Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (H_O=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (H_O=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F_st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.     

Population structure and inbreeding from pedigree analysis of purebred dogs

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Psi for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.     

Mapping of a quantitative trait locus for beef marbling on bovine chromosome 9 in purebred Japanese black cattle

The goal of this study is to detect quantitative trait loci (QTL) for carcass traits applicable for a DNA-based breeding system in a Japanese Black cattle population. A purebred paternal half-sib family from a commercial line composed of 65 steers was initially analyzed using 188 informative microsatellites giving a 16-cM average interval covering 29 autosomes. A significant QTL for marbling was detected in the centromeric portion of bovine chromosome (BTA) 9. After additional marker genotyping across a larger sample size composed of 169 individuals, this locus was refined to a 20-cM confidence interval between microsatellites BM1227 (24 cM) and DIK2741 (50 cM) at a 1% chromosome-wise threshold. The allele substitution effect between Q and q for a beef marbling standard score (1 to 12 range) on BTA9 was 1.0 (5.7% of total phenotypic variance in QTL contribution in this family). This result provides a primary platform for a marker-assisted selection system of the beef marbling trait within the Japanese Black (Wagyu) cattle population.     

Assessment of progesterone profiles and postpartum onset of luteal activity in spring calving Hereford beef suckler cattle

Background  

Reproduction is the single greatest factor limiting beef cattle production. Previous research on beef suckler luteal activity has largely focused on the mechanisms, and duration, of postpartum anoestrus. However, the temporal pattern of luteal activity after resumption of post-partum ovarian activity, and the impact of pattern type on days open (DO) in purebred beef suckler cows, are unknown.     

Contribution of herd characteristics to best linear unbiased estimates of slaughter traits in beef cattle

Genetic evaluations separate phenotypes into their contributing additive genetic effects and non-(additive) genetic effects, with the former termed best linear unbiased predictions, and the latter termed best linear unbiased estimates (BLUEs). For the purpose of the present study, genetic evaluations, along with phenotypic data from 4 137 376 animals, were used to generate herd, year of slaughter and sex contemporary group BLUEs for various slaughter-related traits. These slaughter traits included carcass weight (CW), carcass conformation (CC) and carcass fat (CF). For the 4 665 herds that were consistently slaughtering ≥10 animals/year between the years 2014 and 2018, inclusive, all relevant contemporary group BLUEs were collapsed into a single herd-year value; results herein relate to these herds. The within-year herd-year BLUE correlations between CW and CC, between CW and CF, and between CC and CF were 0.51, 0.10 and −0.04, respectively. The repeatability across years of the herd-year BLUEs for CW, CC and CF was 0.66, 0.59 and 0.50, respectively. Furthermore, when the herds were stratified, within year, on the percentile rank of their herd-year BLUEs, herds had the greatest probability of remaining in the same BLUE stratum from one year to the next. In addition, results from the present study determined that various herd characteristics are associated with differences in the herd BLUEs. Results from the present study could be used to advise beef producers on the most promising strategy to improve the carcass merit of their animals.     

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).     

Endocrine and reproductive responses of beef cattle to a synthetic gonadotropin-releasing hormone agonist (fertirelin acetate)

A synthetic gonadotropin-releasing hormone (GnRH) agonist (fertirelin acetate, FA) was administered to beef cattle within 12 h after onset of estrus (Day = 0) to study effects on subsequent endocrine responses and fertility. In Study 1, 16 crossbred beef heifers were injected with either 100 mug FA (n = 8) or saline (n = 8) at 6 or 12 h (n = 7; n = 9) after onset of estrus. Concentrations of luteinizing hormone (LH) over time were affected (P<0.01) by the interaction of treatment and interval from onset of estrus to treatment. Heifers treated with FA at 6 h after onset of estrus exhibited the greatest increase in LH after treatment. There was no effect of treatment, interval from onset of estrus to treatment or treatment by interval interaction on duration of the estrous cycle, on concentrations of progesterone from Days 1 through 14 posttreatment, or on concentrations of progesterone prior to subsequent estrus (Day -10 through 0, posttreatment estrus). In summary, FA administered to beef cattle within 12 h after onset of estrus effectively increased peripheral plasma concentration of LH, but this increase had no effect on subsequent luteal function as measured by duration of the estrous cycle or concentrations of plasma progesterone. In Study 2, 86 parous beef cows were bred artificially to one of two bulls following natural or prostaglandin F(2)alpha induced estrus. Cows received either no treatment or 50 or 100 mug FA at the time of AI. There was no effect of treatment, breed, parity, technician, service sire or interactions on conception rate (mean = 76.7%). Although not significant, the numerical pattern of conception rate among experimental groups (control = 71.4%, 50 mug FA = 76.7%, 100 mug FA = 82.1%) supports further investigation of this GnRH agonist with larger numbers of cattle.     

Genetic variation within the Hereford breed of cattle

Genetic differentiation among Hereford populations from Britain, Ireland, Sweden, Canada and New Zealand together with six other beef breeds was assessed using blood type polymorphisms. Changes in the genetic structure of the British Hereford population over time were also examined. Loci surveyed were seven red cell antigen systems (A, B, C, F, L, S, Z), and two serum protein loci (transferrin and albumin). Within group variation was measured by the average expected heterozygosity, and between group relationships by genetic distance. There was significant genetic differentiation among Hereford populations from different countries. Differences between Hereford groups, however, were not as large as differences between breeds. There were also significance differences among British herds. The proportion of Canadian genes in the British 'hybrid' population was estimated to have increased from 0·42 (±0·34) in the 1970s to 0·98 (±0·11) in the 1990s. Canadian Hereford groups were found to be less heterozygous than other groups, and replacement of the British population with Canadian animals may lead to loss of variation. Breeding strategies that preserve original native genes in British Hereford populations should be considered by commercial breeders, in order to prevent the long-term loss of genetic variation within the breed.     

Movement orders in spontaneous group movements in cattle: 6-year monitoring of a beef cow herd with changing composition

Journal of Ethology - Few studies have investigated group movements of domestic ungulates in farming conditions where the groups are subjected to repeated composition changes across years. We...     

A review of some factors affecting the expression of libido in beef cattle, and individual bull and herd fertility

This paper examines some of the factors that affect the expression of libido in beef cattle, focusing on the male and the free-ranging situation. The ways in which bull libido is assessed and the relationship between libido test results and fertility are discussed. Genetics play a role in determining libido, but there are many environmental factors affecting its expression, and a number of these factors influence sexual activity in both tests of libido and paddock mating. Herd fertility is multi-factorial and, consequently, it is difficult to draw definitive conclusions about the relationship between libido and fertility. Multiple males increase the expression of libido, but it is uncertain whether this translates into improvements in herd fertility. However, there are consequences for individual bull fertility, as there is ample evidence of inherent differences between bulls. Male:female ratios appear to have minor effects on libido and fertility. Anecdotal evidence indicates that multiple matings with the same or different bulls may reduce the duration of oestrus. Social relationships between bulls can affect the expression of libido, with subordinate bulls being inhibited by the presence of dominant bulls. There is evidence that dominant bulls may achieve more matings at pasture, but this is not necessarily shown in their fertility. Older bulls show greater expression of libido in tests and appear more efficient in serving, although these changes may reflect greater sexual experience. Provided bulls are sexually mature and physically able to mate, age per se appears not to affect fertility, but age interacts with dominance, which can influence fertility. There is evidence of breed differences in expression of libido, but this appears not to be demonstrated in fertility. There is anecdotal evidence that bulls and females prefer to mate with similar genotypes/phenotypes with implications for fertility. Limited research on thermal and nutritional effects indicate some adverse consequences for libido of climatic extremes for unadapted bulls and of over-feeding, but not under-feeding. Limited research has investigated the effects on libido and fertility of multiple stressors associated with relocation; relocation to dramatically different environments has long-lasting detrimental consequences for fertility. Too few studies have been conducted to draw conclusions about the effects of topography and herd dispersion on libido and fertility. Temperament is likely to affect the expression of libido when animals are put into new situations, but this has not been critically researched. In the light of this review, the implications for managing cattle to optimise fertility are discussed and suggestions made as to areas where further research is needed.     

BoLA class I allele diversity and polymorphism in a herd of cattle

Major histocompatibility complex class I genes are among the most polymorphic genes characterized. The high level of polymorphism is essential for generating host immune responses. In humans, three distinct genomic loci encode human leukocyte antigen (HLA) class I genes, allowing individuals to express up to six different HLA class I molecules. In cattle, the number of distinct genomic loci are currently at least six, and the number of different bovine leukocyte antigens (BoLA) class I molecules that are expressed in individual animals are variable. The extent of allele variation within the cattle population is unknown. In this study, the number and variety of BoLA class I sequences expressed by 36 individuals were determined from full-length BoLA class I cDNA clones. Twenty distinct BoLA class I alleles were identified, with only four being previously reported. The number of expressed BoLA class I alleles in individual animals ranged between one and four, with none of the animals having an identical complement of BoLA class I molecules. Variation existed in the number of BoLA class I alleles expressed as well as the composition of expressed alleles, however, several BoLA class I alleles were found in multiple individual animals. Polymorphic amino acid sites were analyzed for positive and negative selection using the ADAPTSITE program. In the antigen recognition sites (ARS), there were eight positions that were predicted to be under positive selection and three positions that were predicted to be under negative selection from 62 positions. In contrast, for non-antigen recognition sites (non-ARS), there were three positions that were predicted to be under positive selection and 20 that were predicted to be under negative selection from 278, indicating that positive selection of amino acids occurs at a greater frequency within the antigen recognition sites.     

Production of recombinant albumin by a herd of cloned transgenic cattle

Purified plasma derived human albumin has been available as a therapeutic product since World War II. However, cost effective recombinant production of albumin has been challenging due to the amount needed and the complex folding pattern of the protein. In an effort to provide an abundant source of recombinant albumin, a herd of transgenic cows expressing high levels of rhA in their milk was generated. Expression cassettes efficiently targeting the secretion of human albumin to the lactating mammary gland were obtained and tested in transgenic mice. A high expressing transgene was transfected in primary bovine cell lines to produce karyoplasts for use in a somatic cell nuclear transfer program. Founder transgenic cows were produced from four independent cell lines. Expression levels varying from 1–2 g/l to more than 40 g/l of correctly folded albumin were observed. The animals expressing the highest levels of rhA exhibited shortened lactation whereas cows yielding 1–2 g/l had normal milk production. This herd of transgenic cattle is an easily scalable and well characterized source of rhA for biomedical uses.     

Genetic disorders in beef cattle: a review

The main purpose of present review is to describe and organize autosomal recessive disorders (arachnomelia, syndactylism, osteopetrosis, dwarfism, crooked tail syndrome, muscular hyperplasia, glycogen storage disease, protoporphyria), which occur among beef cattle, and methods that can be applied to detect these defects. Prevalence of adverse alleles in beef breeds happens due to human activity—selections of favorable features, e.g. developed muscle tissue. Unfortunately, carriers of autosomal recessive diseases are often characterized by these attributes. Fast and effective identification of individuals, that may carry faulty genes, can prevent economical losses.     

Ultra-low-density genotype panels for breed assignment of Angus and Hereford cattle

Angus and Hereford beef is marketed internationally for apparent superior meat quality attributes; DNA-based breed authenticity could be a useful instrument to ensure consumer confidence on premium meat products. The objective of this study was to develop an ultra-low-density genotype panel to accurately quantify the Angus and Hereford breed proportion in biological samples. Medium-density genotypes (13 306 single nucleotide polymorphisms (SNPs)) were available on 54 703 commercial and 4042 purebred animals. The breed proportion of the commercial animals was generated from the medium-density genotypes and this estimate was regarded as the gold-standard breed composition. Ten genotype panels (100 to 1000 SNPs) were developed from the medium-density genotypes; five methods were used to identify the most informative SNPs and these included the Delta statistic, the fixation (F_st) statistic and an index of both. Breed assignment analyses were undertaken for each breed, panel density and SNP selection method separately with a programme to infer population structure using the entire 13 306 SNP panel (representing the gold-standard measure). Breed assignment was undertaken for all commercial animals (n=54 703), animals deemed to contain some proportion of Angus based on pedigree (n=5740) and animals deemed to contain some proportion of Hereford based on pedigree (n=5187). The predicted breed proportion of all animals from the lower density panels was then compared with the gold-standard breed prediction. Panel density, SNP selection method and breed all had a significant effect on the correlation of predicted and actual breed proportion. Regardless of breed, the Index method of SNP selection numerically (but not significantly) outperformed all other selection methods in accuracy (i.e. correlation and root mean square of prediction) when panel density was ⩾300 SNPs. The correlation between actual and predicted breed proportion increased as panel density increased. Using 300 SNPs (selected using the global index method), the correlation between predicted and actual breed proportion was 0.993 and 0.995 in the Angus and Hereford validation populations, respectively. When SNP panels optimised for breed prediction in one population were used to predict the breed proportion of a separate population, the correlation between predicted and actual breed proportion was 0.034 and 0.044 weaker in the Hereford and Angus populations, respectively (using the 300 SNP panel). It is necessary to include at least 300 to 400 SNPs (per breed) on genotype panels to accurately predict breed proportion from biological samples.