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BMC Genomics

, 16:762

Transcriptomic methods


BackgroundThe 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.

ResultsThe 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.

ConclusionsWe 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.

KeywordsRNA-Seq EBSeq Cell wall Auxin Ethylene bZIP AP2-EREBP bHLH WRKY Aux-IAA Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1939-9 contains supplementary material, which is available to authorized users.

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Autor: Ngoc T. Nham - Sergio Tonetto de Freitas - Andrew J. Macnish - Kevin M. Carr - Trisha Kietikul - Angelo J. Guilatco - C

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

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