title: A transcriptome approach towards understanding the development of ripening capacity in 'Bartlett' pears (Pyrus communis L.).
abstract: BACKGROUND
  The capacity of European pear fruit (Pyrus communis L.) to ripen after harvest develops during the final stages of growth on the tree. The objective of this study was to characterize changes in 'Bartlett' pear fruit physico-chemical properties and transcription profiles during fruit maturation leading to attainment of ripening capacity.
  
  
  RESULTS
  The softening response of pear fruit held for 14 days at 20 °C after harvest depended on their maturity. We identified four maturity stages: S1-failed to soften and S2- displayed partial softening (with or without ET-ethylene treatment); S3 - able to soften following ET; and S4 - able to soften without ET. Illumina sequencing and Trinity assembly generated 68,010 unigenes (mean length of 911 bp), of which 32.8 % were annotated to the RefSeq plant database. Higher numbers of differentially expressed transcripts were recorded in the S3-S4 and S1-S2 transitions (2805 and 2505 unigenes, respectively) than in the S2-S3 transition (2037 unigenes). High expression of genes putatively encoding pectin degradation enzymes in the S1-S2 transition suggests pectic oligomers may be involved as early signals triggering the transition to responsiveness to ethylene in pear fruit. Moreover, the co-expression of these genes with Exps (Expansins) suggests their collaboration in modifying cell wall polysaccharide networks that are required for fruit growth. K-means cluster analysis revealed that auxin signaling associated transcripts were enriched in cluster K6 that showed the highest gene expression at S3. AP2/EREBP (APETALA 2/ethylene response element binding protein) and bHLH (basic helix-loop-helix) transcripts were enriched in all three transition S1-S2, S2-S3, and S3-S4. Several members of Aux/IAA (Auxin/indole-3-acetic acid), ARF (Auxin response factors), and WRKY appeared to play an important role in orchestrating the S2-S3 transition.
  
  
  CONCLUSIONS
  We identified maturity stages associated with the development of ripening capacity in 'Bartlett' pear, and described the transcription profile of fruit at these stages. Our findings suggest that auxin is essential in regulating the transition of pear fruit from being ethylene-unresponsive (S2) to ethylene-responsive (S3), resulting in fruit softening. The transcriptome will be helpful for future studies about specific developmental pathways regulating the transition to ripening.
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. ntnham@ucdavis.edu.
authors.forename: Ngoc T
authors.initials: NT
authors.lastname: Nham
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. stonettodefreitas@yahoo.com.br.|Present address: Embrapa Tropical Semi-Arid, Petrolina, PE, 56302-970, Brazil. stonettodefreitas@yahoo.com.br.
authors.forename: Sergio Tonetto
authors.initials: ST
authors.lastname: de Freitas
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. andrew.macnish@daf.qld.gov.au.|Present address: Horticulture and Forestry Science, Queensland Department of Agriculture, Fisheries and Forestry, Maroochy Research Facility, Nambour, QLD, 4560, Australia. andrew.macnish@daf.qld.gov.au.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Macnish
authors.affiliation: Research Technology Support Facility, Michigan State University, East Lansing, MI, 48824, USA. carrk@msu.edu.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Carr
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. tkietikul@ucdavis.edu.
authors.forename: Trisha
authors.initials: T
authors.lastname: Kietikul
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. ajguilatco@ucdavis.edu.
authors.forename: Angelo J
authors.initials: AJ
authors.lastname: Guilatco
authors.affiliation: Agriculture Research Service, United States Department of Agriculture, Davis, CA, 95616, USA. cjiang@ucdavis.edu.
authors.forename: Cai-Zhong
authors.initials: CZ
authors.lastname: Jiang
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. fnegre@ucdavis.edu.
authors.forename: Florence
authors.initials: F
authors.lastname: Zakharov
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. ejmitcham@ucdavis.edu.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Mitcham
mesh_terms: D005030:Ethylenes / Q000494:pharmacology; D005638:Fruit / Q000235:genetics* / Q000254:growth & development; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D007210:Indoleacetic Acids / Q000494:pharmacology; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D031989:Pyrus / Q000235:genetics* / Q000254:growth & development; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005030:Ethylenes; D007210:Indoleacetic Acids; D010940:Plant Proteins; C036216:ethylene