Genetcin Meker and Meiotic Panels

Track Imformation


Hd-rR_female_panel
Hd-rR_male_panel
AA2_panel
Kunming_panel
SSLP marker

These tracks contain Medaka genetic marker information. Hd-rR/HNI female backcross panel and AA2/HNI female backcross panel are 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 isused to segregate genetic markers in these regions. In linkage group (chromosoe 11), recombination is highly supressed in the wide range in Hd-rR/HNI and AA2/HNI meiosis. Hd-rR/kunming panel (female and male backcross panels are mixed) is used for this region. Hd-rR/HNI F2 panel is used to map SSLP markers.

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.

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 typying data.

Genetcin Mekers and Meiotic Panels
Track Name Marker Type Meiotic panel Observed Recombination Covered Region Rererence
Hd-rR female EST, SNPs Hd-rR/HNI female backcross panel 94 Whole Genomic Region 2, 4
Hd-rR male EST, SNPs Hd-rR/HNI male backcross panel 93 Sub-telomeric region on the linkage groups 1, 5, 6, 7, 8, 9, 10, 12, 13, 14、15、16、17、18、19、22、23 and 24. 4
AA2 (Mbase) EST, AFLPs, RAPDs, IRSs, STSs, phenotype AA2/HNI female backcross panel 39 Whole Genomic Region 1
Kunming EST, SNPs Hd-rR/kunming backcross panels
(female and male are mixed)		 44 Linkage group (chromosome) 11 4
SSLP SSLP, microsatelite Hd-rR/HNI F2 panel
Kaga/Hd-rR F2 panel
Hd-rR/kunming backcross panels
(female and male are mixed)		 368
96

44
 Whole Genomic Region 3


References:

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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)