Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.)

Abstract

Estimating maturity in pome fruits is a critical task that directs virtually all postharvest supply chain decisions. This is especially important for European pear (Pyrus communis) cultivars because losses due to spoilage and senescence must be minimized while ensuring proper ripening capacity is achieved (in part by satisfying a fruit chilling requirement). Reliable methods are lacking for accurate estimation of pear fruit maturity, and because ripening is maturity dependent it makes predicting ripening capacity a challenge. In this study of the European pear cultivar ‘d’Anjou’, we sorted fruit at harvest based upon on-tree fruit position to build contrasts of maturity. Our sorting scheme showed clear contrasts of maturity between canopy positions, yet there was substantial overlap in the distribution of values for the index of absorbance difference (IAD), a non-destructive spectroscopic measurement that has been used as a proxy for pome fruit maturity. This presented an opportunity to explore a contrast of maturity that was more subtle than IAD could differentiate, and thus guided our subsequent transcriptome analysis of tissue samples taken at harvest and during storage. Using a novel approach that tests for condition-specific differences of co-expressed genes, we discovered genes with a phased character that mirrored our sorting scheme. The expression patterns of these genes are associated with fruit quality and ripening differences across the experiment. Functional profiles of these co-expressed genes are concordant with previous findings, and also offer new clues, and thus hypotheses, about genes involved in pear fruit quality, maturity, and ripening. This work may lead to new tools for enhanced postharvest management based on activity of gene co-expression modules, rather than individual genes. Further, our results indicate that modules may have utility within specific windows of time during postharvest management of ‘d’Anjou’ pear.

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

“…Orthogroup multiple sequence alignment, phylogenetic tree estimation, homology inference, and gene model evaluation were performed using genes from 16 Rosaceae genomes (the same 15 from [52] plus Malus baccata [53]) plus the scaffolding species following methods from [52]. These top 45 genes were further filtered for primer development following criteria from [54], giving priority to genes in (in no particular order): 1) small orthogroups (ideally < 15 members in Prunus persica), 2) high expression, 3) low variance between biological replicates, and 4) those with linear expression profiles. From these criteria, a set of 15 genes were selected for primer development for a preliminary assessment of potential PTB performance in a novel sample set (Year 2).…”

Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes

“…Combining information such as de novo transcriptome assembly, homologous proteins of closely related species, and protein-coding gene annotations from the two ‘Bartlett’ genomes, we identified a total of 45,981 protein coding genes in d’Anjou ( Table 1 ). Of those putative genes 76.63% were annotated with functional domains from Pfam ( Mistry et al., 2020 ) and the remaining are supported by annotation evidence, primarily d’Anjou RNA-Seq reconstructed transcripts ( Honaas et al., 2021 ). These results indicate that we captured a large majority of the gene space in the d’Anjou genome.…”

“…To supplement ab initio gene predictions, extensive extrinsic gene annotation homology evidence was collected, including (1) d’Anjou RNA-seq data from our previous study ( Honaas et al., 2021 ); (2) homologous protein evidence of closely related species: Malus domestica , Prunus persica , Pyrus betulifolia , Pyrus communis ‘Bartlett’, Pyrus x bretschneideri , Rosa chinensis , and Rubus occidentalis retrieved from the Genome Database for Rosaceae (GDR) ( Jung et al., 2018 ), and (3) protein sequences from the plant model species, Arabidopsis thaliana ( Cheng et al., 2017 ).…”

Mechanism of Peppermint Extract-Induced Delay of ‘Packham’s Triumph’ Pear (Pyrus communis L.) Postharvest Ripening

“…The flesh is soluble and the juice is rich; however, the fruit is prone to spoilage after softening. Therefore, the postharvest storage process of European pears is very important for their industrial development [ 30 ]. Given their specific requirements, delaying fruit senescence cannot be achieved by inhibiting respiratory climacteric changes, which limits the ability to appropriately soften the flesh to achieve the optimal edible state.…”