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The harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. The mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit–pedicel junction. The natural propensity for pedicel-–fruit abscission zone (PFAZ) activation varies by cultivar, and the general molecular basis for PFAZ activation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time-course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In ‘Skeena’, mean PFRF for both control and treatment fruit dropped below the 0.40 kg-force (3.92 N) threshold for mechanical harvesting, indicating the activation of a discrete PFAZ. In ‘Bing’, mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in ‘Chelan’ the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ region followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts, as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for the induction or inhibition of PFAZ activation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.
SeAnna Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.). Horticulturae 2021, 7, 270 .
AMA StyleSeAnna Hewitt, Benjamin Kilian, Tyson Koepke, Jonathan Abarca, Matthew Whiting, Amit Dhingra. Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.). Horticulturae. 2021; 7 (9):270.
Chicago/Turabian StyleSeAnna Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. 2021. "Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.)." Horticulturae 7, no. 9: 270.
Harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. Mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit-pedicel junction. The natural propensity for pedicel-fruit abscission zone (PFAZ) formation varies by cultivar, and the general molecular basis for PFAZ formation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In ‘Skeena’, mean PFRF for both control and treatment fruit dropped below the 0.40kg-force (3.92N) threshold for mechanical harvesting and indicating the formation of a discrete PFAZ. In ‘Bing’, mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in ‘Chelan’ the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for induction or inhibition of PFAZ formation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.
Seanna L Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.). 2020, 1 .
AMA StyleSeanna L Hewitt, Benjamin Kilian, Tyson Koepke, Jonathan Abarca, Matthew Whiting, Amit Dhingra. Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.). . 2020; ():1.
Chicago/Turabian StyleSeanna L Hewitt; Benjamin Kilian; Tyson Koepke; Jonathan Abarca; Matthew Whiting; Amit Dhingra. 2020. "Characterization of ethylene-inducible pedicel-fruit abscission zone formation in non-climacteric sweet cherry (Prunus avium L.)." , no. : 1.
The ancient plant production practice of grafting which instantly imparts new physiological properties to the desirable scion still remains shrouded in mystery. Yet, grafting remains a widely used technique in the production of several horticultural species. In a composite grafted plant, rootstocks control many aspects of scion growth and physiology including yield and quality attributes as well as biotic and abiotic stress tolerance. Broadly, physical, physiological, biochemical and molecular mechanisms have been reviewed to develop an integrated understanding of this enigmatic process that challenges existing genetic paradigms. This review summarizes the reported mechanisms underlying some of the economically important traits and identifies several key points to consider when conducting rootstock scion interaction experiments. Study of the somatogenetic interactions between rootstock and scion is a field that is ripe for discovery and vast improvements in the coming decade. Further, utilization of rootstocks based on a better understanding of the somatogenetic interactions is highly relevant in the current agricultural environment where there is a need for sustainable production practices. Rootstocks may offer a non-transgenic approach to rapidly respond to the changing environment and expand agricultural production of annual and perennial crops where grafting is feasible in order to meet the global food, fiber and fuel demands of the future.
Tyson Koepke; Amit Dhingra. Rootstock scion somatogenetic interactions in perennial composite plants. Plant Cell Reports 2013, 32, 1321 -1337.
AMA StyleTyson Koepke, Amit Dhingra. Rootstock scion somatogenetic interactions in perennial composite plants. Plant Cell Reports. 2013; 32 (9):1321-1337.
Chicago/Turabian StyleTyson Koepke; Amit Dhingra. 2013. "Rootstock scion somatogenetic interactions in perennial composite plants." Plant Cell Reports 32, no. 9: 1321-1337.
Sweet cherry (Prunus avium L.), a non-model crop with narrow genetic diversity, is an important member of sub-family Amygdoloideae within Rosaceae. Compared to other important members like peach and apple, sweet cherry lacks in genetic and genomic information, impeding understanding of important biological processes and development of efficient breeding approaches. Availability of single nucleotide polymorphism (SNP)-based molecular markers can greatly benefit breeding efforts in such non-model species. RNA-seq approaches employing second generation sequencing platforms offer a unique avenue to rapidly identify gene-based SNPs. Additionally, haplotype markers can be rapidly generated from transcript-based SNPs since they have been found to be extremely utile in identification of genetic variants related to health, disease and response to environment as highlighted by the human HapMap project.
Tyson Koepke; Scott Schaeffer; Vandhana Krishnan; Derick Jiwan; Artemus Harper; Matthew Whiting; Nnadozie Oraguzie; Amit Dhingra. Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing. BMC Genomics 2012, 13, 18 -18.
AMA StyleTyson Koepke, Scott Schaeffer, Vandhana Krishnan, Derick Jiwan, Artemus Harper, Matthew Whiting, Nnadozie Oraguzie, Amit Dhingra. Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing. BMC Genomics. 2012; 13 (1):18-18.
Chicago/Turabian StyleTyson Koepke; Scott Schaeffer; Vandhana Krishnan; Derick Jiwan; Artemus Harper; Matthew Whiting; Nnadozie Oraguzie; Amit Dhingra. 2012. "Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing." BMC Genomics 13, no. 1: 18-18.
Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD and SSR markers. This study was carried out to assess the utility of SNP markers generated from 3’UTRs for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars and old cultivars imported from different parts of the world were screened with 7 SSR markers developed from other Prunus species and with 40 SNPs obtained from 3’UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity and polymorphic information content (PIC) values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, ‘Stella’ was separated from ‘Compact Stella’. This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3’ UTR SNPs for genetic fingerprinting, parentage verification, gene mapping and study of genetic diversity in sweet cherry.
Angel Fernandez I Marti; Blessing Athanson; Tyson Koepke; Carolina Font I Forcada; Amit Dhingra; Nnadozie Oraguzie. Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers. Frontiers in Plant Science 2012, 3, 116 .
AMA StyleAngel Fernandez I Marti, Blessing Athanson, Tyson Koepke, Carolina Font I Forcada, Amit Dhingra, Nnadozie Oraguzie. Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers. Frontiers in Plant Science. 2012; 3 ():116.
Chicago/Turabian StyleAngel Fernandez I Marti; Blessing Athanson; Tyson Koepke; Carolina Font I Forcada; Amit Dhingra; Nnadozie Oraguzie. 2012. "Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers." Frontiers in Plant Science 3, no. : 116.