Ben Hayes

..Results indicated an exponentially increasing N in humans and a declining N in dairy cattle. CSH is a valuable statistic for inferring population histories from haplotype data, and has implications for mapping of disease loci...

..This is promising, suggesting that in silico genome re-sequencing is possible in sheep if a suitable pool of key ancestors is sequenced for each breed...

..The objective of this study was to evaluate the use of low-density assays to predict direct genomic value (DGV) on five milk production traits, an overall conformation trait, a survival index, and two profit index traits (APR, ASI)...

..Here we explore to which degree the phenotypic manifestation of local and distant polymorphisms is a dynamic feature of regulatory design...

..The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species...

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..While measures of LD is also crucial for determining the number of markers required for association mapping studies, estimates of recombination rate can be used to assess quality of genomic assemblies...

..Selective breeding for milk production traits is likely to have increased the frequency of this haplotype in the NRC population...

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..Here, we demonstrate the value of selective genotyping strategies which balance the contribution of families across high and low phenotypes to greatly reduce rates of false discovery with a minimal effect on power...

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..The accuracies were obtained both as a function of elements of the inverse coefficient matrix and from the realised accuracies of GEBV...

..The validated marker panels we have reported here will aid selection for high milk production under anticipated climate change scenarios, for example selection of sires whose daughters will be most productive at low levels of feeding...

..Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships...

..3, and N(e)=100, approximately 12474 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0.7 [corrected]...

..Many challenges with genomic selection and its implementation remain, including increasing the accuracy of GEBV, integrating genomic information into national and international genetic evaluations, and managing long-term genetic gain...

..Finally, for the chromosome tested, the location of selection signatures between dairy and beef cattle was correlated with the location of selection signatures within dairy cattle...

..Further, there was evidence for a site of preferential recombination between CSN2 and CSN1S2. The value of the haplotypes for haplotype-assisted selection (HAS) is discussed...

..In this article, we demonstrate with Atlantic salmon and pig EST collections that splitting the EST collection in two, detecting SNPs in both subsets, then accepting only cross-validated SNPs increases validation rates...

..A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes...

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..The approach is demonstrated for an Angus data set with 9,323 SNP markers genotyped...

..We analysed over 7,500 polymorphic single nucleotide polymorphisms (SNP) in beef (Angus) and dairy (Holstein) cattle and outgroup species Bison, Yak and Banteng in an indirect test of inbreeding and positive selection in Domestic cattle...

..Altogether these results argue for an increase in the frequency of the CSN2_67 C allele or haplotypes containing this allele in the Norwegian Red cattle population by selective breeding...

..Our results suggest that the most accurate genomic predictions are achieved when phenotypes from all populations are combined in one training set, while for more diverged populations a higher marker density is required...

..90 between protein yield at the 5th and 95th percentile of THI. The use of response to environment estimated breeding values to improve the accuracy of international sire evaluations is discussed...

..It is likely that breeding companies will move rapidly to alter their breeding schemes to make use of genomic selection because benefits to the breeding companies and to the industry are considerable...

..The multivariate analysis did not appear to increase the precision with which putative QTL were mapped...

..Promising candidate genes have been identified in several of the validated regions...

..Implementation of genomic selection is likely to have major implications for genetic evaluation systems and for genetic improvement programmes generally and these are discussed...

..Potential gene candidates and application of the markers is discussed. About one-third of the significant markers affect intercept and slope in opposite directions, and some of these facilitate marker-assisted selection for robustness...

..Persistency is a good candidate for genomic selection because the trait is expressed late in lactation...

..The differences in expression are in accordance with the evolutionary history of this gene cluster, where TLR10 diverged from the common ancestral gene before the duplication event that created TLR1 and TLR6...

..e. SPP1, IBSP and MEPE) are of particular interest and we suggest that these genes are screened in candidate gene studies for dystocia and stillbirth in cattle as well as other species...

..Selective genotyping also resulted in a significant increase in false positives, even when pedigree structure was accounted for...

..The estimates of N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago...

..This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation...