs) are prone to be preferentially bound with such introns. To our knowledge, this is the first transcriptome-wide study to analyze and evaluate the effect of alternative splicing on RNA subcellular localization. Our findings reveal that alternative splicing plays a promising role in regulating RNA subcellular localization.

scholarly journals EFFECTS OF HYDROGEN CYANAMIDE ON APPLE AND PLUM FRUIT THINNING

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 690a-690
Author(s):  
Esmaeil Fallahi ◽  
Brenda R. Simons ◽  
John K. Fellman ◽  
W. Michael Colt
Keyword(s):  
Malus Domestica ◽  
Fruit Set ◽  
Fruit Size ◽  
Apple Fruit ◽  
Fruit Weight ◽  
Full Bloom ◽  
Hydrogen Cyanamide ◽  
Fruit Thinning ◽  
Prunus Salicina

Influence of various concentrations of hydrogen cyanamide (HC) on fruit thinning of `Rome Beauty' apple (Malus domestica Borkh.), `Friar,' and `Simka' plums (Prunus salicina Lindley) were studied. A full bloom application of HC at all tested concentrations decreased `Rome Beauty' apple fruit set and yield, and increased fruit weight. Hydrogen cyanamide at 0.25% (V/V) resulted in adequate apple thinning, indicated by the production of an ideal fruit weight. Prebloom and full bloom applications of HC at greater than 0.75% reduced plum fruit set and yield in `Friar.' Full bloom application of HC at 0.25% to 0.50% showed a satisfactory fruit set, yield, and fruit size in `Friar' plum. Full bloom application decreased fruit set and yield in `Simka' plum. Hand thinning, as well as chemical thinning, is recommended for plums.

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