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Title:   Author  item
                                            NHAM, NGOC - University Of Californiaitem
                                            DE FREITAS, SERGIO TONETTO - University Of Californiaitem
                                            MACNISH, ANDREW - University Of Californiaitem
                                            CARR, KEVIN - Michigan State Universityitem
                                            KIETIKUL, TRISHA - University Of Californiaitem
                                            GUILATCO, ANGELO - University Of Californiaitem
                                            Jiang, Cai-Zhongitem
                                            ZAKHAROY, FLORENCE - University Of Californiaitem
                                            MITCHAM, ELIZABETH - University Of California
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 9/19/2015
                                    Publication  Date: 10/9/2015
                                    Publication URL: http://www.biomedcentral.com/1471-2164/16/762Citation: Nham, N.T., De Freitas, S., Macnish, A.J., Carr, K.M., Kietikul, T., Guilatco, A.J., Jiang, C., Zakharoy, F., Mitcham, E.J. 2015. A transcriptome approach towards understanding the development of ripening capacity in European pears (Pyrus communis L. cv Bartlett). BMC Genomics. 16:762 doi: 10.1186/s12864-015-1939-9.Interpretive Summary: European pears are economically significant fruit in the United States, with a production value of $437 million in 2012. As a climacteric fruit, pears ripen in association with a substantial increase in rates of respiration and ethylene biosynthesis. Unlike many climacteric fruit such as apple and mango, European pears develop poor texture and flavor if left to ripen on the tree. Therefore, most European pears are harvested at the mature-green stage and then usually exposed to ethylene or cold temperatures (e.g., -1 to 10'C) to facilitate ripening. Early maturity ‘Bartlett’ and ‘d’Anjou’ pear might not respond to ethylene or cold treatment while late maturity fruit could ripen without any conditioning treatment. However, the underlying molecular mechanisms governing this developmental shift are still not well understood. Furthermore, as a climacteric fruit, pear fruit ripening includes the transition from auto-inhibitory ethylene (also known as “System 1”) to autocatalytic ethylene (“System 2”) that regulates the numerous metabolic processes associated with fruit ripening. The intrinsic developmental factors that regulate the transition from System 1 to System 2 remain mostly unknown.
In the last 5 years, next generation sequencing (NGS) technologies accompanied by sophisticated bioinformatics tools have been developed and provide a powerful approach to examine the transcriptomes of non-model plants. Accordingly, these tools have been utilized to determine transcriptional changes during fruit growth and development in a variety of species including Chinese bayberry (Myrica rubra), orange (Citrus sinensis), and Korean black raspberry (Rubus coreanus).
In the present study, NGS technology was used to characterize the molecular mechanisms regulating the development of ripening capacity in ‘Bartlett’ pear fruit. We identified four maturity stages: S1, S2 - unable to soften (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. The transcription factor families AP2/EREBP (APETALA 2/ethylene response element binding protein) and bHLH (basic helix-loop-helix) were enriched in all three transitions S1-S2, S2-S3, and S3-S4. 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. 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.
                                Technical Abstract: 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. 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, S2 - unable to soften (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. The transcription factor families AP2/EREBP (APETALA 2/ethylene response element binding protein) and bHLH (basic helix-loop-helix) were enriched in all three transitions S1-S2, S2-S3, and S3-S4. 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. 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.


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