Properties of different selection signature statistics and a new strategy for combining them.

Identifying signatures of recent or ongoing selection is of high relevance in livestock population genomics. From a statistical perspective, determining a proper testing procedure and combining various test statistics is challenging. On the basis of extensive simulations in this study, we discuss the statistical properties of eight different established selection signature statistics. In the considered scenario, we show that a reasonable power to detect selection signatures is achieved with high marker density (>1 SNP/kb) as obtained from sequencing, while rather small sample sizes (~15 diploid individuals) appear to be sufficient. Most selection signature statistics such as composite likelihood ratio and cross population extended haplotype homozogysity have the highest power when fixation of the selected allele is reached, while integrated haplotype score has the highest power when selection is ongoing. We suggest a novel strategy, called de-correlated composite of multiple signals (DCMS) to combine different statistics for detecting selection signatures while accounting for the correlation between the different selection signature statistics. When examined with simulated data, DCMS consistently has a higher power than most of the single statistics and shows a reliable positional resolution. We illustrate the new statistic to the established selective sweep around the lactase gene in human HapMap data providing further evidence of the reliability of this new statistic. Then, we apply it to scan selection signatures in two chicken samples with diverse skin color. Our analysis suggests that a set of well-known genes such as BCO2, MC1R, ASIP and TYR were involved in the divergent selection for this trait.

Bos indicus introgression into (peri-)alpine cattle breeds - evidence from the analysis of bovine whey protein variants.

The major bovine whey proteins, α-lactalbumin (α-LA) and ß-lactoglobulin (ß-LG), exhibit breed-specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA-based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non-synonymous nucleotide exchange were identified. Furthermore, two known α-LA variants (A and B) and four known ß-LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri-)alpine cattle breeds.

An evaluation of a novel estimator of linkage disequilibrium.

The analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker-phenotype associations. This article introduces a new estimator of a LD parameter (ρ(2)) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution of the estimator of ρ(2) could be less frequency dependent than that of the estimator of r(2), a widely used metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein-Friesian cattle using 771 single-nucleotide polymorphism (SNP) markers and of HapMap III data on 21,991 SNPs (chromosome 3) observed in 88 unrelated individuals from Tuscany. Also, 1600 haplotypes over a region of 1 Mb simulated under the coalescent were used to estimate LD using the two measures. Subsequently, a simulation study compared the new estimator with that of r(2) using several scenarios of LD and allelic frequencies. From these studies, it is concluded that ρ(2) provides a useful metric for the study of LD as the distribution of its estimator is less frequency dependent than that of the standard estimator of r(2).

DNA-based identification of novel bovine casein gene variants.

In cattle, at least 39 variants of the 4 casein proteins (α(S1)-, ß-, α(S2)- and κ-casein) have been described to date. Many of these variants are known to affect milk-production traits, cheese-processing properties, and the nutritive value of milk. They also provide valuable information for phylogenetic studies. So far, the majority of studies exploring the genetic variability of bovine caseins considered European taurine cattle breeds and were carried out at the protein level by electrophoretic techniques. This only allows the identification of variants that, due to amino acid exchanges, differ in their electric charge, molecular weight, or isoelectric point. In this study, the open reading frames of the casein genes CSN1S1, CSN2, CSN1S2, and CSN3 of 356 animals belonging to 14 taurine and 3 indicine cattle breeds were sequenced. With this approach, we identified 23 alleles, including 5 new DNA sequence variants, with a predicted effect on the protein sequence. The new variants were only found in indicine breeds and in one local Iranian breed, which has been phenotypically classified as a taurine breed. A multidimensional scaling approach based on available SNP chip data, however, revealed an admixture of taurine and indicine populations in this breed as well as in the local Iranian breed Golpayegani. Specific indicine casein alleles were also identified in a few European taurine breeds, indicating the introgression of indicine breeds into these populations. This study shows the existence of substantial undiscovered genetic variability of bovine casein loci, especially in indicine cattle breeds. The identification of new variants is a valuable tool for phylogenetic studies and investigations into the evolution of the milk protein genes.

A genome-wide scan for signatures of recent selection in Holstein cattle.

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.

The pattern of linkage disequilibrium in German Holstein cattle.

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) > or = 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 < or =100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r(2). It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r(2) estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to approximately 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed.

Analysis of relationship between bovine lymphocyte antigen DRB3.2 alleles, somatic cell count and milk traits in Iranian Holstein population.

The major histocompatibility complex (MHC) is a gene complex closely linked to the vertebrate immune system due to its importance in antigen recognition and immune response to pathogens. To improve our understanding of the MHC and disease resistance in dairy cattle, we gathered 5119 test day records of somatic cell count (SCC) and performance traits of 262 Holstein dairy cows to determine whether the DRB region of the MHC contains alleles that are associated with elevated SCC, milk yield, protein and fat percent of milk. To this purpose, genotyping of animals for DRB3 gene was investigated by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) assay. A two-step PCR was carried out so as to amplify a 284 base-pair fragment of exon 2 of the target gene. Second PCR products were treated with three restriction endonuclease enzymes RsaI, BstYI and HaeIII. Twenty-eight BoLA-DRB3 alleles were identified including one novel allele (*40). The results in general are in good accordance with allele frequencies of Holstein cattle populations reported by previous studies. Analyses of associations were modeled based on repeated measurement anova and generalized logistic linear methods for production traits and SCC data, respectively. The results of this study showed a significant relationship between the elevated SCC reflecting an increased probability of occurrence to subclinical mastitis and DRB3.2 allele *8 (p < 0.03). The results also revealed significant positive relationships of alleles*22 (p < 0.01) and allele*11 (p < 0.05) with milk fat percent as well as of alleles*24 (p < 0.03) and *22 (p < 0.05) with protein percent. The present study failed to find any association between milk yield and tested alleles. Because of the lack of consistency among results of similar studies, we suggest further investigations to determine the precise nature of these associations with the high polymorphic bovine MHC region to be performed based on haplotypes.

Power of microsatellite markers for analysis of genetic variation and parentage verification in sheep.

We report the genetic analysis of 100 individuals of an elite breeding flock of Afshari sheep with a selected set of eighteen microsatellite markers. A full characterization of this set of eighteen loci was carried out generating allele frequency distributions that were used to estimate the genetic information content of these loci, including genetic variability, inbreeding, individual and parent verification parameters. Disregarding MCMA26 monomorphic pattern, microsatellite loci showed moderate level of polymorphism, as such totally 102 alleles were detected with a mean number of 6 alleles per locus. The average expected heterozygosity was 0.72 (SD = 0.07) and the average Polymorphism Information Content (PIC) was 0.67 (SD = 0.08). Total value of inbreeding based on marker data was estimated as -0.02 so it indicates that inbreeding occurred less than would be expected at random. The overall probability of identity considering all twelve independent loci combined was 3.148E-13 meaning lower than 1 in 31 trillions. The results of this study indicate, despite the selective breeding and closed flock system over a number of generations, a relatively high level of heterozygosity still exists in the representative sheep flock. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide a powerful system for the unique identification of Afshari sheep individuals for fingerprinting purposes and parentage testing.