Abstract
The high-value apple cultivar ‘Honeycrisp’ is prone to bitter pit, a physiological disorder characterized by the development of dark, sunken lesions on fruit particularly towards the calyx-end. Identifying the genetic basis of bitter pit is critical for mitigation of the disorder and development of bitter pit-free varieties. To this end, we performed an RNA sequencing experiment to compare the peel and flesh transcriptomes of healthy and bitter pit-affected ‘Honeycrisp’ fruit, with the objective of identifying bitter pit candidate genes. A similar number of genes were expressed in flesh and peel (~ 27,000), and we detected flesh- and peel-specific expression. Within the flesh and peel datasets, 2.6% and 1% of genes were differentially expressed between healthy and bitter pit apples, respectively. We identified over 1000 differentially expressed genes in both flesh and peel datasets that are distributed throughout the genome, sixteen of which are within a previously identified bitter pit QTL, making them potential candidate genes. Both MdMADS5 and MdIDL1, the orthologs of Arabidopsis APETALA1 and INFLORESCENCE DEFICIENT IN ABSCISSION-LIKE 1, respectively, which are possibly involved in fruit development and organ abscission, stand out as candidate genes for bitter pit, based on their proposed function, differential expression, and location within a bitter pit QTL. The RNA-seq data also revealed that many genes involved with defense response and stress are upregulated in bitter pit-affected tissues. We discuss how these differentially expressed genes could provide important information about the physiology, development, and progression of bitter pit.
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Acknowledgements
We thank Cherry Lawn Fruit Farms in Western New York for their cooperation on fruit sample collection.
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This work is supported in part by USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative project “AppleRoot2Fruit: Accelerating the development, evaluation and adoption of new apple rootstocks” (2016–51181-25406) and New York Apple Research and Development Program.
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Raw transcriptome sequencing reads have been deposited into the NCBI BioProject database under the accession PRJNA725518.
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Orcheski, B., Meng, D., Bai, Y. et al. The transcriptomes of healthy and bitter pit-affected ‘Honeycrisp’ fruit reveal genes associated with disorder development and progression. Tree Genetics & Genomes 17, 37 (2021). https://doi.org/10.1007/s11295-021-01518-7
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DOI: https://doi.org/10.1007/s11295-021-01518-7