Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

This corrects the article DOI: 10.1038/hdy.2016.79.

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.

Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: application in cattle breeds.

The genetic identification of the population of origin of individuals, including animals, has several practical applications in forensics, evolution, conservation genetics, breeding and authentication of animal products. Commercial high-density single nucleotide polymorphism (SNP) genotyping tools that have been recently developed in many species provide information from a large number of polymorphic sites that can be used to identify population-/breed-informative markers. In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out-of-bag (OOB) error rate for both ranking methods and SNP densities ranged from 0.0 to 0.1% in the reference population. Application of this approach in a test population (10% of individuals pre-extracted from the whole data set) achieved 100% of correct assignment with both classifiers. Linkage disequilibrium between selected SNPs was relevant (r(2) > 0.6) only in few pairs of markers indicating that most of the selected SNPs captured different fractions of variance. Several informative SNPs were in genes/QTL regions that affect or are associated with phenotypes or production traits that might differentiate the investigated breeds. The combination of PCA and RF to perform SNP selection and breed assignment can be easily implemented and is able to identify subsets of informative SNPs useful for population assignment starting from a large number of markers derived by high-throughput genotyping platforms.

Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds.

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.

A new and unusual reciprocal translocation in cattle: rcp(11;25)(q11;q14-21).

A new and unusual reciprocal translocation was detected in a heifer of the Agerolese cattle breed during a routine cytogenetic screening carried out on 13 animals (2 males and 11 females) kept at the ConSDABI Conservation Center in Benevento (Southern Italy). The 13 animals investigated had a normal karyotype except for a 1-year-old female, which carried one autosome smaller than the smallest normal bovine autosomes. This small autosome showed very little C-banding in comparison to the other autosomes, while another medium-sized autosome showed 2 distinct and prominent C-bands. RBA-banding and karyotype analysis revealed that these 2 chromosomes were the result of a reciprocal translocation between chromosomes 11 and 25. FISH analysis with BAC142G06 mapping to the proximal (subcentromeric) region of both BTA25 and der11, BAC513H08 (ELN) mapping to BTA25q22dist and der25, and BAC533C11 mapping to the proximal region of BTA11 and der11 confirmed the localization of the breakpoints on band q11 (centromere) of chromosome 11 and q14-21 of chromosome 25. Ag-NOR and sequential RBA/Ag-NOR techniques detected the presence of NORs on both BTA11 and BTA25 and both der11 and der25. To our knowledge, this is the first report of a reciprocal translocation event in cattle with the breakpoint located in the centromeric region.

A first comparative map of copy number variations in the sheep genome.

We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant (P<0.0001), suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVRs include genes with important biological functions. Further studies are needed to evaluate their functional relevance.

Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs.

DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F(ST)), and Reynolds genetic distances. A highly significant average F(ST) of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of F(ST) across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity.

Genetic diversity within and between European pig breeds using microsatellite markers.

An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43-0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy-Weinberg expectations (P < 0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright F(ST) index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers.

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.

Chemical composition of pig meat from the genetic type 'Casertana' and its crossbreeds.

The meat quality of the autochthonous genetic type Casertana (Ca) and its crossbreeds was evaluated for the production of pork for fresh consumption and/or processing. The chemical composition of the fresh meat was determined on eight muscles of 143 pigs of six genetic types, of both sexes and slaughtered at three different live weights. The most important results of fixed analysis of variance showed that the first order interactions are statistically important in determining most of the analytical data considered; muscle is an important factor for ash content. On average, the dry matter percentage is higher in the Casertana; the opposite is observed in the Ca × [Landrace (L) × Large White (LW)]. The protein content, in relation to dry matter, is lower in the Casertana and higher in Ca × (L × LW) and L × (L × LW). The opposite results were observed for lipid contents and energy value. The ash content ranges from 4.8% in Ca to 5.3% in Ca × Duroc (Du). However, the above trends vary in relation to sex, live weight at slaughter and muscle. Females, compared with males, supply meat with high lipid contents and energy values. The protein content, by contrast, is higher in males. As the live weight at slaughter increases from 80-90 to 120-130 kg, the protein content rises, while the ash value decreases. In meat obtained from females no significant differences are observed in the analytical data from 80-90 to 120-130 kg, while in that from males the protein content increases, and the lipid content and energy value decrease. The Longissimus dorsi muscle (both at thoracic and lumbar level) has the highest content of dry matter, while the Supraspinatus and the Rectus femoris have the lowest. The Rectus femoris has the highest protein content and Semitendinosus the lowest. The opposite holds for lipid content and energy value; such results confirm the histochemical individuality of the muscle. The dry matter content of the 'bacon' cut is higher in the Casertana pigs and lower in L × (L × LW), which is due, in part, to the higher lipid content and lower protein content found in the former.

Effect of dietary energy content on the intramuscular fat depots and triglyceride composition of river buffalo meat.

The production of river buffalo meat in Italy has long been under discussion due to poor acceptance by consumers. In order to understand whether dietary energy content may affect the organoleptic characteristics of buffalo meat, two groups of river buffalo calves were fed on two diets, with high (H) and low (L) energy contents. The animals were slaughtered at 4-monthly intervals starting from 6 months old (10, 14 and 18 months) and five muscles were dissected on the half-carcass: Caput longum tricipitis brachii (CloTB), Gluteobiceps (Gb), Semitendinosus (St), Semimembranosus (Sm) and Longissimus dorsi (LD). The results showed that from 6 to 10 months of age the meat lipid content decreases and protein content increases for both diets. The lipid content increases slowly with both diets from 10 to 14 months. In the last experimental period (from 14 to 18 months) an increase in the percentage of lipids with diet H and a decrease with diet L was observed. At all slaughtering ages the meat from the animals fed on diet H had a higher energy content. The different energy content of the two diets did not significantly influence the composition of triglycerides only formed by SFA and triglycerides with a higher degree of unsaturation. The triglycerides with an unsaturated fatty acid in position sn 2 did not show the same behaviour in relation to age and diet. The energy content of the feed did influence the unsaturated fatty acid composition: MUFA increased with an increased energy level of the diet, while PUFA increased with a reduction in the energy level of the diet. The muscle LD showed a significantly higher (P<0.05) content of SFA and lower (P<0.05) of MUFA and PUFA than the other muscles. On the basis of our results, the better TAG's composition is found in the meat of animals fed on diet H and slaughtered at 4 months of age.

Sister chromatid exchange in chromosomes of sheep (Ovis aries).

Blood lymphocyte cultures from 32 Comisana and Laticauda sheep breeds (15 males and 17 females) raised in Southern Italy were studied using sister chromatid exchange (SCE) test. Of the 932 cells studied, the SCE-mean value was 7.20 +/- 2.5 per cell for both breeds. Indeed, the SCE mean values were 7.12 +/- 2.45 and 7.28 +/- 2.55 in Comisana and Laticauda breeds, respectively, and the differences were not significant. No statistical differences were noticed between male and female cells (7.25 +/- 2.39 and 7.16 +/- 2.60, respectively). The SCE frequency distribution did not follow a Poisson distribution. The number of SCE were significantly higher than expected in chromosomes 1, 2 and 3 (p < 0.001) and significantly lower than expected in the X and remaining chromosomes (p < 0.001) on the basis of relative chromosome lengths.

Measurement of micronuclei by cytokinesis-block method in bovine lymphocytes.

The present study was carried out in order to set up a standardized quantitative assay for spontaneous micronuclei in bovine lymphocytes. For this purpose the cytokinesis-block micronucleus (MN) method, originally proposed by Fenech and Morley (1985) for human lymphocytes, was applied to peripheral blood lymphocytes of 20 healthy cows of Italian Friesian breed. The results demonstrate that the optimal concentration of cytochalasin B to obtain the highest frequency of binucleated cells (mean = 400.26 +/- 23.76/1000 cells scored) was 6 micrograms/ml. The baseline frequency of spontaneous MN formation in 500 binucleated cells was 12.3 +/- 4.1, i.e., 3 times higher than that reported in human lymphocytes (Fenech and Morley, 1985; Scarfi et al., 1991). The possible reason(s) for this difference (sensitivity to cytochalasin B, chromosome number, environmental genotoxic pollutants) is discussed.

R-banding pattern of the prometaphase chromosomes of the goat.

R-banded prometaphase karyotypes of the goat are presented using both fluorescent and light staining techniques. A model for the standardization of the R-banded prometaphase goat karyotype is suggested.

Chromosome instability in a calf affected by congenital malformation.

High rates of structural chromosome aberrations were associated with increased yields of sister chromatid exchanges (SCE) in metaphase chromosomes of a new born female calf affected by a congenital malformation. The frequency of abnormal cells was 25 per cent in the abnormal calf, 8 per cent in its dam and 3 per cent in a group of four healthy cows. Chromatid and chromosome breaks were the most frequent types of chromosome aberration found in the malformed calf; centric fusions, chromosome fragments and deletions were much less common. The mean rate of SCE/cell in the malformed calf was nearly twice that of the control and the difference was statistically significant. Possible factors involved in the occurrence of such a malformation are discussed.

Ag-NORs variation and banding homologies in two species of Bovidae: Bubalus bubalis and Bos taurus.

G,Q and R-binding pattern comparisons between the Murrah type of Bubalus bubalis L. (2n - 50) and the Holstein Friesian breed of Bos taurus L. (2n = 60) chromosomes revealed that the autosomes are similar in both species; in the former, the five pairs of submetacentrics correspond to centric fusions of chromosomes 1-29, 2-22, 8-19, 5-28 and 16-25 in the latter. Silver staining on somatic cells of buffalo revealed telomeric AG-NORs located on six pairs of autosomes, identified as 3p, 4p, 8, 21, 23 and 24. Only one pair of nucleolus organizer chromosomes is common to both species, namely the 4p of buffalo which corresponds to the 28 of cattle. The remaining NORs are located on different pairs. Out of 18 individuals, the number of Ag-NORs per cell varied between 3 and 10, with a mean value of 6.3 +/- 1.7; the mean number of nucleolar associations per cell was between 0.1 and 1.8. In the total population of 317 cells the two variables followed the binomial and the Poisson distributions, respectively, and their correlation coefficient was not statistically significant (r = +0.36). In addition to the mean number of Ag-NORs, the mean number of nucleolar associations per cell should be used for a better understanding of the differences among individuals.