GeneticMarkers

Track Imformation

Mase
mappedGeneticMarkers
SSLP marker

These tracks contain Medaka genetic marker information.

Mbase:
This track shows genetic markers which are shown in the Mbase in Prof. Mitani lab. AA2/HNI female backcross panel are used to map genetic markers for whole genomic region.
Click on an individual marker within a track opens a details page containing the marker type (SSLP, RFLP, SNPs), primer sequences, PCR condition, restriction enzyme information and links to Mbase.

mappedGeneticMarkers:
Hd-rR/HNI female backcross panel is used to map genetic markers for whole genomic region. Three additional meiotic panels are used for the specific region. In subtelomeric region, recombination is more supressed in the female meiosis than the male one. Hd-rR/HNI male backcross panel is used to segregate genetic markers in these regions. In linkage group (chromosoe 11), recombination is highly supressed in the wide range in Hd-rR/HNI meiosis. Hd-rR/kunming panel (female and male backcross panels are mixed) is used for this region.
Click on an individual marker within a track opens a typing panel using Hd-rR/HNI female backcross panel.

SSLP markers:
Microstelite markers and Simple sequence length polymorphism (SSLP) markers are mapped using Hd-rR/HNI F2 panel, Hd-rR/HNI male backcross panel and Hd-rR/kunming panel (female and male backcross panels are mixed) are also used as the markers in the mappedGeneticMarkers track. Click on an individual marker within a track opens a details page containing primer sequences.
Acknowledgement:
These marker information was published in reference 3, Copyright Elsevier.

Polymorphic EST fragments are mapped by conventional polyacrylamide gel electrophoresis and DNA fragments containing SNP polymorphism are mapped using MassARRAY system. SSLP markers,including microstelite markers are mapped using ABI3700.

All PCR primer sequence information can be downloaded from our download site.

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Genetcin Mekers and Meiotic Panels
Track Name Marker Type Meiotic panel Rererence
mappedGeneticMarkers EST, SNPs Hd-rR/HNI female backcross panel
Hd-rR/HNI male backcross panel
Hd-rR/kunming backcross panels (female and male are mixed)		 2, 4
Mbase EST, AFLPs, RAPDs, IRSs, STSs, phenotype AA2/HNI female backcross panel 1
SSLP SSLP, microsatelite Hd-rR/HNI F2 panel
Kaga/Hd-rR F2 panel
Hd-rR/kunming backcross panels
(female and male are mixed)		 3


References:

(1) Naruse K., Fukamachi S., Mitani H., Kondo M., Matsuoka T., Kondo S., Hanamura N., Morita Y., Hasegawa K., Nishigaki R., Shimada A., Wada H., Kusakabe T., Suzuki N., Kinoshita M., Kanamori A., Terado T., Kimura H., Nonaka M. and Shima A.
A Detailed Linkage Map of Medaka, Oryzias latipes. Comparative genomics and genome evolution.
Genetics 154:1773-1784 (2000)
(2)Kimura T, Jindo T, Narita T, Naruse K, Kobayashi D, Shin-I T, Kitagawa T, Sakaguchi T, Mitani H, Shima A, Kohara Y and Takeda H.
Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics.
Mech. Dev. 121:915-32 (2004)
(3) Kimura T, Yoshida K, Shimada A, Jindo T, Sakaizumi M, Mitani H, Naruse K, Takeda H, Inoko H, Tamiya G, Shinya M.
Genetic linkage map of medaka with polymerase chain reaction length polymorphisms.
Gene 363 24-31 (2005)
(4) Kasahara M., Naruse K., Sasaki S., Nakatani Y., Qu W., Ahsan B., Yamada T., Nagayasu Y., Doi K., Kasai Y., Jindo T., Kobayashi D., Shimada A., Toyoda A., Kuroki Y., Fujiyama A., Sasaki T., Shimizu A., Asakawa S., Shimizu N., Hashimoto S., Yang J., Lee Y., Matsushima K., Sugano S., Sakaizumi M., Narita T., Ohishi K., Haga S., Ohta F., Nomoto H., Nogata K., Morishita T., Endo T., Shin-I T., Takeda H., Morishita S. and Kohara Y.
The medaka draft genome and insights into vertebrate genome evolution
Nature 447:714-719 (2007)