Metabolomic Profiling of Bos taurus Beef, Dairy, and Crossbred Cattle: A Between-Breeds Meta-Analysis.

Cattle breeds may differ substantially in their metabolism. However, the metabolomes of dairy and beef cattle are not well-known. Knowledge of breed-specific metabolic features is essential for biomarker identification and to adopt specific nutritional strategies. The muscle hypertrophy (mh), a beef cattle phenotype present in Asturiana de los Valles (AV) but absent in Asturiana de la Montaña (AM) and Holsteins, may underlie such differences. We compared the plasma metabolomes of Holstein, AV, AM, and crossbred cattle recipients selected for meta-analysis within an embryo transfer (ET) program. Blood samples were collected on day 0 (oestrus) and day 7 (prior to ET) (N = 234 samples × 2 days). Nuclear magnetic resonance quantified N = 36 metabolites in plasma, and more metabolic differences between breeds were found on day 0 (N = 19 regulated metabolites) than on day 7 (N = 5). AV and AM largely differed from Holstein cattle (N = 55 and 35 enriched metabolic pathways, respectively); however, AV and AM differed in N = 6 enriched pathways. Metabolic activity was higher in AV than in Holstein cattle, as explained in part by the mh phenotype. The metabolomic characterization of breeds facilitates biomarker research and helps to define the healthy ranges of metabolite concentrations.

Differences in genetic structure assessed using Y-chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires.

Up to 173 African sires belonging to 11 different subpopulations representative of four cattle groups were analysed for six Y-specific microsatellite loci and a mitochondrial DNA fragment. Differences in Y-chromosome and mtDNA haplotype structuring were assessed. In addition, the effect of such structuring on contributions to total genetic diversity was assessed. Thirty-five Y-chromosome and 71 mtDNA haplotypes were identified. Most Y-chromosomes analysed (73.4%) were of zebu origin (11 haplotypes). Twenty-two Y-haplotypes (44 samples) belonged to the African taurine subfamily Y2a. All mtDNA haplotypes belonged to the "African" taurine T1 haplogroup with 16 samples and nine haplotypes belonging to a recently identified subhaplogroup (T1e). Median-joining networks showed that Y-chromosome phylogenies were highly reticulated with clear separation between zebu and taurine clusters. Mitochondrial haplotypes showed a clear star-like shape with small number of mutations separating haplotypes. Mitochondrial-based FST -statistics computed between cattle groups tended to be statistically non-significant (p > .05). Most FST values computed among groups and subpopulations using Y-chromosome markers were statistically significant. AMOVA confirmed that divergence between cattle groups was only significant for Y-chromosome markers (ΦCT  = 0.209). At the mitochondrial level, African sires resembled an undifferentiated population with individuals explaining 94.3% of the total variance. Whatever the markers considered, the highest contributions to total Nei's gene diversity and allelic richness were found in West African cattle. Genetic structuring had no effect on patterns of contributions to diversity.

Resistance to gastrointestinal parasite infection in Djallonké sheep.

Gastrointestinal parasitism places serious constraints on small ruminant production. The situation has been exacerbated by development of drug resistance in many parasite populations, leading to interest in identification of animals with genetically mediated resistance or tolerance to nematode infections. This study assessed the response to natural infection with gastrointestinal nematodes (GIN) in Djallonké sheep during the rainy season in the Sudan-Guinea Savannah region of Burkina Faso. Haemonchus contortus is the most prevalent GIN at this site and time. Djallonké lambs (n=434) were sampled from 40 households and evaluated at a common location in southern Burkina Faso. Lambs were dewormed with levamisole at 2 to 6 months of age and returned to infected pastures. Fecal egg counts (FEC), packed cell volumes (PCV), and FAffa Malan CHArt (FAMACHA©) scores were determined 28 and 35 days after deworming. Lamb mortality was monitored throughout the experiment. Least-squares means for BW increased from 13.8±0.2 kg at 28 days to 14.0±0.2 kg at 35 days (P<0.01). Simple means and medians for FEC were 615 and 100, respectively, at 28 days and 850 and 175, respectively, at 35 days. The FEC exhibited strong right skewness. Following logarithmic transformation and back-transformation of resulting least-squares means to the original scale, FEC were higher (P<0.01) for males (208±27) than females (122±10). Least-squares means for PCV decreased (P<0.001) from 28 (36.3±0.5%) to 35 days (33.7±0.5%), and were higher (P<0.01) for females (36.0±0.4%) than males (33.9±0.7%). Correlations (r) between repeated measurements of BW, FEC, PCV and FAMACHA scores at 28 and 35 days were all positive (P<0.001). The correlation between FAMACHA scores and PCV was negative at 28 (r=-0.14) and 35 days (r=-0.18) (P<0.001). This study revealed that BW was an easily measured predictor of the ability of the lamb to resist infection with GIN and maintain PCV, and confirmed that FAMACHA scores are useful indicators of differences in FEC. Approximately 40% of female and 30% of male lambs did not show detectable levels of infection (i.e. FEC=0) under field conditions. The great variability that was observed in FEC and PCV suggests potential to use Djallonké sheep in breeding programs to enhance resistance to GIN.

Protein in culture and endogenous lipid interact with embryonic stages in vitro to alter calf birthweight after embryo vitrification and warming.

Short-term protein removal in vitro improves long-term blastocyst competence to survive vitrification. We investigated the mechanisms and effects underlying protein removal. Day-6 morulae and early blastocysts were cultured individually with and without protein for 24h. Development and lipid content were analysed in expanded blastocysts derived from morulae (M-XB) and from early blastocysts (EB-XB). Expression of genes involved in lipid metabolism, stress responses and apoptosis was analysed in fresh and vitrified-warmed M-XB produced with and without protein. Pregnancy rates, birth rates and birthweight (BW) were recorded after transfer of embryos. Day-7 EB-XB production rates (with, 66.9±6.2 and without, 68.8±6.0 protein) were higher than M-XB rates (with, 21.4±4.6 and without, 9.4±4.6 protein; P<0.005). EB-XB showed fewer lipids than M-XB (P=0.03). In fresh M-XB, expression of sterol regulatory element binding protein (SREBP1) was lower with (4.1±2.2) than without (13.6±2.2) protein, contrary to results obtained for Patatin-like phospholipase domain containing 2, Hormone-sensitive lipase and Bcl-2-associated X protein (P<0.05). Protein did not affect pregnancy rates and birth phenotypes (P>0.05). However, BW was higher (P<0.01) in calves born from vitrified M-XB (48.6±3.4kg) than from EB-XB (39.8±2.9kg). Such effects were more pronounced in females (P<0.001). Calves from fresh embryos did not show BW differences. These results indicate that embryonic kinetics and vitrification impact birth phenotypes, at least in females. Alterations might involve exogenous protein and mobilisation of lipid stocks.

Genetic relationships among American donkey populations: insights into the process of colonization.

This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed.

Lack of haplotype structuring for two candidate genes for trypanotolerance in cattle.

Bovine trypanotolerance is a heritable trait associated to the ability of the individuals to control parasitaemia and anaemia. The INHBA (BTA4) and TICAM1 (BTA7) genes are strong candidates for trypanotolerance-related traits. The coding sequence of both genes (3951 bp in total) were analysed in a panel including 79 Asian, African and European cattle (Bos taurus and B. indicus) to identify naturally occurring polymorphisms on both genes. In general, the genetic diversity was low. Nineteen of the 33 mutations identified were found just one time. Seventeen different haplotypes were defined for the TICAM1 gene, and 9 and 12 were defined for the exon 1 and the exon 2 of the INHBA gene, respectively. There was no clear separation between cattle groups. The most frequent haplotypes identified in West African taurine samples were also identified in other cattle groups including Asian zebu and European cattle. Phylogenetic trees and principal component analysis confirmed that divergence among the cattle groups analysed was poor, particularly for the INHBA sequences. The European cattle subset had the lowest values of haplotype diversity for both the exon1 (monomorphic) and the exon2 (0.077 ± 0.066) of the INHBA gene. Neutrality tests, in general, did not suggest that the analysed genes were under positive selection. The assessed scenario would be consistent with the identification of recent mutations in evolutionary terms.

Elements of functional genital asymmetry in the cow.

Asymmetry in the cow affects ovarian function and pregnancy. In this work we studied ovarian and uterine asymmetry. Synchronised animals, in which in vitro-produced embryos (n=30-60) had been transferred on Day 5 to the uterine horn ipsilateral to the corpus luteum (CL), were flushed on Day 8. Ovulatory follicle diameter, oestrus response and total protein flushed did not differ between sides. However, a corpus luteum in the right ovary led to plasma progesterone concentrations that were higher than when it was present in the left ovary. Fewer embryos were recovered from the left than the right horn. Among 60 uterine proteins identified by difference gel electrophoresis, relative abundance of nine (acyl-CoA dehydrogenase, very long chain; twinfilin, actin-binding protein, homologue 1; enolase 1; pyruvate kinase isozymes M1/M2 (rabbit); complement factor B Bb fragment ; albumin; fibrinogen gamma-B chain; and ezrin differed (P<0.05) between horns. Glucose concentration was higher, and fructose concentration lower, in the left horn. In a subsequent field trial, pregnancy rates after embryo transfer did not differ between horns (51.0±3.6, right vs 53.2±4.7, left). However, Day 7 blood progesterone concentrations differed (P=0.018) between pregnant and open animals in the left (15.9±1.7 vs 8.3±1.2) but not in the right horn (12.4±1.3 vs 12.4±1.2). Progesterone effects were independent of CL quality (P=0.55). Bilateral genital tract asymmetry in the cow affects progesterone, proteins and hexoses without altering pregnancy rates.

Assessing introgression of Sahelian zebu genes into native Bos taurus breeds in Burkina Faso.

A total of 350 samples were analyzed to estimate zebu gene proportions into two different taurine cattle breeds of Burkina Faso (Lobi and N'Dama) using 38 microsatellites and various statistical methodologies. West African and East African zebu samples were sequentially used as reference parental populations. Furthermore, N'Dama cattle from Congo, the composite South African Bonsmara cattle breed and a pool of European cattle were used successively as second parental populations. Independently of the methodology applied: (a) the use of West African zebu samples gave higher admixture coefficients than the East African zebu; (b) the higher zebu proportions were estimated when the European cattle was used as parental population 2; and (c) the use of the N'Dama population from Congo as parental population 2 gave the more consistent zebu proportion estimates for both the Lobi and the N'Dama breeds. In any case, the zebu admixture proportions estimated were not negligible and were always higher in the N'Dama cattle than in the Lobi cattle of Burkina Faso. This suggested that the introgression of Sahelian zebu genes into the taurine cattle of Southern West Africa can follow a complex pattern that can depend on local agro-ecological features. The current research pointed out that the estimation of admixture coefficients is highly dependent on both the assumptions underlying the methodologies applied and the selection of parental populations. Our analyses suggest that either too high or nil genetic identity between the parental and the expectedly derived populations must be avoided.

Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication.

A total of 132 mtDNA sequences from 10 Balkan donkey populations were analysed to ascertain their regional genetic structure and to contribute to the knowledge of the spreading of the species after domestication. The Balkan donkey sequences were compared with those from 40 Burkina Faso donkeys as an African outgroup to account for possible local Balkan scenarios. The 172 sequences gave 62 different haplotypes (55 in Balkan donkey). Virtually all the analysed populations had haplotypes assigned to either Clade 1 or Clade 2 even though the relative proportion of Clade 1 or 2 haplotypes differed across populations. Geographical maps constructed using factors computed via principal component analysis showed that the Balkan donkey populations are not spatially structured. AMOVA confirmed a lack of genetic structure in Balkan donkey mtDNA. Balkan populations were poorly differentiated (ΦST  = 0.071). Differentiation between the Balkan donkey and the African outgroup also was low. The lack of correspondence between geographical areas and maternal genetic structure is consistent with the hypothesis suggesting a very quick spread of the species after domestication. The current research illustrates the difficulties to trace routes of expansion in donkey, as the species has no geographical structure.

Mitochondrial DNA and Y-chromosome diversity in East Adriatic sheep.

Variation in mitochondrial DNA (mtDNA) and Y-chromosome haplotypes was analysed in nine domestic sheep breeds (159 rams) and 21 mouflon (Ovis musimon) sampled in the East Adriatic. Mitochondrial DNA analyses revealed a high frequency of type B haplotypes, predominantly in European breeds, and a very low frequency of type A haplotypes, which are more frequent in some Asian breeds. Mitochondrial haplotype Hmt-3 was the most frequent (26.4%), and 37.1%, 20.8% and 7.6% of rams had haplotypes one, two and three mutations remote from Hmt-3 respectively. In contrast, Y-chromosome analyses revealed extraordinary paternal allelic richness: HY-6, 89.3%; HY-8, 5.0%; HY-18, 3.1%; HY-7, 1.3%; and HY-5, 1.3%. In fact, the number of haplotypes observed is comparable to the number found in Turkish breeds and greater than the number found in European breeds so far. Haplotype HY-18 (A-oY1/135-SRYM18), identified here for the first time, provides a link between the haplotype HY-12 (A-oY1/139-SRYM18) found in a few rams in Turkey and haplotype HY-9 (A-oY1/131-SRYM18) found in one ram in Ethiopia. All mouflons had type B mtDNA haplotypes, including the private haplotype (Hmt-55), and all were paternally monomorphic for haplotype HY-6. Our data support a quite homogeneous maternal origin of East Adriatic sheep, which is a characteristic of European breeds. At the same time, the high number of haplotypes found was surprising and intriguing, and it begs for further analysis. Simultaneous analysis of mtDNA and Y-chromosome information allowed us to detect a large discrepancy between maternal and paternal lineages in some populations. This is most likely the result of breeder efforts to 'upgrade' local populations using rams with different paternal origins.

Mitochondrial analysis sheds light on the origin of hair sheep.

A total of 180 mtDNA sequences from hair Caribbean (93), West African (73) and Canarian-wooled (14) sheep were analysed to shed light on the origin of hair sheep. A comparison of 360 Iberian sheep sequences retrieved from GenBank was performed to assess a possible European origin of the Caribbean hair sheep. These 180 sequences gave 48 different haplotypes (16 in Caribbean sheep). All Caribbean and Canarian-wooled sequences and 91.8% of the West African samples belonged to haplogroup B. The sheep analysed showed wide haplotypic identity. Caribbean sheep shared roughly two-thirds of their samples with Canarian-wooled and West African samples, respectively. Principal component analysis showed that the Caribbean and the Canarian-wooled sheep clustered together. Additional analyses showed that hair and Iberian sheep had wide genetic identity. It was not possible to ascertain a single Canarian, African or European origin of the Caribbean hair sheep using mtDNA markers only. European, African and Caribbean hair sheep maternal genetic backgrounds likely result from related domestication events.

Founder and present maternal diversity in two endangered Spanish horse breeds assessed via pedigree and mitochondrial DNA information.

Pedigree information and 179 mtDNA sequences from two endangered Spanish horse breeds, the Asturcón pony (143) and the Mallorquí horse (36), were analysed to asses: (i) the pedigree and molecular maternal genetic diversity of the two breeds; (ii) the concordance between the dam lines recorded in the corresponding studbooks and the mtDNA haplotypes identified; and (iii) to assess the losses of maternal genetic variability occurred from the foundation of the studbooks to present. Up to 50 Asturcón and 18 Mallorquí founder dam lines were identified in the studbooks analysed. Up to 315 Asturcón mares and 51 Mallorquí mares that foaled in the last 5 years of recording formed a reference population. Only 35 Asturcón and 13 Mallorquí founder dam lines were represented in their reference populations. Sequences from a total of 38 Asturcón and 12 Mallorquí dam lines could be obtained. The 179 sequences obtained gave 15 different haplotypes, 11 and 9 of them being identified, respectively, in the Asturcón pony and in the Mallorquí horse. Five different haplotypes (roughly two-thirds of the sequences) were shared by the two horse breeds. Most dam lines analysed had a single mtDNA haplotype. However, more than one haplotype was detected within eight of the dam lines in Asturcón pony. The found inconsistencies are likely to result from deficiencies in genebank management. The maternal N(e) (mN(e)) computed using the dam line information was higher in the Asturcón pony (20.5) than in the Mallorquí horse (15.9), while these figures were on the opposite direction for the haplotypic line information (6.4 and 9.4, respectively). The ratio of the computed mN(e) values to the actual number of founder dam lines were always higher in the Mallorquí horse probably due to a more balanced distribution of individuals kept for reproduction among studs. Consequences for the conservation programmes of the analysed breeds are discussed.

Assessing priorities for conservation in Tuscan cattle breeds using microsatellites.

Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (Dm) matrices showed that the pair Calvana-Chianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (CT = 1.8%). The Calvana breed made null or negative within-breed contributions (W = 0.0%; CW = -0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (T = -0.7%; CT = -1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (T = 2.1%; CT = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (T = 0.47%; CT = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock.

Usefulness of molecular-based methods for estimating effective population size in livestock assessed using data from the endangered black-coated Asturcón pony.

Empirical evidence of the usefulness of different molecular-based methods to estimate the effective population size (N(e)) for conservation purposes in endangered livestock populations is reported. The black-coated Asturcón pony pedigree (1,981 individuals) was available. Additionally, a total of 267 Asturcón individuals born in 1998, 2002, and 2008 were typed for 15 microsatellites. These yearly cohorts (cohort(1998, 2002, 2008)) included almost all individuals kept for reproduction at the end of the corresponding foaling season. The genealogical realized N(e) was estimated for each cohort by using the individual increase in inbreeding. Molecular N(e) was computed by using 1) linkage disequilibrium [N(e)(()(D)())], 2) a temporal method based on F-statistics [N(e)(()(T)())], 3) an unbiased temporal method [N(e)(()(JR)())], and 4) a Bayesian temporal method [N(e)(()(B)())]. Estimates of increased from cohort(1998) (18.8 ± 5.1) to cohort(2008) (24.9 ± 5.2), illustrating the history of the population and its breeding policy of avoiding matings between close relatives. The estimates of N(e)(()(D)()) were highly biased upward, with the maximum N(e)(()(D)()) value obtained for cohort(2002) (137.0). The estimates of N(e)(()(T)()), N(e)(()(JR)()), and N(e)(()(B)()) showed similar performance. However, N(e)(()(JR)()) estimates were very consistent across cohorts, varying from 14.9 to 15.5 after correcting for the effect of overlapping generations. When the drift signal was not strong (pair cohort(1998)-cohort(2002)), estimates of N(e)(()(T)()) and N(e)(()(B)()) were not realistic. Estimates of N(e)(()(B)()) tended to be biased downward (being 9.0 or below for the sampling pairs including cohort(2008)). Results of N(e)(()(D)()) are more likely to be estimates of the effective number of breeders producing the sample, rather than the effective size for a generation. The temporal methods were strongly affected by a weak drift signal, particularly when samplings were not spaced a sufficient number of generations or a sufficient time apart. The use of molecular-based estimates of N(e) is not straightforward, and their use in livestock conservation programs should be carried out with caution. Sampling strategies (including sampling sizes, sampling periods, and the age structure of the sampled individuals) must be carefully planned to ensure that robust estimates of N(e) are obtained.

Estimation of effective population size from the rate of coancestry in pedigreed populations.

We introduce a simple method to estimate effective population size from increase in coancestry (Δc(jk)) for all pairs of individuals j and k in a reference subpopulation. An increase in pairwise coancestry for any pair of individuals j and k can be defined assuming that a hypothetical mating between them would give an individual with an inbreeding coefficient equal to c(jk), where c(jk) is the coancestry coefficient between the individuals j and k. The equivalent measure to discrete generations value (g(jk)) corresponding to the individual jk can be computed by averaging discrete equivalents generations of its parents (g(j) and g(k)). The mean increase in coancestry for all pairs of individuals in a reference subpopulation can be used to estimate a realized effective population size based on coancestries that would provide information on the effective size of a population under random mating. Performance of the new parameter was tested on simulated and empirical (horse) populations with different mating strategies and population structures. The routines needed to compute the introduced parameters have been included in a new version of the program ENDOG.

Analysis of the existence of major genes affecting alpaca fiber traits.

The aim of this study was to determine the presence of major genes for fiber diameter (FD), SD of FD (SDFD), CV of FD, and comfort factor (CF) in Huacaya (HU) and Suri (SU) Peruvian alpaca breeds. Bayesian segregation analyses with relaxed transmission probabilities were performed using 1,906 and 6,592 available records for SU and HU breeds. Evidence for the presence of major genes was statistically supported when the 95% posterior density did not include zero. Significant major genes were found associated with decreased FD, SDFD, CV values, and increased CF values. Additive effects of the major genes were 4.18 and 4.23 µm for FD, 1.67 and 1.61 µm for SDFD, 3.32 and 3.76% for CV, and 15.03 and 14.90% for CF in HU and SU breeds, respectively. Dominance effects were -1.98 and -2.03 µm for FD, -0.88 and -1.11 µm for SDFD, -1.37 and -2.17% for CV, and 13.0 and 11.8% for CF in HU and SU breeds, respectively. Major gene variance was larger than the polygenic variance for all traits. Major gene allelic frequencies for FD, SDFD, and CV ranged from 0.81 to 0.86 for HU breed and from 0.70 to 0.77 for the SU breed and were 0.24 and 0.36, respectively, for CF. It can be concluded that a major gene affecting these traits could be segregating. Then, molecular identification and monitoring of animals carrying favorable genes throughout the worldwide alpaca population would allow for a quick genetic improvement.

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites.

In this study, we show how Y-specific interspersed multilocus microsatellites, which are loci that yield several amplified bands differing in size from the same male individual and PCR reaction, are a powerful source of information for tracing the history of cattle. Our results confirm the existence of three main groups of sires, which are separated by evolutionary time and clearly predate domestication. These three groups are consistent with the haplogroups previously identified by Götherström et al. (2005) using five Y-specific segregating sites: Y1 and Y2 in taurine (Bos taurus) cattle and Y3 in zebu (Bos indicus) cattle. The zebu cattle cluster clearly originates from a domestication process that was geographically and temporally separated from that of taurine clusters. Our analyses further suggest that: (i) introgression of wild sire genetic material into domesticated herds may have a significant role in the formation of modern cattle, including the formation of the Y1 haplogroup; (ii) a putative domestication event in Africa probably included local Y2-like wild sires; (iii) the West African zebu cattle Y-chromosome may have partially originated from an ancient introgression of humped cattle into Africa; and (iv) the high genetic similarity among Asian zebu sires is consistent with a single domestication process.

Pedigree estimation of the (sub) population contribution to the total gene diversity: the horse coat colour case.

A method to quantify the contribution of subpopulations to genetic diversity in the whole population was assessed using pedigree information. The standardization of between- and within-subpopulation mean coancestries was developed to account for the different coat colour subpopulation sizes in the Spanish Purebred (SPB) horse population. The data included 166264 horses registered in the SPB Studbook. Animals born in the past 11 years (1996 to 2006) were selected as the 'reference population' and were grouped according to coat colour into eight subpopulations: grey (64 836 animals), bay (33 633), black (9414), chestnut (1243), buckskin (433), roan (107), isabella (57) and white (37). Contributions to the total genetic diversity were first assessed in the existing subpopulations and later compared with two scenarios with equal subpopulation size, one with the mean population size (13 710) and another with a low population size (100). Ancestor analysis revealed a very similar origin for the different groups, except for six ancestors that were only present in one of the groups likely to be responsible for the corresponding colour. The coancestry matrix showed a close genetic relationship between the bay and chestnut subpopulations. Before adjustment, Nei's minimum distance showed a lack of differentiation among subpopulations (particularly among the black, chestnut and bay subpopulations) except for isabella and white individuals, whereas after adjustment, white, roan and grey individuals appeared less differentiated. Standardization showed that balancing coat colours would contribute preserving the genetic diversity of the breed. The global genetic diversity increased by 12.5% when the subpopulations were size standardized, showing that a progressive increase in minority coats would be profitable for the genetic diversity of this breed. The methodology developed could be useful for the study of the genetic structure of subpopulations with unbalanced sizes and to predict their genetic importance in terms of their contribution to genetic variability.