TY  - JOUR
AB  - Summary This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r(2) statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r(2) = 0.30 +/- 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r(2) >/= 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance
AU  - Qanbari, S.*
AU  - Pimentel, E.C.G.*
AU  - Tetens, J.*
AU  - Thaller, G.*
AU  - Lichtner, P.
AU  - Sharifi, A.R.*
AU  - Simianer, H.*
C1  - 915
C2  - 26975
SP  - 346-356
TI  - The pattern of linkage disequilibrium in German Holstein cattle.
JO  - Anim. Genet.
VL  - 41
IS  - 4
PB  - Wiley-Blackwell Publishing, Inc.
PY  - 2010
SN  - 0003-3480
ER  - 

TY  - JOUR
AB  - The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.
AU  - Qanbari, S.*
AU  - Pimentel, E.C.*
AU  - Tetens, J.*
AU  - Thaller, G.*
AU  - Lichtner, P.
AU  - Sharifi, A.R.*
AU  - Simianer, H.*
C1  - 5851
C2  - 27911
SP  - 377-389
TI  - A genome-wide scan for signatures of recent selection in Holstein cattle.
JO  - Anim. Genet.
VL  - 41
IS  - 4
PB  - Wiley-Blackwell Publishing
PY  - 2010
SN  - 0003-3480
ER  -