Functional Genomics

Trainotti, Livio; Cagnin, Stefano; Forcato, Claudio; Bonghi, Claudio; Dhingra, Amit; Koepke, Tyson; Prat, Loreto; Maldonado, Jonathan; Silva, Herman

doi:10.1201/b13104-12

Cited by 3 publications

(1 citation statement)

References 112 publications

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“…These genome initiatives coupled with transcriptomic analyses of these fruit species are enabling scientists to identify candidate genes, signal transduction pathways and metabolic pathways that may play an important role in fruit quality and production (Gonzalez-Aguero et al, 2008;Tittarelli et al, 2009;Vizoso et al, 2009;Illa et al, 2011a;Alkio et al, 2012;Barakat et al, 2012;Diez-de-Medina and Silva, 2012;Dirlewanger et al, 2012;Habu et al, 2012;Leida et al, 2012;Trainotti et al, 2012;Koepke et al, 2013;Eduardo et al, 2013;Martinez-Garcia et al, 2013;Sanchez et al, 2013). Identifi cation of polymorphisms between members of the Rosaceae, members of the same genus (i.e.…”

Section: Genome Sequencing and Transcriptome Initiati-ves In Prunmentioning

confidence: 99%

Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective

et al. 2013

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This review is an overview of traditional and modern breeding methodologies being used to develop new Prunus cultivars (stone fruits) with major emphasis on peach, sweet cherry and Japanese plum. To this end, common breeding tools used to produce seedlings, including in vitro culture tools, are discussed. Additionally, the mechanisms of inheritance of many important agronomical traits are described. Recent advances in stone fruit transcriptomics and genomic resources are providing an understanding of the molecular basis of phenotypic variability as well as the identifi cation of allelic variants and molecular markers. These have potential applications for understanding the genetic diversity of the Prunus species, molecular marker-assisted selection and transgenesis. Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNPs) molecular markers are described as useful tools to describe genetic diversity in peach, sweet cherry and Japanese plum. Additionally, the recently sequenced peach genome and the public release of the sweet cherry genome are discussed in terms of their applicability to breeding programs.

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Section: Genome Sequencing and Transcriptome Initiati-ves In Prunmentioning

confidence: 99%

Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective

et al. 2013

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Transcriptional regulatory networks controlling woolliness in peach in response to preharvest gibberellin application and cold storage

et al. 2015

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BackgroundPostharvest fruit conservation relies on low temperatures and manipulations of hormone metabolism to maintain sensory properties. Peaches are susceptible to chilling injuries, such as ‘woolliness’ that is caused by juice loss leading to a ‘wooly’ fruit texture. Application of gibberellic acid at the initial stages of pit hardening impairs woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcriptional profiling to investigate the effects of gibberellic acid application and cold storage on harvested peaches.ResultsApproximately half of the investigated genes exhibited significant differential expression in response to the treatments. Cellular and developmental process gene ontologies were overrepresented among the differentially regulated genes, whereas sequences in cell death and immune response categories were underrepresented. Gene set enrichment demonstrated a predominant role of cold storage in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone responses exhibited a more complex transcriptional response, indicating an extensive network of crosstalk between hormone signaling and low temperatures. Time course transcriptional analyses demonstrate the large contribution of gene expression regulation on the biochemical changes leading to woolliness in peach.ConclusionOverall, our results provide insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach and suggest that hormone mediated reprogramming previous to pit hardening affects the onset of chilling injuries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0659-2) contains supplementary material, which is available to authorized users.

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Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold ^|^amp; Zucc.) and Peach [Prunus persica (L.) Batsch]: A Summary of Recent Studies

Yamane

2014

J. Japan. Soc. Hort. Sci.

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Bud dormancy allows most deciduous fruit tree species to avoid injury in unsuitable environments, synchronize their annual growth, and adapt to a temperate zone climate. Because bud dormancy affects next season's fruit production and vegetative growth, it is considered one of the most important physiological factors that control fruit production. Recent global climate changes require us to better understand the genetic factors regulating bud dormancy, especially those that induce dormancy release and subsequent bud break. In this review, environmental factors that affect the seasonal dormancy depth of Japanese apricot (P. mume Siebold & Zucc.) and peach [P. persica (L.) Batsch] are first outlined. Next, recent progress of genetic, biochemical, and molecular biological studies of Prunus dormancy regulation is described. Recent advances in functional genomics have promoted the discovery of gene function and gene networks associated with bud dormancy regulation. A group of candidate genes for bud dormancy regulation, the DORMANCY-ASSOCIATED MADS-box (DAM) genes in Prunus, are focused. Recently reported expressional analysis suggests a significant role for DAMs in dormancy release and bud break of Japanese apricot and peach vegetative buds. Transformation studies of PmDAM6 have demonstrated that it has an inhibitory effect on the apical growth of poplar (Populus spp.). As bud dormancy is a quantitative polygenic trait, not only DAMs, but also other genes and gene networks appear to regulate bud dormancy. Ongoing and future studies will undoubtedly facilitate the unveiling of the molecular aspects of bud dormancy regulation in temperate fruit tree species of Prunus.

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Functional Genomics

Cited by 3 publications

References 112 publications

Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective

Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective

Transcriptional regulatory networks controlling woolliness in peach in response to preharvest gibberellin application and cold storage

Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold ^|^amp; Zucc.) and Peach [Prunus persica (L.) Batsch]: A Summary of Recent Studies

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