Dataset Information

Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate.

ABSTRACT: Abscission, organ separation, is a developmental process that is modulated by endogenous and environmental factors. To better understand the molecular events underlying the progression of abscission in soybean, an agriculturally important legume, we performed RNA sequencing (RNA-seq) of RNA isolated from the leaf abscission zones (LAZ) and petioles (Non-AZ, NAZ) after treating stem/petiole explants with ethylene for 0, 12, 24, 48, and 72 h. As expected, expression of several families of cell wall modifying enzymes and many pathogenesis-related (PR) genes specifically increased in the LAZ as abscission progressed. Here, we focus on the 5,206 soybean genes we identified as encoding transcription factors (TFs). Of the 5,206 TFs, 1,088 were differentially up- or down-regulated more than eight-fold in the LAZ over time, and, within this group, 188 of the TFs were differentially regulated more than eight-fold in the LAZ relative to the NAZ. These 188 abscission-specific TFs include several TFs containing domains for homeobox, MYB, Zinc finger, bHLH, AP2, NAC, WRKY, YABBY, and auxin-related motifs. To discover the connectivity among the TFs and highlight developmental processes that support organ separation, the 188 abscission-specific TFs were then clustered based on a >four-fold up- or down-regulation in two consecutive time points (i.e., 0 and 12 h, 12 and 24 h, 24 and 48 h, or 48 and 72 h). By requiring a sustained change in expression over two consecutive time intervals and not just one or several time intervals, we could better tie changes in TFs to a particular process or phase of abscission. The greatest number of TFs clustered into the 0 and 12 h group. Transcriptional network analysis for these abscission-specific TFs indicated that most of these TFs are known as key determinants in the maintenance of organ polarity, lateral organ growth, and cell fate. The abscission-specific expression of these TFs prior to the onset of abscission and their functional properties as defined by studies in Arabidopsis indicate that these TFs are involved in defining the separation cells and initiation of separation within the AZ by balancing organ polarity, roles of plant hormones, and cell differentiation.

SUBMITTER: Kim J

PROVIDER: S-EPMC4756167 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate.

Kim Joonyup J Yang Jinyoung J Yang Ronghui R Sicher Richard C RC Chang Caren C Tucker Mark L ML

Frontiers in plant science 20160217

Abscission, organ separation, is a developmental process that is modulated by endogenous and environmental factors. To better understand the molecular events underlying the progression of abscission in soybean, an agriculturally important legume, we performed RNA sequencing (RNA-seq) of RNA isolated from the leaf abscission zones (LAZ) and petioles (Non-AZ, NAZ) after treating stem/petiole explants with ethylene for 0, 12, 24, 48, and 72 h. As expected, expression of several families of cell wal ...[more]

PMID: 26925069

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Project description:Background and aimsThe stimulatory and inhibitory role of ethylene and auxin, respectively, in leaf abscission (leaf drop) is well documented. More recently, IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) peptides and their putative interacting receptor-like-kinase partners, HAESA and HAESA-like2, were shown to be essential components in Arabidopsis floral organ abscission. Prior to research on IDA, it was reported that bean (Phaseolus vulgaris) leaf abscission required a diffusible signal that emanated from the vascular tissue. We were interested in determining whether the IDA signalling path might regulate abscission in plants other than Arabidopsis and whether IDA might act as a diffusible signal in abscission.MethodologyQuantitative polymerase chain reaction was used to monitor gene expression and a GUS reporter gene construct used to determine the need for a diffusible signal in tomato.Principal resultsWe identified 12 IDA-like and 11 HAESA-like genes in soybean (Glycine max) and monitored their gene expression in abscission in relation to the expression of several cell-wall-modifying proteins and aminocyclopropane-1-carboxylic acid synthases. Ethylene evoked the expression of several IDA-like genes in abscission zones (AZ), but also to a lesser degree in the adjacent petiole tissue. Surprisingly, IDA-like gene expression was very high in senescent soybean leaves. We identified five IDA-like genes in tomato (Solanum lycopersicum). Only one IDA-like gene was expressed in the tomato AZ and its expression was approximately equal in the AZ and petioles, but no IDA-like gene showed significant expression in leaves at up to 96 h of exposure to ethylene.ConclusionsIDA-like gene expression is up-regulated during soybean and tomato abscission but up-regulation was not limited to the AZ. Cell separation in the AZ cortex of tomato does not require a diffusible signal emanating from the stele. A role for IDA in soybean and tomato leaf abscission is discussed.

Project description:BackgroundSugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest.ResultsTo determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants.ConclusionOur results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane.

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Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate.

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Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate.

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