EST-SSRs from Cornell and KSU

From Ju-Kyung Yu, Ramesh Kantety, Mauricio La Rota, Sukhwinder Singh, Bikram Gill and Mark Sorrells
17 Oct 2003
Updated 18 Feb 2005, and again 1 Mar 2005

References:

Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME. 2004. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805-18.

Yu JK, La Rota M, Kantety RV, Sorrells ME. 2004. EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742-51.

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Downloadable Files (spreadsheets and presentation files)

• SUMMARY_CNL_KSUM_EST_SSR_MARKER.xls Updated, 1 Mar
  Overall functional marker information including primer sequences.
  (Please note: Some cnl probes have one primer in common, to amplify SSRs from the same supercluster in different species. So check to be sure you don't order the same primer more than once.)

• CORNELL_EST_SSR.xls
  The first two sheets are organized not by individual rows but by blocks of rows corresponding to the superclusters (SpCl) of EST contigs from Wheat (W), Barley, Rice, Maize and Sorghum. Data in some columns refers to the SpCl itself, in other columns to the particular row.
  • Sheet "ESTinfo"
  • Sheet "primer"
    For each SpCl multiple primer sequences are given, each with a Primer Name. The primer pairs tested are given by name in the Primer Combination column.
  • Sheet "PCR"
    Results (amplification or not) of the named Primer Combinations in barley, maize, rice and wheat.
  Hovering your mouse over the column headers in these tables will pop up a helpful comment.

• KSU_EST_SSR.xls Updated
  Simpler, row-organized. Data for individual ESTs, not superclusters.
  • Sheet "EST_info"
    Note: Some primer pairs are derived from the same EST contig. See the "Cornell SpCl" column to help identify these.
  • Sheet "PCR"

• WHEAT_RICE_MAP_INFO.xls
  Map locations (chromosome) and map scoring data for wheat Synthetic × Opata and rice IR64 × Azucena.
  • Sheet "POLY"
    Polymorphism and chromosome locations for the wheat and rice genetic maps, plus chromosome locations in Chinese Spring nulli-tetrasomics.
  • Sheet "WHEAT" -- mapping scores.
  • Sheet "RICE" -- mapping scores.

• WHEAT_MAP.ppt
  Wheat Synthetic x Opata map figure with these EST-SSRs added.

• RICE_MAP.ppt
  Rice IR64 x Azucena map figure with these EST-SSRs added.

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Triticeae EST-SSR Coordination page