Connectedness among herds of beef cattle bred under natural service

Background

A procedure to measure connectedness among herds was applied to a beef cattle population bred by natural service. It consists of two steps: (a) computing coefficients of determination (CDs) of comparisons among herds; and (b) building sets of connected herds.

Methods

The CDs of comparisons among herds were calculated using a sampling-based method that estimates empirical variances of true and predicted breeding values from a simulated n-sample. Once the CD matrix was estimated, a clustering method that can handle a large number of comparisons was applied to build compact clusters of connected herds of the Bruna dels Pirineus beef cattle. Since in this breed, natural service is predominant and there are almost no links with reference sires, to estimate CDs, an animal model was used taking into consideration all pedigree information and, especially, the connections with dams. A sensitivity analysis was performed to contrast single-trait sire and animal model evaluations with different heritabilities, multiple-trait animal model evaluations with different degrees of genetic correlations and models with maternal effects.

Results

Using a sire model, the percentage of connected herds was very low even for highly heritable traits whereas with an animal model, most of the herds of the breed were well connected and high CD values were obtained among them, especially for highly heritable traits (the mean of average CD per herd was 0.535 for a simulated heritability of 0.40). For the lowly heritable traits, the average CD increased from 0.310 in the single-trait evaluation to 0.319 and 0.354 in the multi-trait evaluation with moderate and high genetic correlations, respectively. In models with maternal effects, the average CD per herd for the direct effects was similar to that from single-trait evaluations. For the maternal effects, the average CD per herd increased if the maternal effects had a high genetic correlation with the direct effects, but the percentage of connected herds for maternal effects was very low, less than 12%.

Conclusions

The degree of connectedness in a bovine population bred by natural service mating, such as Bruna del Pirineus beef cattle, measured as the CD of comparisons among herds, is high. It is possible to define a pool of animals for which estimated breeding values can be compared after an across-herds genetic evaluation, especially for highly heritable traits.     

Pedigree analysis of eight Spanish beef cattle breeds

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña – Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).     

Bayes factor for testing between different structures of random genetic groups: A case study using weaning weight in Bruna dels Pirineus beef cattle

The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null intraclass correlation. It compares two nested models, a model with a given structure of genetic groups against a model without genetic groups. The calculation of the Bayes factor between different structures of genetic groups can be quickly and easily obtained from the Bayes factor between the nested models. We applied this approach to a weaning weight data set of the Bruna dels Pirineus beef cattle, comparing several structures of genetic groups, and the final results showed that the preferable structure was an only group for unknown dams and different groups for unknown sires for each year of calving.     

The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers

Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.     

Proteomic analysis reveals oxidative stress response as the main adaptative physiological mechanism in cows under different production systems

Three groups of cows representing three ranges of welfare in the production system were included in the study: two groups of Bruna dels Pirineus beef cattle maintained under different management systems (good and semiferal conditions) and a group of Alberes cows, a breed that lives in the mountains (hardest conditions). In order to identify new stress/welfare biomarkers, serum from Bruna cows living in both environments was subjected to DIGE labelling, two-dimensional electrophoresis and MALDI-MS or ion trap MS. Identification was achieved for 15 proteins, which mainly belonged to three biological functions, the oxidative stress pathway (glutathione peroxidase (GPx) and paraoxonase (PON-1)), the acute phase protein family (Heremans Schmid glycoprotein alpha2 (α2-HSG)) and the complement system. Biological validation included the Alberes breed. GPx and PON-1 were validated by an enzymatic assay and found to be higher and lower, respectively, in cows living in hard conditions. α2-HSG was validated by ELISA and found to be reduced in hard conditions. Other biomarkers of the redox status were also altered by living conditions: protein carbonyl content, superoxide dismutase (SOD) and glutathione reductase (GR). Our results show that changes in the redox system are the main adaptation of cows living in challenging environmental conditions.     

Y chromosome diversity and paternal origin of Chinese cattle

To determine the Y chromosome genetic diversity and paternal origin of Chinese cattle, 369 bulls from 17 Chinese native cattle breeds and 30 bulls from Holstein and four bulls from Burma were analyzed using a recently discovered USP9Y marker that could distinguish between taurine and indicine cattle more efficiently. In total, the taurine Y1, Y2 haplogroup and indicine Y3 haplogroup were detected in 7 (1.9 %), 193 (52.3 %) and 169 (45.8 %) individuals of 17 Chinese native breeds, respectively, although these frequencies varied amongst the Chinese native cattle breeds examined. Y2 dominates in northern China (91.4 %), while Y3 dominates in southern China (81.2 %). Central China is an admixture zone with Y2 predominating overall (72.0 %). Our results demonstrate that Chinese cattle have two paternal origins, one from B. taurus (Y2) and the other from B. indicus (Y3). The Y1 haplogroup may originate from the imported beef cattle breeds in western countries. The geographical distributions of the Y2 and Y3 haplogroup frequencies reveal a pattern of male indicine introgression from south to north China, and male taurine introgression from north to south China.     

Complementarity between microhistological analysis and PCR-capillary electrophoresis in diet analysis of goats and cattle using faecal samples

An evaluation is made of the complementarity between two non-invasive techniques, cuticle microhistological analysis (CMA) and PCR-capillary electrophoresis (PCR-CE) DNA-based analysis, for the determination of herbivore diet composition from faecal samples. Cuticle microhistological analysis is based on the different microanatomical characteristics of the epidermal fragments remaining in the faeces. The PCR-CE technique combines PCR amplification of a trnL(UAA) genomic DNA region with amplicon length determination by CE, with this length being characteristic for each species or taxon. A total of 37 fresh stool samples were analyzed, including 16 from feral goats (Capra hircus) from the Tramuntana mountain range (Mallorca, Baleares) and 11 from Bruna dels Pirineus cattle breed (Bos taurus) from the surrounding Montserrat mountain range (Barcelona, Spain). All the animals were in a free grazing Mediterranean pine habitat, dominated by Aleppo pine (Pinus halepensis). The results showed that both techniques detected a similar number of plant components in the faeces of goats and cows. In the case of goats, a positive correlation was obtained between the percentage of samples in which a particular taxon is detected by CMA and the percentage of samples in which that taxon is detected by PCR-CE. This correlation was not observed in the case of cows. It is concluded that PCR-CE is a fast and reliable method to detect the different plant components in the faeces of herbivores. However, it cannot be considered as an alternative to CMA, but as a complementary method, since both techniques can detect some taxa that are not detected by the other technique. In addition, CMA detected the presence of the different taxa in a greater number of samples, and at the same time, it enables quantitative data to be obtained for plant diet composition. The species of herbivore also seems to influence the results obtained by PCR-CE, so more studies are required to address this aspect.     

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.     

Survival of XO mouse fetuses: effect of parental origin of the X chromosome or uterine environment?

Using a recombinant product from the structurally abnormal Y chromosome, Y*, female mice with a single X of either maternal or paternal origin were generated. The two types of females were produced on the same genetic background and differ only in the origin of the X chromosome. Hence it has been possible to assess the effect of parental origin of the X on survival of females with a single X chromosome. A highly significant prenatal loss of females with a single X of paternal origin, but no comparable loss of females with a single X of maternal origin was observed. The reduced viability of females with a paternally derived X could be mediated by the parental origin of the X (i.e. X chromosome imprinting) or alternatively, since the mothers of females with a single paternally derived X have only a single X chromosome, the effect could be mediated by the genotype of the mother (i.e. maternal uterine effect).     

Design of a bovine low-density SNP array optimized for imputation

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.     

The evolution of X-linked genomic imprinting

We develop a quantitative genetic model to investigate the evolution of X-imprinting. The model compares two forces that select for X-imprinting: genomic conflict caused by polygamy and sex-specific selection. Genomic conflict can only explain small reductions in maternal X gene expression and cannot explain silencing of the maternal X. In contrast, sex-specific selection can cause extreme differences in gene expression, in either direction (lowered maternal or paternal gene expression), even to the point of gene silencing of either the maternal or paternal copy. These conclusions assume that the Y chromosome lacks genetic activity. The presence of an active Y homologue makes imprinting resemble the autosomal pattern, with active paternal alleles (X- and Y-linked) and silenced maternal alleles. This outcome is likely to be restricted as Y-linked alleles are subject to the accumulation of deleterious mutations. Experimental evidence concerning X-imprinting in mouse and human is interpreted in the light of these predictions and is shown to be far more easily explained by sex-specific selection.     

Prader-Willi-Syndrom und Angelman-Syndrom

Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are two distinct neurogenetic disorders caused by the loss of function of imprinted genes in the chromosomal region 15q11q13. An approximately 2 Mb region inside 15q11q13 is subject to genomic imprinting. As a consequence the maternal and paternal copies in this region are different in DNA methylation and gene expression. The most frequent genetic lesions in both disorders are an interstitial de novo deletion of the chromosomal region 15q11q13, uniparental disomy 15, an imprinting defect or, in the case of AS, a mutation of the UBE3A gene. Microdeletions in a small number of patients with PWS and AS with an imprinting defect have led to the identification of the chromosome 15 imprinting centre (IC) upstream of the SNURF-SNRPN gene, which acts in cis to regulate imprinting in the whole 15q imprinted domain. The IC consists of two critical elements: one in the more centromeric part which is deleted in patients with AS and which is thought to be responsible for the establishment of imprinting in the female germ line, and one in the more telomeric part which is deleted in patients with PWS and which is required to maintain the paternal imprint.     

Genetic correlations between reproduction of crossbred ewes and the growth and carcass performance of their progeny

Genetic correlations were estimated between first cross ewe reproduction traits and growth and carcass traits of their second cross lamb progeny. The 2460 crossbred ewes were progeny of 74 maternal breed sires and mainly Merino dams. The ewes had 3 joinings to terminal sire rams with 6824 joining records resulting in 9002 lambs born and 7176 lambs slaughtered. The ewe reproduction traits included: fertility, litter size, ewe rearing ability or lamb survival, number of lambs born (NLBj) and weaned (NLWj) per ewe joined, with traits reflecting ewe productivity being total litter weight weaned (TWWj) per ewe joined and the component trait average lamb weaning weight in the litter (AWW). The lamb growth traits included weight of the lambs at birth (BWT), weaning (WWT) and post weaning (PWWT) as well as growth rate pre and post weaning. The lamb carcass traits included hot carcass weight (HCWT), dressing yield (DRESS%), fat depth (FatGR, FatC), eye muscle depth (EMD) and area (EMA) and meat quality traits (colour and pH). The genetic correlations were estimated by bivariate mixed models using ASReml. The genetic correlations between the composite reproduction traits of the ewes and the post-weaning growth rate of their lambs were high (0.67 for NLBj and 0.65 for NLWj). There were moderate positive correlations between NLWj and WWT (0.36), PWWT (0.49) and pre weaning growth (0.36) and NLBj with PWWT (0.31). BWT was negatively correlated with litter size (−0.34) and positively with ewe rearing ability (0.38). Most of the other genetic correlations were smaller than their standard errors which generally ranged from 0.2 to 0.3. The genetic correlations for HCWT with all the ewe reproduction traits were positive and moderate (0.29–0.53) and high with the ewe productivity traits that included weight of lambs (TWWj 0.98 and AWW 0.96). The genetic correlations among the other traits were variable and had high standard errors, generally ranging from 0.1 to 0.5. However there were generally negative and unfavourable genetic correlations between the reproduction traits and DRESS% and meat colour L*, whereas those with carcass fat (FatC and FatGR) were generally negative and favourable.     

Genome‐wide variability and selection signatures in Italian island cattle breeds

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo‐Bruna and Sardo‐Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within‐breed genetic heterogeneity. The F_ST comparison revealing the largest number of significant SNPs was Sardo‐Bruna vs. Sardo‐Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo‐Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo‐Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi‐dimensional scaling and the admixture analysis the Sardo‐Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo‐Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.     

PATERNAL EFFECTS ON THE EXPRESSION OF A MALE POLYPHENISM

Polyphenic traits are widespread, but compared to other traits, relatively few studies have explored the mechanisms that influence their inheritance. Here we investigated the relative importance of additive, nonadditive genetic, and parental sources of variation in the expression of polyphenic male dimorphism in the mite Rhizoglyphus echinopus, a species in which males are either fighters or scramblers. We established eight inbred lines through eight generations of full‐sibling matings, and then crossed the inbred lines in a partial diallel design. Nymphs were isolated and raised to adulthood with ad libitum food. At adulthood, male morph was recorded for all male offspring. Using a Cockerham–Weir model, we found strong paternal effects for this polyphenic trait that could be either linked to the Y chromosome of males or an indirect genetic effect that is environmentally transmitted. In additional analyses, we were able to corroborate the paternal effects but also detected significant additive effects questioning the Cockerham–Weir analysis. This study reveals the potential importance of paternal effects on the expression of polyphenic traits and sheds light on the complex genetic architecture of these traits.     

Effects of genetic variants and mapping assignments of the ovine calpain regulatory subunit gene on chromosome 14

The aim of this study was to search genetic variants, to map the ovine calpain regulatory subunit gene (CAPN4S) on chromosomes, and to find associations between single nucleotide (nt) polymorphisms (SNPs) and weight traits. Genotyping was performed with 226 purebred, 133 crossbred and 122 animals from eight sheep reference families. The polymerase chain reaction–single strand conformational polymorphism analysis detected genetic variants in the genomic regions between exons 4 and 8. Nt polymorphisms were confirmed at positions 115 (G/C) with CAPN445, 71 (A/G) with CAPN456, and 25 (A/G) and 44 (A/T) with the CAPN478 segments. The Polypay and Targhee purebreds showed significantly different allele frequencies while the mixed population was placed between pure breeds. The two-point linkage analysis using the CRI-MAP version 2.4 identified locations of the CAPN4S segments, showing that CAPN4S is closely linked with the LSCV30 microsatellite marker on chromosome 14. The genotypes of g.45923178G>C had significant mean differences for BWT and WWT, meaning that the identified SNP may be used in marker assisted selection programs. A significant haplo-block was constructed between g.45924950T>C and g.45924969A>T, and major frequencies were observed as AA (0.727) and GT (0.267).     

A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data

Genomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have received little consideration in animal breeding programmes, although their relevance to some agricultural important traits has been demonstrated. A recently proposed model (imprinting model) with two path-of-transmission (male and female)-specific breeding values for each animal accounts for all types of imprinting simultaneously (paternal, maternal, full and partial). Imprinting effects (or more generally: parent-of-origin effects (POE)) are determined by taking the difference between the two genetic effects in each animal. However, the computation of their prediction error variance (PEV) is laborious; thus, we propose a new model that is equivalent to the aforementioned imprinting model, which facilitates the direct estimation of imprinting effects instead of taking the differences and the PEV is readily obtained. We applied the new model to slaughterhouse data for Brown Swiss cattle, among which imprinting has never been investigated previously. Data were available for up to 173 051 fattening bulls, where the pedigrees contained up to 428 710 animals representing the entire Brown Swiss population of Austria and Germany. The traits analysed comprised the net BW gain, fat score, EUROP class and killing out percentage. The analysis demonstrated that the net BW gain, fat score and EUROP class were influenced significantly by POE. After estimating the POE, the new model yielded estimates with reliabilities ranging between 0.4 and 0.9. On average, the imprinting variances accounted for 9.6% of the total genetic variance, where the maternal gamete was the main contributor. Moreover, our results agreed well with those obtained using linear models when the EUROP class and fat score were treated as categorical traits by applying a GLMM with a logit link function.     

Contribution of Lidia cattle breed historical castes to the paternal genetic stock of Spain

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.     

DNA fingerprint bands applied to linkage analysis with quantitative trait loci in chickens

Summary
An efficient approach to detect association between quantitative traits and bands of DNA fingerprint patterns uses intra-family tail analysis, which compares fingerprints of DNA mixes from individuals at the two tails of a phenotypic distribution. In analysis of 67 paternal half-sibs of a meat-type chicken family, of 57 sire bands generated by two probes, one sire-specific band (S6–6) was associated with abdominal fat deposition. The band effect was estimated by a linear model analysis to be 0–88 standard deviations, or about 30% of the family mean. The association between band S6–6 and abdominal fat was further examined by testing progeny of paternal half-sibs of the chickens which were used in the tail analysis, establishing genetic linkage between the DNA marker and a genetic locus affecting abdominal fat deposition.