W435 Mining and mapping of SSR motifs from BAC-end sequences of watermelon

Date: Saturday, January 14, 2012
Time: 5:10 PM
Room: Town and Country
Padma Nimmakayala , Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV
Chantel Scheuring , Texas A&M University
Abhishek Bhandari , Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV
Nischit Aryal , Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV
Gopinath Vajja , Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV
Yang Zhang , Texas A&M University, College Station, TX
Hongbin Zhang , Texas A&M University, College Station, TX
Umesh Reddy , Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV
BAC end sequences (BES) provide robust markers, when mapped and will provide a framework for map based cloning strategies as well as for the whole genome sequencing. BES is very useful for marker development and also to identify protein coding regions, transposable elements, and Simple Sequence Repeats(SSRs). A 10X genome coverage BAC library was constructed for watermelon (Variety: Charleston Grey) to generate 4,999 BES. Watermelon BES contained approximately 10% protein coding regions, 20.1% transposable elements and 15% of them contained tandem repeats. We located 111, 115, 180 and 31 repeats of di, tri, tetra and penta units respectively.  One hundred and eighty four SSRs were located in the open reading frames and 254 were found in the non coding areas. Mapping data and location of the BEC-SSRs on various chromosomes resolved using the FISH will be presented.
Back to: Large Insert DNA Library (LIL)
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