Exploring Candidate Genes for Pericarp Russet Pigmentation of Sand Pear (Pyrus pyrifolia) via RNA-Seq Data in Two Genotypes Contrasting for Pericarp Color

Sand pear (Pyrus pyrifolia) russet pericarp is an important trait affecting both the quality and stress tolerance of fruits. This trait is controlled by a relative complex genetic process, with some fundamental biological questions such as how many and which genes are involved in the process remaining elusive. In this study, we explored differentially expressed genes between the russet- and green-pericarp offspring from the sand pear (Pyrus pyrifolia) cv. ‘Qingxiang’ × ‘Cuiguan’ F1 group by RNA-seq-based bulked segregant analysis (BSA). A total of 29,100 unigenes were identified and 206 of which showed significant differences in expression level (log2fold values>1) between the two types of pericarp pools. Gene Ontology (GO) analyses detected 123 unigenes in GO terms related to ‘cellular_component’ and ‘biological_process’, suggesting developmental and growth differentiations between the two types. GO categories associated with various aspects of ‘lipid metabolic processes’, ‘transport’, ‘response to stress’, ‘oxidation-reduction process’ and more were enriched with genes with divergent expressions between the two libraries. Detailed examination of a selected set of these categories revealed repressed expressions of candidate genes for suberin, cutin and wax biosynthesis in the russet pericarps.Genes encoding putative cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POD) that are involved in the lignin biosynthesis were suggested to be candidates for pigmentation of sand pear russet pericarps. Nine differentially expressed genes were analyzed for their expressions using qRT-PCR and the results were consistent with those obtained from Illumina RNA-sequencing. This study provides a comprehensive molecular biology insight into the sand pear pericarp pigmentation and appearance quality formation.

• Publication year

  2014

• Venue

  PLoS ONE

• Publication date

  2014-01-06

• Fields of study

  Biology, Agricultural and Food Sciences, Medicine

• Identifiers
  DOI 10.1371/journal.pone.0083675PMID 24400075PMCID 3882208
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The genome of the pear (Pyrus bretschneideri Rehd.)

  2013cited by this paper
• Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks.

  2012cited by this paper
• Plant cell biology: the ABC of monolignol transport.

  2012cited by this paper
• Analysis of Enzyme Activity and Lignin Content and Expression of CCoAOMT Gene in the Pericarp of‘Dangshan Suli’and Its Russet Mutant

  2012cited by this paper
• Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis

  2012cited by this paper
• Suppression of CCR impacts metabolite profile and cell wall composition in Pinus radiata tracheary elements

  2012cited by this paper
• Solving the puzzles of cutin and suberin polymer biosynthesis.

  2012cited by this paper
• Tomato GDSL1 Is Required for Cutin Deposition in the Fruit Cuticle[C][W]

  2012cited by this paper
• Environmental Stresses of Field Growth Allow Cinnamyl Alcohol Dehydrogenase-Deficient Nicotiana attenuata Plants to Compensate for their Structural Deficiencies1[C][W][OA]

  2012cited by this paper
• Identification of differentially expressed genes in a spontaneous mutant of ‘Nanguoli’ pear (Pyrus ussuriensis Maxim) with large fruit

  2011cited by this paper
• An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice

  2011cited by this paper
• A Member of the PLEIOTROPIC DRUG RESISTANCE Family of ATP Binding Cassette Transporters Is Required for the Formation of a Functional Cuticle in Arabidopsis[W]

  2011cited by this paper
• Identification of functional BrFAD2-1 gene encoding microsomal delta-12 fatty acid desaturase from Brassica rapa and development of Brassica napus containing high oleic acid contents

  2011cited by this paper
• Transcriptional networks for lignin biosynthesis: more complex than we thought?

  2011cited by this paper
• SHINE Transcription Factors Act Redundantly to Pattern the Archetypal Surface of Arabidopsis Flower Organs

  2011cited by this paper
• A potato skin SSH library yields new candidate genes for suberin biosynthesis and periderm formation

  2011cited by this paper
• Fatty acid elongase is required for shoot development in rice.

  2011cited by this paper
• The Arabidopsis ABCG13 transporter is required for flower cuticle secretion and patterning of the petal epidermis.

  2011cited by this paper
• Tissue-specific transcriptome profiling of the citrus fruit epidermis and subepidermis using laser capture microdissection

  2010cited by this paper
• Mining the surface proteome of tomato (Solanum lycopersicum) fruit for proteins associated with cuticle biogenesis

  2010cited by this paper
• EgMYB1, an R2R3 MYB transcription factor from eucalyptus negatively regulates secondary cell wall formation in Arabidopsis and poplar.

  2010cited by this paper
• Arabidopsis ABCG Transporters, Which Are Required for Export of Diverse Cuticular Lipids, Dimerize in Different Combinations[W]

  2010cited by this paper
• The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots.

  2010cited by this paper
• Lignin Biosynthesis and Structure1

  2010cited by this paper
• Transport barriers made of cutin, suberin and associated waxes.

  2010cited by this paper
• Multivariate analysis of digital gene expression profiles identifies a xylem signature of the vascular tissue of white spruce (Picea glauca)

  2010cited by this paper
• RDML: structured language and reporting guidelines for real-time quantitative PCR data

  2009cited by this paper
• The Arabidopsis DCR Encoding a Soluble BAHD Acyltransferase Is Required for Cutin Polyester Formation and Seed Hydration Properties1[C][W][OA]

  2009cited by this paper
• A Genomewide Analysis of the Cinnamyl Alcohol Dehydrogenase Family in Sorghum [Sorghum bicolor (L.) Moench] Identifies SbCAD2 as the Brown midrib6 Gene

  2009cited by this paper
• TopHat: discovering splice junctions with RNA-Seq

  2009cited by this paper
• RNA-Seq: a revolutionary tool for transcriptomics

  2009cited by this paper
• Salicylic acid improves acclimation to salt stress by stimulating abscisic aldehyde oxidase activity and abscisic acid accumulation, and increases Na+ content in leaves without toxicity symptoms in Solanum lycopersicum L.

  2009cited by this paper
• Observation on Exocarp Growth of Korean Pear During Young Fruit Period

  2009cited by this paper
• Two Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynthesis, but differentially controlled by osmotic stress.

  2009cited by this paper
• Spontaneous mapping of number and space in adults and young children.

  2009influential reference
• Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester

  2009cited by this paper
• Functional Characterization of Poplar Wood-Associated NAC Domain Transcription Factors1[C][OA]

  2009cited by this paper
• A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis

  2009influential reference
• Suppression of 4-Coumarate-CoA Ligase in the Coniferous Gymnosperm Pinus radiata1[W]

  2008cited by this paper
• Gene Expression and Metabolism in Tomato Fruit Surface Tissues1[C][W]

  2008cited by this paper
• Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array

  2008cited by this paper
• Self-assembly of the plant cell wall requires an extensin scaffold

  2008cited by this paper
• Wax Crystal-Sparse Leaf1 encodes a β–ketoacyl CoA synthase involved in biosynthesis of cuticular waxes on rice leaf

  2008cited by this paper
• Silencing of StKCS6 in potato periderm leads to reduced chain lengths of suberin and wax compounds and increased peridermal transpiration

  2008cited by this paper
• Sealing plant surfaces: cuticular wax formation by epidermal cells.

  2008cited by this paper
• Building lipid barriers: biosynthesis of cutin and suberin.

  2008influential reference
• A Genomic Approach to Suberin Biosynthesis and Cork Differentiation1[C][W][OA]

  2007cited by this paper
• Monoacylglycerols Are Components of Root Waxes and Can Be Produced in the Aerial Cuticle by Ectopic Expression of a Suberin-Associated Acyltransferase1[W][OA]

  2007cited by this paper
• Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion.

  2007cited by this paper
• The Transcription Factor WIN1/SHN1 Regulates Cutin Biosynthesis in Arabidopsis thaliana[W]

  2007cited by this paper
• The Developmental Pattern of Tomato Fruit Wax Accumulation and Its Impact on Cuticular Transpiration Barrier Properties: Effects of a Deficiency in a β-Ketoacyl-Coenzyme A Synthase (LeCER6)1[C]

  2007cited by this paper
• Expression profiling of the lignin biosynthetic pathway in Norway spruce using EST sequencing and real-time RT-PCR

  2007cited by this paper
• Plant ATP-binding cassette transporters.

  2007cited by this paper
• The Arabidopsis DESPERADO/AtWBC11 Transporter Is Required for Cutin and Wax Secretion1[C][W]

  2007cited by this paper
• Identification of RAPD marker linked to fruit skin color in Japanese pear (Pyrus pyrifolia Nakai)

  2006cited by this paper
• Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis.

  2006cited by this paper
• Genetic and biochemical evidence for involvement of HOTHEAD in the biosynthesis of long-chain alpha-,omega-dicarboxylic fatty acids and formation of extracellular matrix.

  2006cited by this paper
• GENETIC TRANSFORMATION AND HYBRIDIZATION

  2006cited by this paper
• Phloem and xylem specification: pieces of the puzzle emerge.

  2005cited by this paper
• A coumaroyl-ester-3-hydroxylase Insertion Mutant Reveals the Existence of Nonredundant meta-Hydroxylation Pathways and Essential Roles for Phenolic Precursors in Cell Expansion and Plant Growth1[W][OA]

  2005cited by this paper
• Flavonoids: a colorful model for the regulation and evolution of biochemical pathways.

  2005cited by this paper
• Changes in Transcriptional Profiles Are Associated with Early Fruit Tissue Specialization in Tomato1[w]

  2005cited by this paper
• DEVELOPMENT OF MOLECULAR MARKERS LINKED TO SEVERAL FRUIT TRAITS IN ORIENTAL PEAR

  2005cited by this paper
• Expression of viral EPS-depolymerase reduces fire blight susceptibility in transgenic pear

  2005cited by this paper
• Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation.

  2005cited by this paper
• EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis.

  2005cited by this paper
• Tomato fruit cuticular waxes and their effects on transpiration barrier properties: functional characterization of a mutant deficient in a very-long-chain fatty acid beta-ketoacyl-CoA synthase.

  2004cited by this paper
• Biosynthesis and accumulation of sterols.

  2004cited by this paper
• Coordinated Genetic Regulation of Growth and Lignin Revealed by Quantitative Trait Locus Analysis of cDNA Microarray Data in an Interspecific Backcross of Eucalyptus1

  2004cited by this paper
• Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana

  2003cited by this paper
• Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w]

  2003cited by this paper
• Improvement of rice (Oryza sativa L.) seed oil quality through introduction of a soybean microsomal omega-3 fatty acid desaturase gene

  2003cited by this paper
• PIP1 plasma membrane aquaporins in tobacco: from cellular effects to function in plants.

  2002cited by this paper
• Identification of the Structure and Origin of Thioacidolysis Marker Compounds for Cinnamyl Alcohol Dehydrogenase Deficiency in Angiosperms* 210

  2002cited by this paper
• A direct approach to false discovery rates

  2002cited by this paper
• Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity.

  2002cited by this paper
• Climatic Impact of Tropical Lowland Deforestation on Nearby Montane Cloud Forests

  2001cited by this paper
• Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF

  2001cited by this paper
• Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

  2001cited by this paper
• Structural determinants of water permeation through aquaporin-1

  2000cited by this paper
• Aldehyde oxidase and xanthine dehydrogenase in a flacca tomato mutant with deficient abscisic acid and wilty phenotype

  1999cited by this paper
• The macromolecular aromatic domain in suberized tissue: a changing paradigm.

  1998cited by this paper
• Antifungal lignans from the arils of Virola oleifera

  1998cited by this paper
• Isolation of antifungal and larvicidal constituents of Diplolophium buchanani by centrifugal partition chromatography.

  1995cited by this paper
• Molybdenum Cofactor Mutants, Specifically Impaired in Xanthine Dehydrogenase Activity and Abscisic Acid Biosynthesis, Simultaneously Overexpress Nitrate Reductase

  1995cited by this paper
• Antifungal aryltetralin lignans from leaves of Podophyllum hexandrum

  1995cited by this paper
• Chemical composition and variability of cork from Quercus suber L.

  1988cited by this paper
• Biopolyester Membranes of Plants: Cutin and Suberin

  1980cited by this paper
• Edinburgh Research Explorer Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106

  year unknowncited by this paper
• Journal of Experimental Botany Advance Access published July 3, 2007 Journal of Experimental Botany, Page 1 of 15

  year unknowncited by this paper

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  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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  2018cites this paper
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  2018cites this paper
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  2016cites this paper
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  2015cites this paper
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  year unknowncites this paper