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The aim of this work was to perform a thorough analysis of the diversity of Y-haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y-specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y-haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle., (© 2017 Stichting International Foundation for Animal Genetics.)

The main objective of this work was to determine whether the five founding castes defined in the Lidia cattle breed actually have an important contribution to the Spanish paternal genetic stock as well as to the paternal genetic origin support. A total of 1300 Bos taurus male individuals were genotyped for five microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1) and one indel (ZFY10). Microsatellite and indel alleles were combined into haplotypes, identifying a total of 38 haplotypes, 11 of them belonging to haplogroup Y1 and 27 to haplogroup Y2. Ten different haplotypes were found in the Lidia cattle breed, with five being exclusive to this breed. Our results agree with different male genetic stocks in the Lidia breed: one hypothetically representing the ancient Iberian bovine genetic stock (Gallardo, Navarra and Cabrera castes and some encastes from Vistahermosa) and a second one that is the result of the more recent breeding strategy of choosing the most aggressive individuals from traditional herds (including some Vistahermosa encastes and the Vazqueña caste). In terms of conservation, it would be better to not consider this breed as a unit but to consider the caste, or even better the encaste, as the target of putative conservation efforts., (© 2015 Stichting International Foundation for Animal Genetics.)

Meat is a significant source of high-quality nutrients, which are very important in the diet. Among meat products, one of the most prized is bovine meat, of which male beef has been designated to be of a higher quality. However, because of its similarity with female beef, deliberate or unintentional substitutions can occur. To avoid this, methodology based on the fast real-time polymerase chain reaction has been developed to authenticate the species and gender origin of beef. This technique consists of two polymerase chain reactions: one bovine-specific reaction and another Y-chromosome-specific multiplex reaction. This methodology has been validated for all kinds of beef products, including those subjected to intensive processing treatments, and it has subsequently been applied to 10 commercial samples labelled as ox to determine whether they are properly labelled. This assay has been shown to have high specificity, sensitivity and rapidity, with the potential to be a powerful tool in enforcing food labelling regulations.

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.

Five cattle Y-specific microsatellites, totalling six loci, were selected from a set of 44 markers and genotyped on 608 Bos taurus males belonging to 45 cattle populations from Europe and Africa. A total of 38 haplotypes were identified. Haplogroups (Y1 and Y2) previously defined using single nucleotide polymorphisms did not share haplotypes. Nine of the 27 Y2-haplotypes were only present in African cattle. Network and correspondence analyses showed that this African-specific subfamily clustered separately from the main Y2-subfamily and the Y1 haplotypes. Within-breed genetic variability was generally low, with most breeds (78%) showing haplotypes belonging to a single haplogroup. AMOVA analysis showed that partitioning of genetic variation among breeds can be mainly explained by their geographical and haplogroup assignment. Between-breed genetic variability summarized via Principal Component Analysis allowed the identification of three principal components explaining 94.2% of the available information. Projection of principal components on geographical maps illustrated that cattle populations located in mainland Europe, the three European Peninsulas and Mediterranean Africa presented similar genetic variation, whereas those breeds from Atlantic Europe and British Islands (mainly carrying Y1 haplotypes) and those from Sub-Saharan Africa (belonging to Y2-haplogroup) showed genetic variation of a different origin. Our study confirmed the existence of two large Y-chromosome lineages (Y1 and Y2) in taurine cattle. However, Y-specific microsatellites increased analytical resolution and allowed at least two different Y2-haplotypic subfamilies to be distinguished, one of them restricted to the African continent.

Here we tested the segregation and paternal compatibility of markers INRA124 and INRA126 on female DNA in 10 different cattle families, in order to clarify the usefulness of these microsatellites for the study of male-mediated population processes in cattle. Their performance was compared with that of four microsatellites located in the PAR-BTAY (UMN0108, UMN0803, UMN0929 and UMN0905) and another one male-specific microsatellite (INRA189). INRA124 and INRA126 amplified the same sized fragment in both sexes. Same size alleles were sequenced and the high homology found allowed us to rule out non-specific female amplification. INRA124 showed full parental compatibility, whilst the locus INRA126 showed 55% parental incompatibility. Based on these observations, it is recommended that markers INRA124 and INRA126 should not be used in studies to characterize male-mediated genetic events in cattle.

The aim of this paper was to estimate direct and maternal genetic parameters for calving ease (CE), birth weight (BrW), weaning weight (WW), and calving interval (CI) to assess the possibility of including this information in beef cattle improvement programs. Field data, including a total of 59,813 animals (1,390 sires and 1,147 maternal grand sires) from the Asturiana de los Valles beef cattle breed, were analyzed with a multivariate linear model. Estimates of heritability for direct genetic effects (CED, CID, BrWD, and WWD) were 0.191 +/- 0.019, 0.121 +/- 0.013, 0.390 +/- 0.030, and 0.453 +/- 0.035, respectively, whereas those for maternal genetic effects (CEM, BrWM, and WWM) were 0.140 +/- 0.015, 0.208 +/- 0.020, and 0.138 +/- 0.022, respectively. Genetic correlations between direct or maternal genetic effects across traits were, in general, positive and moderate to low. However, genetic correlation for the pair CED-BrWD was positive and high (0.604 +/- 0.064). Genetic correlations between the direct and maternal genetic effects within a trait were negative and moderate (-0.219 +/- 0.097 for CE, -0.337 +/- 0.080 for BrW, and -0.440 +/- 0.102 for WW). Genetic correlations for CED-BrWM and CED-WWM were -0.121 +/- 0.090 and -0.097 +/- 0.113, respectively. The genetic correlation for CEM-CID was unfavorable (0.485 +/- 0.078), and those for CEM-BrWD (-0.094 +/- 0.079) and CEM-WWD (-0.125 +/- 0.082) were low and negative. The genetic correlation between CID and WWM was favorable (-0.148 +/- 0.106). Overall, the data presented here support the hypothesis that maternal effects for CE and BrW are not the same and that the genetic relationships between CI and maternal effects for WW in beef cattle follow a similar pattern to that reported between CI and milk yield in dairy cattle. Moreover, the need to include direct and maternal breeding values in beef cattle selection programs is suggested.

The aim of this study was to ascertain the role of the Agouti signaling peptide (ASIP) gene coding region in the Agouti locus variation within wild-type coat colour in cattle. We determined the Extension genotype in 241 individuals from six Spanish and three French brown cattle breeds representative of wild-type coat variation. Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis was carried out in individuals of each Extension genotypes within the same breed in an attempt to identify variants in the three coding exons of the ASIP gene. No SSCP variants were found. Results were confirmed by sequencing the coding exons of the ASIP gene in 20 individuals. Our results suggest that the ASIP coding region does not play a central role in coat colour variation in cattle.