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BMC Genomics

, 14:841

Plant genomics

Abstract

BackgroundAbscisic acid ABA can regulate the expressions of many stress-responsive genes in plants. However, in defense responses to pathogens, mounting evidence suggests that ABA plays variable roles. Little information exists about genome-wide gene expression in ABA responses in tomato Solanum lycopersicum L., a model fruit crop plant.

ResultsGlobal transcriptome profiles of tomato leaf responses to exogenous ABA were generated using Illumina RNA-sequencing. More than 173 million base pair reads were mapped onto the tomato reference genome and the expression pattern differences between treated and control leaves were assessed. In total, 50,616 transcripts were generated. Among them, 42,583 were functionally annotated in the NCBI non-redundant database and 47,877 in the tomato genome reference. Additionally, 31,107 transcripts were categorized into 57 functional groups based on Gene Ontology terms, and 14,371 were assigned to 310 Kyoto Encyclopedia of Genes and Genomes pathways. In both the ABA treatment and control samples, 39,671 transcripts were available to analyze their expressions, of which 21,712 54.73% responded to exogenous ABA. Of these transcripts, 2,787 were significantly differently expressed genes DEGs. Many known and novel ABA-induced and -repressed genes were found. Exogenous ABA can influence the ABA signaling pathway with PYR-PYL-RCARs-PP2Cs-SnRK2s as the center. Eighteen PYL genes were detected. A large number of genes related to various transcription factors, heat shock proteins, pathogen resistance, and the salicylic acid, jasmonic acid, and ethylene signaling pathways were up-regulated by exogenous ABA.

ConclusionsThe results indicated that ABA has the potential to improve pathogen-resistance and abiotic stress tolerance in tomato. This study presents the global expression analysis of ABA-regulated transcripts in tomato and provides a robust database for investigating the functions of genes induced by ABA.

KeywordsTomato Exogenous ABA RNA-Seq ABA signaling pathway Transcription factors Heat shock proteins Pathogen-related proteins ROS scavenging enzymes AbbreviationsABAAbscisic acid

a1dABA-treatment after 1 day

ABFABA responsive element ABRE binding factors

ABREABA responsive promoter element

ABRTABA responsive transcription factor

ANTADP-ATP translocator-like

AP2-ERFapetala 2-ethylene -responsive element-binding factor

APXAscorbate peroxidase

AREBABA-responsive element binding protein

bHLHBasic helix-loop-helix

bZIPBasic leucine zipper

c1dControl sample after 1 day

CATCatalase

cDNAComplementary DNA deoxyribonucleic acid

COGClusters of orthologous groups of proteins

DEGSignificantly differentially expressed genes

DHARDehydroascorbate reductase

DREBDehydration responsive element binding protein

ERF-EREBPEthylene response factor

ETethylene

ETRethylene receptor

FPKMFragments Per Kilobase of exon model per Million mapped fragments

GAPDHGlyceraldehyde-3-phosphate dehydrogenase

GLRGlutaredoxin

GLUBeta-1:3-glucanase

GOGene ontology

GPXGlutathione peroxidase

GRGlutathione reductase

GSH-AsAglutathione-ascorbate

GSTGlutathione-S-transferase

HSFHeat shock factor

HSPHeat shock protein

JAJasmonic acid

JAR1Jasmonate resistant

JAZJasmonate ZIM-domain protein

KEGGKyoto Encyclopedia of genes and genomes

MDARMonodehydroascorbate reductase

MYBMyeloblastosis oncogene

MYCMyelocytomatosis oncogene

NACNo apical meristem-ATAF-CUP-shaped cotyledons

NATsNatural antisense transcripts

NRNon-redundant protein database in National Center of Biotechnology Information NCBI

ORFOpen reading frame

PALPhenylalanine ammonia-lyase

PCRPolymerase chain reaction

PODPeroxidase

PP2CsProtein phosphatases which fall under the category of type 2C

PPOPolyphenol oxidase

PR1Pathogenesis-related proteins

PrxRPeroxiredoxin

RCARs-PYR1-PYLRegulatory components of ABA receptor-pyrabactin resistance protein1-PYR-like protein

RNARibonucleic acid

ROSReactive oxygen species

qRT-PCRQuantitative real time - PCR

SASalicylic acid

sHSPSmall heat shock protein

SnRK2The sucrose nonfermenting1–related protein kinase 2

SODSuperoxide

STINGSearch tool for the retrieval of interacting genes

TGATGACG-as-1: binding

TrxThioredoxin.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-841 contains supplementary material, which is available to authorized users.

Yan Wang, Xiang Tao contributed equally to this work.

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Autor: Yan Wang - Xiang Tao - Xiao-Mei Tang - Liang Xiao - Jiao-long Sun - Xue-Feng Yan - Dan Li - Hong-Yuan Deng - Xin-Rong Ma

Fuente: https://link.springer.com/







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