Identification of cherry incompatibility alleles by microarray

Pasquer, Frédérique; Frey, Beatrice; Frey, Juerg E.

doi:10.1111/j.1439-0523.2007.01476.x

Cited by 6 publications

(3 citation statements)

References 13 publications

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“…Finally, this technology has been used in sweet and sour cherry species in the identification of flower incompatibility alleles using other microarray containing only 80 oligonucleotide probes (can be considered a macroarray) corresponding to the first and the second intron of the S-RNase gene (Pasquer et al 2008).…”

Section: Early Transcriptome Analysis Inmentioning

confidence: 99%

New approaches to Prunus transcriptome analysis

et al. 2011

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The recent sequencing of the complete genome of the peach offers new opportunities for further transcriptomic studies in Prunus species in the called post-genomics era. First works on transcriptome analysis in Prunus species started in the early 2000s with the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. Later, new strategies of massive analysis (high throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single experiment. One of these systems is massive transcriptome analysis using cDNA biochips (microarrays) to analyze thousands of genes by hybridization of mRNA labelled with fluorescence. However, the recent emergence of a massive sequencing methodology ("deep-sequencing") of the transcriptome (RNA-Seq), based on lowering the costs of DNA (in this cases complementary, cDNA) sequencing, could be more suitable than the application of microarrays. Recent papers have described the tremendous power of this technology, both in terms of profiling coverage and quantitative accuracy in transcriptomic studies. Now this technology is being applied to plant species, including Prunus. In this work, we analyze the potential in using this RNA-Seq technology in the study of Prunus transcriptomes and the development of genomic tools. In addition, the strengths and limitations of RNA-Seq relative to microarray profiling have been discussed.

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Section: Early Transcriptome Analysis Inmentioning

confidence: 99%

New approaches to Prunus transcriptome analysis

et al. 2011

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“…Microarrays have been extensively used in the past years to study the expression levels of transcripts in many plants including Prunus species [25], [26], [27], [28], [29]. It notably permitted to show in Arabidopsis thaliana that the same set of genes confers resistance or susceptibility to diseases, and that the difference of phenotype is due to the timing and magnitude of the expression of those genes [30].…”

Section: Introductionmentioning

confidence: 99%

Comparative RNA-Seq Analysis of Early-Infected Peach Leaves by the Invasive Phytopathogen Xanthomonas arboricola pv. pruni

et al. 2013

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Xanthomonas arboricola pv. pruni is a quarantine bacterial pathogen that threatens peach production by causing necrotic spots on leaves and fruits, thus with the potential of severely reducing yields. The current understanding of the host plant defense responses to the pathogen is very limited. Using whole transcriptome sequencing, differential gene expression was analyzed at two time points, 2 h and 12 h post inoculation (hpi), by comparing the inoculated samples to their respective controls. On the total of 19,781 known peach genes that were expressed in all time points and conditions, 34 and 263 were differentially expressed at 2 and 12 hpi, respectively. Of those, 82% and 40% were up-regulated, respectively; and 18% and 60% were down-regulated, respectively. The functional annotation based on gene ontology (GO) analysis highlighted that genes involved in metabolic process and response to stress were particularly represented at 2 hpi whereas at 12 hpi cellular and metabolic processes were the categories with the highest number of genes differentially expressed. Of particular interest among the differentially expressed genes identified were several pathogen-associated molecular pattern (PAMP) receptors, disease resistance genes including several RPM1-like and pathogenesis related thaumatin encoding genes. Other genes involved in photosynthesis, in cell wall reorganization, in hormone signaling pathways or encoding cytochrome were also differentially expressed. In addition, novel transcripts were identified, providing another basis for further characterization of plant defense-related genes. Overall, this study gives a first insight of the peach defense mechanisms during the very early stages of infection with a bacterial disease in the case of a compatible interaction.

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“…High-throughput methods have also been developed for S-RNase-based S-genotyping. For instance, microarray platforms based on intron and cDNA sequences have been developed to identify S-RNase alleles in sweet cherry (Pasquer et al, 2008) and Asian pear (Pyrus pyrifolia Nakai) (Nan et al, 2015), respectively. In apple, Larsen et al (2016) identified 25 S-RNase alleles in 432 accessions by using multiplex PCR and fragment detection on a capillary DNA sequencer ( Table 1).…”

Section: Molecular S-genotyping For Successful Crossing and Marker-asmentioning

confidence: 99%

Self-(In)compatibility Systems: Target Traits for Crop-Production, Plant Breeding, and Biotechnology

et al. 2020

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Self-incompatibility (SI) mechanisms prevent self-fertilization in flowering plants based on specific discrimination between self-and non-self pollen. Since this trait promotes outcrossing and avoids inbreeding it is a widespread mechanism of controlling sexual plant reproduction. Growers and breeders have effectively exploited SI as a tool for manipulating domesticated crops for thousands of years. However, only within the past thirty years have studies begun to elucidate the underlying molecular features of SI. The specific S-determinants and some modifier factors controlling SI have been identified in the sporophytic system exhibited by Brassica species and in the two very distinct gametophytic systems present in Papaveraceae on one side and in Solanaceae, Rosaceae, and Plantaginaceae on the other. Molecular level studies have enabled SI to SC transitions (and vice versa) to be intentionally manipulated using marker assisted breeding and targeted approaches based on transgene integration, silencing, and more recently CRISPR knock-out of SI-related factors. These scientific advances have, in turn, provided a solid basis to implement new crop production and plant breeding practices. Applications of self-(in)compatibility include widely differing objectives such as crop yield and quality improvement, marker-assisted breeding through SI genotyping, and development of hybrids for overcoming intra-and interspecific reproductive barriers. Here, we review scientific progress as well as patented applications of SI, and also highlight future prospects including further elucidation of SI systems, deepening our understanding of SI-environment relationships, and new perspectives on plant self/non-self recognition.

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Identification of cherry incompatibility alleles by microarray

Cited by 6 publications

References 13 publications

New approaches to Prunus transcriptome analysis

New approaches to Prunus transcriptome analysis

Comparative RNA-Seq Analysis of Early-Infected Peach Leaves by the Invasive Phytopathogen Xanthomonas arboricola pv. pruni

Self-(In)compatibility Systems: Target Traits for Crop-Production, Plant Breeding, and Biotechnology

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