A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits

Additional File 2:

Excel spreadsheet containing mapping information and homology of sequences mapped on the 12 k WG-RH map of BTA6. Entitled: Mapping information and homology of sequences mapped on the 12 k WG-RH map of BTA6. The order of loci is given according to the 12 k WG-RH map presented in this study. (1) Loci in cells highlighted light green represent framework markers in the 12 k WG-RH map. (2) Accession numbers in bold blue: Homology of BAC contigs from human chromosome 4 (HSA4) was identified by blasting the bovine anonymous sequences directly against the human genome sequence. Accession numbers in underlined blue: Homology on HSA4 was obtained using identified bovine whole-genome sequences (WGS) sequences containing the sequences of targeted anonymous loci as intermediary sequence for blasting against the human genome sequence. Empty cells: no significant homology was found. (3) Loci with identical retention pattern and position on the 12 k WG-RH map of BTA6 are indicated in green. (4) Identified bovine WGS containing the sequences of targeted anonymous loci, which did not find homologous human sequences by direct sequence similarity search. WGS were used as intermediary sequence for blasting against the human genome sequence. (5) Sequence contigs given in black were retrieved from the available sequence map of BTA6 at NCBI (build 2.1, [27]). Sequence contigs marked in bold red represent new assignments of loci to BTA6 specific sequence contigs. Sequence contigs marked in ordinary red letters are assigned on the currently available bovine STS map. Sequence contigs given in blue indicate new loci assignments to unplaced bovine contigs. Cells highlighted in yellow indicate sequence contigs that have been assigned to other chromosomes than BTA6. Empty cells: no significant homology was found.

Format: XLS Size: 70KB Download file

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Additional File 1:

Excel spreadsheet containing loci mapped on the 12 k WG-RH map of BTA6, primer sequences and PCR conditions. Entitled: Loci mapped on BTA6, primer sequences and PCR conditions. Loci given in red represent novel genes and ESTs mapped on BTA6 without previous mapping information on bovine physical maps. Loci given in green represent newly developed targeted anonymous markers (STS) and BAC end sequences (BES). Loci indicated in black were previously mapped on BTA6 [9,21,24,25,52-58]. Accession numbers (AccNo) indicate sequences used for primer design. Black AccNo: bovine sequence, Blue AccNo: human sequence. Size: amplicon length in bp, TA: annealing temperature in °C.

Format: XLS Size: 54KB Download file

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Additional File 3:

Excel spreadsheet containing BTA6-specific BAC clones and BAC end sequences. Entitled: BTA6-specific BAC clones and BAC end sequences.

Format: XLS Size: 19KB Download file

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