Dataset Information

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

ABSTRACT: Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

PROVIDER: PRJNA1150595 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30334126_1.fastq.gz	Fastqsanger.gz
	SRR30334126_2.fastq.gz	Fastqsanger.gz
	SRR30334127_1.fastq.gz	Fastqsanger.gz
	SRR30334127_2.fastq.gz	Fastqsanger.gz
	SRR30334128_1.fastq.gz	Fastqsanger.gz

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Project description:Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Most of the existing varieties of olive are traditional and their architecture is poorly suited for modern growing and harvesting systems. This study focuses on the identification of candidate genes involved in determining plant architecture in olive that could help in selecting phenotypes adapted to modern cultivation practices. We previously developed the first microarray for olive, as a means to discover candidate genes involved in relevant agronomical traits. The microarray has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. In the present study, made in the framework of an olive breeding program, varieties displaying differences in architecture and pooled seedlings grouped by their architecture-related phenotypes, were analysed using microarray analysis of meristematic tissue. We identify 2,258 differentially expressed genes potentially involved in determining plant architecture. Varieties with opposite architecture phenotypes and individuals from segregating progenies displaying extreme architecture features, constitute our key to linking phenotype to expression. We analyze some of the genes with potentially interesting functional annotation using quantitative RT-PCR assays, in the reference varieties and individual seedlings. Arabidopsis mutants in putative orthologs of some of the candidate genes show altered architecture, indicating functional conservation between the two species and supporting both, the biological relevance of the results, and the potential of the identified genes as markers for assisted breeding for olive varieties suited for high density orchards. Active or dormant meristems to be used for expression analysis were collected from individual olive trees from four varieties Picual, Arbequina, Arbosana and Chiquitita and from seedlings of a Picual x Arbequina progeny, all of the showing variability for growth habit. Plant material was provided by the olive breeding program of Cordoba. Harvesting was carried out between 8:00 to 11:00 a.m., at the end of Spring. Samples were immediately frozen in liquid nitrogen, and maintained afterwards at -80 ÂºC. Samples of the Picual x Arbequina seedlings used to generate pools were harvested individually and 0.2 g of tissue per individual mixed and processed together to obtain RNA to be used for microarray analysis.

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Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

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