Prevalence of sex-chromosome aneuploidy estimated using SNP genotype intensity information in a large population of juvenile dairy and beef cattle.

Aneuploidy is a genetic condition characterized by the loss or gain of one or more chromosomes. Aneuploidy affecting the sex chromosomes can lead to infertility in otherwise externally phenotypically normal cattle. Early identification of cattle with sex chromosomal aneuploidy is important to minimize the costs associated with rearing infertile cattle and futile breeding attempts. As most livestock breeding programs routinely genotype their breeding populations using single nucleotide polymorphism (SNP) arrays, this study aimed to assess the feasibility of integrating an aneuploidy screening tool into the existing pipelines that handle dense SNP genotype data. A further objective was to estimate the prevalence of sex chromosome aneuploidy in a population of 146,431 juvenile cattle using available genotype intensity data. Three genotype intensity statistics were used: the LogR Ratio (LRR), R-value (the sum of X and Y SNP probe intensities), and B-allele frequency (BAF) measurements. Within the female-verified population of 124,958 individuals, the estimated prevalence rate was 0.0048% for XO, 0.0350% for XXX, and 0.0004% for XXY. The prevalence of XXY in the male-verified population was 0.0870% (i.e., 18 out of 20,670 males). Cytogenetic testing was used to verify 2 of the XXX females who were still alive. The proposed approach can be readily integrated into existing genomic pipelines, serving as an efficient, large-scale screening tool for aneuploidy. Its implementation could enable the early identification of infertile animals with sex-chromosome aneuploidy.

Risk factors for, and genetic association with, intestinal atresia in dairy calves.

Intestinal atresia is an under-diagnosed congenital defect in cattle. It results in complete occlusion of the intestinal lumen and, unless surgically corrected, results in death or euthanasia of the affected calf. There is limited information on the incidence of this condition or on risk factors, including predisposing alleles, associated with the defect. In this study, active surveillance of 39 dairy farms over 8 years identified 197 cases of intestinal atresia among 56 454 calves born, an incidence of 0.35%. The majority of cases (83%) had occlusion of the jejunum, although cases with blockage of the colon (14%) or anus (4%) were also identified. The defect was twice as common in male as in female calves (p < 0.0001), and was more common in progeny of older cows than in progeny of first or second lactation cows (p < 0.001). Year and farm of birth were also significantly associated with incidence (p < 0.05). The incidence of intestinal atresia was highest among the progeny of three related Jersey sires, suggesting that a gene for intestinal atresia was segregating within this family. Linkage analysis utilising 28 affected progeny of two half-sib putative carrier sires identified two putative quantitative trait loci associated with the defect, on chromosomes 14 and 26, although no clear candidate genes were identified. There was no evidence of a sire-effect among the progeny of Holstein-Friesian sires. However, a case-control genome-wide association study involving 91 cases and 375 healthy controls, identified 31 SNP in 18 loci as associated with the defect in this breed. These data suggest that intestinal atresia in dairy calves is not a simple Mendelian trait as previously reported but a complex multigenic disorder.

Predicting carcass cut yields in cattle from digital images using artificial intelligence.

Deep Learning (DL) has proven to be a successful tool for many image classification problems but has yet to be applied to carcass images. The aim of this study was to train DL models to predict carcass cut yields and compare predictions to more standard machine learning (ML) methods. Three approaches were undertaken to predict the grouped carcass cut yields of Grilling cuts and Roasting cuts from a large dataset of 54,598 and 69,246 animals respectively. The approaches taken were (1) animal phenotypic data used as features for a range of ML algorithms, (2) carcass images used to train Convolutional Neural Networks, and (3) carcass dimensions measured directly from the carcass images, combined with the associated phenotypic data and used as feature data for ML algorithms. Results showed that DL models can be trained to predict carcass cuts yields but an approach that uses carcass dimensions in ML algorithms performs slightly better in absolute terms.

Genetic benefits of genomic selection breeding programmes considering foreign sire contributions.

BACKGROUND: In modern dairy breeding programmes, high contributions from foreign sires are nearly always present. Genotyping, and therefore genomic selection (GS), concern only a subpopulation of the breeding programme's wider dairy population. These features of a breeding programme contribute in different ways to the rate of genetic gain for the wider industry. METHODS: A deterministic recursive gene flow model across subpopulations of animals in a dairy industry was created to predict the commercial performance of replacement heifers and future artificial insemination bulls. Various breeding strategies were assessed by varying the reliability of breeding values, the genetic contributions from subpopulations, and the genetic trend and merit of the foreign subpopulation. RESULTS: A higher response in the true breeding goal measured in standard deviations (SD) of true merit (G) after 20 years of selection can be achieved when genetic contributions shift towards higher merit alternatives compared to keeping them fixed. A foreign annual genetic trend of 0.08 SD of the breeding goal, while the domestic genetic trend is 0.10 SD, results in the overall net present value of genetic gain increasing by 1.2, 2.3, and 3.4% after 20 years as the reliability of GS in the domestic population increased from 0.3 to 0.45, 0.60 and 0.75. With a foreign genetic trend of 0.10 SD, these increases are more modest; 0.9, 1.7, and 2.4%. Increasing the foreign genetic trend so that it is higher than the domestic trend erodes the benefits of increasing the reliability of domestic GS further. CONCLUSIONS: Having a foreign source of genetic material with a high rate of genetic progress contributes substantially to the benefits of domestic genetic progress while at the same time reducing the expected returns from investments to improve the accuracy of genomic prediction in the home country.

Analysis of a large dataset reveals haplotypes carrying putatively recessive lethal and semi-lethal alleles with pleiotropic effects on economically important traits in beef cattle.

BACKGROUND: In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. METHODS: In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production. RESULTS: We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype. CONCLUSIONS: We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.

Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology.

BACKGROUND: Negative energy balance (NEB) is an imbalance between energy intake and energy requirements for lactation and body maintenance affecting high-yielding dairy cows and is of considerable economic importance due to its negative impact on fertility and health in dairy herds. It is anticipated that the cow hypothalamus experiences extensive biochemical changes during the early post partum period in an effort to re-establish metabolic homeostasis. However, there is variation in the tolerance to NEB between individual cows. In order to understand the genomic regulation of ovulation in hypothalamic tissue during NEB, mRNA transcriptional patterns between tolerant and sensitive animals were examined. A short term dietary restriction heifer model was developed which induced abrupt onset of anoestrus in some animals (Restricted Anovulatory; RA) while others maintained oestrous cyclicity (Restricted Ovulatory; RO). A third control group (C) received a higher level of normal feeding. RESULTS: A total of 15,295 genes were expressed in hypothalamic tissue. Between RA and C groups 137 genes were differentially expressed, whereas between RO and C, 32 genes were differentially expressed. Differentially expressed genes were involved in the immune response and cellular motility in RA and RO groups, respectively, compared to C group. The largest difference between groups was observed in the comparison between RA and RO heifers, with 1094 genes shown to be significantly differentially expressed (SDE). Pathway analysis showed that these SDE genes were associated with 6 canonical pathways (P < 0.01), of which neuroactive ligand-receptor interaction was the most significant. Within the comparisons the main over-represented pathway functions were immune response including neuroprotection (CXCL10, Q1KLR3, IFIH1, IL1 and IL8; RA v C and RA v RO); energy homeostasis (AgRP and NPY; RA v RO); cell motility (CADH1, DSP and TSP4; RO v C) and prevention of GnRH release (NTSR1 IL1α, IL1ß, NPY and PACA; RA v RO). CONCLUSIONS: This information will assist in understanding the genomic factors regulating the influence of diet restriction on fertility and may assist in optimising nutritional and management systems for the improvement in reproductive performance.

The effects of short term dietary restriction on haematological responses and leukocyte gene expression of anovulatory and ovulatory beef heifers.

The study objective was to characterise the impact of negative energy balance (NEB) on immune-stress responsiveness in beef heifers. A short term (18-day) dietary restriction model was used. Dietary restriction (0.4 maintenance (Mn) energy requirements) induced abrupt onset of anoestrus in nine heifers (Restricted Anovulatory; RA) while nineteen heifers maintained oestrous cyclicity (Restricted Ovulatory; RO). In addition a control (C) group of 12 heifers received a higher level of feeding (1.2 Mn). Haematological related biomarkers of husbandry stress, leukocyte gene expression of seven cytokine genes and five immunological biomarkers were investigated. After 18 days of differential feeding of the heifers alterations in eosinophil and monocyte numbers and altered expression of CXCL8, IL2 and TNFα could be attributed to diet restriction. More specifically, changes in these five variables were found in heifers that became anovulatory (RA) and are therefore considered to be more sensitive biomarkers to an energy deficit.