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Absence of major epigenetic and transcriptomic changes accompanying the interspecific cross between peach and almond

ABSTRACT: Absence of major epigenetic and transcriptomic changes accompanying the interspecific cross between peach and almond

PROVIDER: PRJNA813872 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18272047_1.fastq.gz	Fastqsanger.gz
	SRR18272047_2.fastq.gz	Fastqsanger.gz
	SRR18272048_1.fastq.gz	Fastqsanger.gz
	SRR18272048_2.fastq.gz	Fastqsanger.gz
	SRR18272049_1.fastq.gz	Fastqsanger.gz

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Absence of major epigenetic and transcriptomic changes accompanying the interspecific cross between peach and almond

Project description:We analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in their F1 hybrid using high-throughput sequencing tecnhologies. We can conclude that the merging of the two parental genomes in the P. persica x P. dulcis hybrid does not result in a “genomic shock” with significant changes in the DNA methylation or in the transcription.

2022-08-10 | GSE198152 | GEO

Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond.

Project description:Hybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (Prunus persica). The merging of two different genomes in a hybrid often triggers a so-called "genomic shock" with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in an F1 hybrid using high-throughput sequencing technologies. Contrary to the "genomic shock" expectations, we found that the overall levels of DNA methylation in the transposable elements in the hybrid are not significantly altered compared with those of the parental genomes. We also observed that the levels of transcription of the transposable elements in the hybrid are in most cases intermediate as compared with that of the parental species and we have not detected cases of higher transcription in the hybrid. We also found that the proportion of genes whose expression is altered in the hybrid compared with the parental species is low. The expression of genes potentially involved in the regulation of the activity of the transposable elements is not altered. We can conclude that the merging of the two parental genomes in this Prunus persica x Prunus dulcis hybrid does not result in a "genomic shock" with significant changes in the DNA methylation or in the transcription. The absence of major changes may facilitate using interspecific peach x almond crosses for peach improvement.

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Almond x Peach interspecific hybrid

Project description:Identification of putative markers of noninfectious bud failure in almond (Prunus dulcis [Mill] D.A. Webb) through genome wide DNA methylation profiling and gene expression analysis in an almond x peach hybrid population

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Involvement of different plant viruses in the activation of RNA silencing-related genes and the defensive response against Plum pox virus of ‘GF305’ peach (Prunus persica) grafted with ‘Garrigues’ almond (P. dulcis)

Project description:Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. A recent study tried to identify genes responsible for this effect by studying mRNA expression through RNAseq data in peach and almond plants, before and after grafting, and before and after PPV infection. In this work, we used the same peach and almond samples, but focused the high-throughput analyses on small RNAs (sRNAs) expression. We studied massive sequencing data and found an interesting pattern of sRNAs overexpression linked to antiviral defense genes that suggested activation of these genes followed by downregulation to basal levels. We also discovered that ‘Garrigues’ almond plants were infected by different plant viruses that were transferred to peach plants. The large amounts of viral sRNAs found in grafted peaches indicated a strong RNA silencing antiviral response and led us to postulate that these plant viruses could be collaborating by cross-protection in the observed ‘Garrigues’ effect.

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Project description:The cultivated almond exhibits self-incompatibility of the gametophytic type regulated by the S-locus, and expressed in pistil (S-RNase) and in pollen (SFB protein). The aim of this study is to clarify the transcription pattern of these 2 S-genes and to identify additional components of the gametophytic self-incompatibility system in almond. With this aim, A2-198 (self compatible) and ITAP-1 (self incompatible) almond selections were used: RNA-seq of pistils of these two accessions both un-pollinated and pollinated with A2-198 pollen were carried out.

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