UTGBMedaka/Track: GeneticMappingPanel & Markers.2.html

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10<title>Genetcin Meker and Meiotic Panels</title>
11
12<h1>Track Imformation</h1>
13<h2><b><br>Hd-rR_female_panel
14<br>Hd-rR_male_panel
15<br>AA2_panel
16<br>Kunming_panel
17<br>SSLP marker</b></h2>
18
19<p>
20These 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.
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23Polymorphic 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.
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26Click 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.
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28
29<b>Genetcin Mekers and Meiotic Panels</b>
30
31<Table Border>
32<Tr>
33<Td align=center ><b>Track Name</b></Td>
34<Td align=center ><b>Marker Type</b></Td>
35<Td align=center ><b>Meiotic panel</b></Td>
36<Td align=center ><b>Observed Recombination</b></Td>
37<Td align=center ><b>Covered Region</b></Td>
38<Td align=center ><b>Rererence</b></Td>
39</Tr>
40<Tr>
41<Td align=center >Hd-rR female</Td>
42<Td align=center >EST, SNPs</Td>
43<Td align=center >Hd-rR/HNI female backcross panel</Td>
44<Td align=center >94</Td>
45<Td align=center >Whole Genomic Region</Td>
46<Td align=center >2, 4</Td>
47</Tr>
48<Tr>
49<Td align=center >Hd-rR male</Td>
50<Td align=center >EST, SNPs</Td>
51<Td align=center >Hd-rR/HNI male backcross panel</Td>
52<Td align=center >93</Td>
53<Td align=center >Sub-telomeric region on the linkage groups 1, 5, 6, 7, 8, 9, 10, 12, 13, 14A15A16A17A18A19A22A23 and 24.</Td>
54<Td align=center >4</Td>
55</Tr>
56<Tr>
57<Td align=center >AA2 (<a href = "http://mbase.bioweb.ne.jp/~dclust/ml_base.html">Mbase</a>)</Td>
58<Td align=center >EST, AFLPs, RAPDs, IRSs, STSs, phenotype</Td>
59<Td align=center >AA2/HNI female backcross panel</Td>
60<Td align=center >39</Td>
61<Td align=center >Whole Genomic Region</Td>
62<Td align=center >1</Td>
63</Tr>
64<Tr>
65<Td align=center >Kunming</Td>
66<Td align=center >EST, SNPs</Td>
67<Td align=center >Hd-rR/kunming backcross panels<br>(female and male are mixed)</Td>
68<Td align=center >44</Td>
69<Td align=center >Linkage group (chromosome) 11</Td>
70<Td align=center >4</Td>
71</Tr>
72<Tr>
73<Td align=center >SSLP</Td>
74<Td align=center >SSLP, microsatelite</Td>
75<Td align=center >Hd-rR/HNI F2 panel<br> Kaga/Hd-rR F2 panel<br>Hd-rR/kunming backcross panels<br>(female and male are mixed)</Td>
76<Td align=center >368<br>96<br><br>44<br></Td>
77<Td align=center >Whole Genomic Region</Td>
78<Td align=center >3</Td>
79</Tr>
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81
82
83</Table Border>
84
85<br><br>References:<br>
86<font size="3">
87<br>(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.
88<br>A Detailed Linkage Map of Medaka, Oryzias latipes. Comparative genomics and genome evolution.
89<br>Genetics 154:1773-1784  (2000)
90<br>(2)Kimura T, Jindo T, Narita T, Naruse K, Kobayashi D, Shin-I T, Kitagawa T, Sakaguchi
91T, Mitani H, Shima A, Kohara Y and Takeda H.
92<br>Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics.
93<br>Mech. Dev. 121:915-32 (2004)
94<br>(3) Kimura T, Yoshida K, Shimada A, Jindo T, Sakaizumi M, Mitani H, Naruse K, Takeda H, Inoko H, Tamiya G, Shinya M.
95<br>Genetic linkage map of medaka with polymerase chain reaction length polymorphisms.
96<br>Gene 363 24-31 (2005)
97<br>(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.
98<br>The medaka draft genome and insights into vertebrate genome evolution
99<br>Nature 447:714-719 (2007)
100
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