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Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.
Pubmed ID: 26811909 RIS Download
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Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
View all literature mentionsIndependent body that funds investigator-driven frontier research in the European Union (EU). It is part of the Seventh Research Framework Programme (FP7).
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsNASCArrays is the Nottingham Arabidopsis Stock Centre''s microarray database. Currently most of the data is for Arabidopsis thaliana experiments run by the NASC Affymetrix Facility. There are also experiments from other species, and experiments run by other centres too. NASCArrays is an Affymetrix microarray database. It contains free Affymetrix microarray data, and also features a series of tools allowing you to query that data in powerful ways. Most of the data currently comes from NASC''s Affymetrix Service. It also includes data from other sources, notably the AtGenExpress project. They currently distribute over 30,000 tubes of seed a year. There are currently the following data mining tools available. All of these tools allow you to type in a gene(s) of interest, and identify experiments or slides that you might be interested in: -Spot History: This tool allows you to see the pattern of gene expression over all slides in the database. Easily identify slides (and therefore experimental treatments) where genes are highly, lowly, or unusually expressed -Two gene scatter plot: This tool allows you to see the pattern of gene expression over all slides for two genes as a scatter plot. If you are interested in two genes, you can find out if they act in tandem, and highlight slides (and therefore experimental conditions) where these two genes behave in an unusual manner. -Gene Swinger: If you have a gene of interest, this tool will show you which experiment the gene expression varied most -Bulk Gene Download: This tool allows you to download the expression of a list of genes over all experiments. You can get all genes over all experiments (the entire database!) from the Super Bulk Gene Download Sponsors: This is a BBSRC funded consortium to provide services to the Arabidopsis community.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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