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Gasterosteus aculeatus aculeatus

ABSTRACT: Marine stickleback fish Restriction-site associated DNA (RAD) sequencing (Sbf1)

PROVIDER: PRJNA237034 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1151540.fastq.gz	Fastqsanger.gz
	SRR1151550.fastq.gz	Fastqsanger.gz
	SRR1151560.fastq.gz	Fastqsanger.gz
	SRR1151570.fastq.gz	Fastqsanger.gz
	SRR1151580.fastq.gz	Fastqsanger.gz

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Project description:In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. Four to five fish from each population were used as biological replicates for each of the seven tissues. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. All fish were of similar age and were raised in the same aquarium (salinity: 3.5 ppt), with a plastic divider separating the marine and freshwater groups. One male and four females were sampled from each population. Microarray experiments were performed in a 2-color format on custom Agilent arrays: experimental RNA samples were labeled with Cy5, and the common reference RNA sample was labeled with Cy3. The reference RNA was total RNA isolated from a large number of 7-day-post-hatch embryos from the freshwater population of Bear Paw Lake, Alaska (BEPA). One technical replicate was used for each array, and one of the hypothalamus samples (Hyp_FTC#3) was excluded from further analysis due to poor quality indicators. FTC#1 liver and LITC#2 pectoral muscle samples did not yield RNA of sufficient quality for the microarray experiment, and were also excluded from hybridization.

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Project description:RAD methods paper - Threespine Stickleback Lateral Plate Mapping

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Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping

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