Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

Nilsen, H., Hayes, B., Berg, P. R., Roseth, A., Sundsaasen, K. K., Nilsen, K. and Lien, S. (2008) Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence. Animal Genetics, 39 2: 97-104. doi:10.1111/j.1365-2052.2007.01686.x


Author Nilsen, H.
Hayes, B.
Berg, P. R.
Roseth, A.
Sundsaasen, K. K.
Nilsen, K.
Lien, S.
Title Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence
Journal name Animal Genetics   Check publisher's open access policy
ISSN 0268-9146
1365-2052
Publication date 2008-04
Sub-type Article (original research)
DOI 10.1111/j.1365-2052.2007.01686.x
Open Access Status Not yet assessed
Volume 39
Issue 2
Start page 97
End page 104
Total pages 8
Place of publication Chichester, West Sussex, United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Formatted abstract
A linkage map was constructed for bovine chromosome 6 (BTA6), using 399 single nucleotide polymorphisms (SNPs) detected primarily from PCR-resequencing. The efficiency of SNP detection was highly dependent on the source of sequence information chosen for primer design (BAC-end sequences, introns or promoters). The SNPs were used to build a linkage map comprising 104 cM on BTA6. The SNP order in the linkage map corresponded very well with radiation hybrid (RH) maps available for BTA6 as well as with expected positions in the human comparative map, but diverged significantly from the current assembly of the bovine genome (Btau_3.1). When performing linkage analysis with the marker order suggested from the Btau_3.1 we observed an expansion of the genetic map from 104 cM to 137 cM, strongly suggesting a reordering of scaffolds in the current version of the bovine genome assembly. The extent of LD on BTA6 was evaluated by calculating the average r2 for SNP pairs separated by given distances. The decline of LD was rapid with distance, such that r2 was 0.1 at 100 kb. Our results indicate that linkage mapping will be a valuable source of information for correcting errors in the current bovine assembly. These errors were sufficiently frequent to be of concern for the accuracy of mapping QTL with panels of SNPs whose positions are based on the current assembly.
Keyword Bovine chromosome 6
Genetic map
Single nucleotide polymorphisms
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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