Genomic Prediction Using Imputed Whole-Genome Sequence Data in Australian Angus Cattle.

Whole-genome sequence (WGS) data was used to estimate genomic breeding values for growth and carcass traits in Australian Angus cattle. The study aimed to compare the accuracy and bias of genomic predictions with three marker densities, including 50K, high-density (HD) and WGS. The dataset used in this study consisted of animals born between 2013 and 2022.

The Impact of Genetic and Non-Genetic Factors on Lamb Loin Shear Force.

Shear force is commonly used to evaluate tenderness, one of the most crucial eating quality aspects of sheep meat. The effect size of various factors on tenderness is still unknown. Studies have suggested that both genetic and environmental factors contribute to the variation in meat tenderness, and there are possible interactions between these factors.

Genotyping both live and dead animals to improve post-weaning survival of pigs in breeding programs.

Background: In this study, we tested whether genotyping both live and dead animals (GSD) realises more genetic gain for post-weaning survival (PWS) in pigs compared to genotyping only live animals (GOS).

Methods: Stochastic simulation was used to estimate the rate of genetic gain realised by GSD and GOS at a 0.01 rate of pedigree-based inbreeding in three breeding schemes, which differed in PWS (95%, 90% and 50%) and litter size (6 and 10).

Segregation GWAS to linearize a non-additive locus with incomplete penetrance: an example of horn status in sheep.

Background: The objective of this study was to introduce a genome-wide association study (GWAS) in conjunction with segregation analysis on monogenic categorical traits. Genotype probabilities calculated from phenotypes, mode of inheritance and pedigree information, are expressed as the expected allele count (EAC) (range 0 to 2), and are inherited additively, by definition, unlike the original phenotypes, which are non-additive and could be of incomplete penetrance. The EAC are regressed on the single nucleotide polymorphism (SNP) genotypes, similar to an additive GWAS.

The predicted benefits of genomic selection on pig breeding objectives.

The premise was tested that the additional genetic gain was achieved in the overall breeding objective in a pig breeding program using genomic selection (GS) compared to a conventional breeding program, however, some traits achieved larger gain than other traits. GS scenarios based on different reference population sizes were evaluated. The scenarios were compared using a deterministic simulation model to predict genetic gain in scenarios with and without using genomic information as an additional information source.

Parameter estimation and assessment of bias in genetic evaluation of carcass traits in Hanwoo cattle using real and simulated data.

Most carcass and meat quality traits are moderate to highly heritable, indicating that they can be improved through selection. Genetic evaluation for these types of traits is performed using performance data obtained from commercial and progeny testing evaluation. The performance data from commercial farms are available in large volume, however, some drawbacks have been observed.

Genetic diversity, population structure and origin of the native goats in Central Laos.

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip.

Comparison between multiple-trait and random regression models for genetic evaluation of weight traits in Australian meat sheep.

Random regression (RR) models are recommended as an alternative to multiple-trait (MT) models for better capturing the variance-covariance structure over a trajectory and hence more accurate genetic evaluation of traits that are repeatedly measured and genetically change gradually over time. However, a limited number of studies have been done to empirically compare RR over a MT model to determine how much extra benefit could be achieved from one method over another. We compared the prediction accuracy of RR and MT models for growth traits of Australian meat sheep measured from 60 to 525 d, using 102,579 weight records from 24,872 animals.

Validation of reaction norm breeding values for robustness in Australian sheep.

Background: There can be variation between animals in how stable their genetic merit is across different environments due to genotype-by-environment (G×E) interactions. This variation could be used in breeding programs to select robust genotypes that combine high overall performance with stable genetic ranking across environments. There have been few attempts to validate breeding values for robustness in livestock, although this is a necessary step towards their implementation in selection decisions.

Micro-genetic environmental sensitivity across macro-environments of chickens reared in Burkina Faso and France.

Background: Commercial poultry production systems follow a pyramidal structure with a nucleus of purebred animals under controlled conditions at the top and crossbred animals under commercial production conditions at the bottom. Genetic correlations between the same phenotypes on nucleus and production animals can therefore be influenced by differences both in purebred-crossbred genotypes and in genotype-by-environment interactions across the two environments, known as macro-genetic environmental sensitivity (GES). Within each environment, genotype-by-environment interactions can also occur due to so-called micro-GES.

Increased Yearling Weight Gain Is Associated with a Distinct Faecal Microbial Profile.

Microbial communities inhabiting the gut have the ability to influence physiological processes contributing to livestock production and performance. Livestock enterprises rely on animal production traits such as growth performance for profit. Previous studies have shown that gut microbiota are correlated to growth performance and could even influence it.

Including genomic information in the genetic evaluation of production and reproduction traits in South African Merino sheep.

Genomic selection (GS) has become common in sheep breeding programmes in Australia, New Zealand, France and Ireland but requires validation in South Africa (SA). This study aimed to compare the predictive ability, bias and dispersion of pedigree BLUP (ABLUP) and single-step genomic BLUP (ssGBLUP) for production and reproduction traits in South African Merinos. Animals in this study originated from five research and five commercial Merino flocks and included between 54,072 and 79,100 production records for weaning weight (WW), yearling weight (YW), fibre diameter (FD), clean fleece weight (CFW) and staple length (SL).

An effective hyper-parameter can increase the prediction accuracy in a single-step genetic evaluation.

The H-matrix best linear unbiased prediction (HBLUP) method has been widely used in livestock breeding programs. It can integrate all information, including pedigree, genotypes, and phenotypes on both genotyped and non-genotyped individuals into one single evaluation that can provide reliable predictions of breeding values. The existing HBLUP method requires hyper-parameters that should be adequately optimised as otherwise the genomic prediction accuracy may decrease.

Partitioning the forms of genotype-by-environment interaction in the reaction norm analysis of stability.

The reaction norm analysis of stability can be enhanced by partitioning the contribution of different types of G × E to the variation in slope. The slope of regression in a reaction norm model, where the performance of a genotype is regressed over an environmental covariable, is often used as a measure of stability of genotype performance. This method could be developed further by partitioning variation in the slope of regression into the two sources of genotype-by-environment interaction (G × E) which cause it: scale-type G × E (heterogeneity of variance) and rank-type G × E (heterogeneity of correlation).

Genome-wide association study for carcass traits in Hanwoo cattle using additional relatives' information of non-genotyped animals.

The aim of this study was to find significant genomic regions associated with carcass traits in Hanwoo cattle and to compare the benefit of using additional information from non-genotyped animals. Imputed whole-genome sequence data were used along with phenotypic data on 13 715 genotyped animals as well as phenotypes of 440 284 non-genotyped animals that were offspring of 454 genotyped sires. For carcass weight, 15 083 SNPs in 33 QTL regions and 313 candidate genes were identified.

Genomic analysis of the slope of the reaction norm for body weight in Australian sheep.

Background: Selection of livestock based on their robustness or sensitivity to environmental variation could help improve the efficiency of production systems, particularly in the light of climate change. Genetic variation in robustness arises from genotype-by-environment (G × E) interactions, with genotypes performing differently when animals are raised in contrasted environments. Understanding the nature of this genetic variation is essential to implement strategies to improve robustness.

Economic values for production, fertility and mastitis traits for temperate dairy cattle breeds in tropical Sri Lanka.

Economic values for annual milk yield (MY, kg), annual fat yield (FY, kg), annual protein yield (PY, kg), age at first calving (AFC, days), number of services per conception (NSC), calving interval (CI, days) and mastitis episodes (MS) were derived for temperate dairy cattle breeds in tropical Sri Lanka using a bio-economic model. Economic values were calculated on a per cow per year basis. Derived economic values in rupees (LKR) for MY, FY and PY were 107, -162 and -15, while for AFC, NSC, CI and MS, economic values were -59, -270, -84 and -8,303.

The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations.

Background: South Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. Combining genomic resources could facilitate development for across country selection, but the influence of population structures could be important to the compatability of genomic data from varying origins.

Accuracy of Genomic Prediction for Milk Production Traits in Philippine Dairy Buffaloes.

The objective of this study was to compare the accuracies of genomic prediction for milk yield, fat yield, and protein yield from Philippine dairy buffaloes using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) with the accuracies based on pedigree BLUP (pBLUP). To also assess the bias of the prediction, the regression coefficient (slope) of the adjusted phenotypes on the predicted breeding values (BVs) was also calculated. Two data sets were analyzed.

Genomic prediction in a numerically small breed population using prioritized genetic markers from whole-genome sequence data.

The objective of this study was to investigate the accuracy of genomic prediction of body weight and eating quality traits in a numerically small sheep population (Dorper sheep). Prediction was based on a large multi-breed/admixed reference population and using (a) 50k or 500k single nucleotide polymorphism (SNP) genotypes, (b) imputed whole-genome sequencing data (~31 million), (c) selected SNPs from whole genome sequence data and (d) 50k SNP genotypes plus selected SNPs from whole-genome sequence data. Furthermore, the impact of using a breed-adjusted genomic relationship matrix on accuracy of genomic breeding value was assessed.

A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits.

Background: Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants and genes that underpin economically important traits. Merino wool is globally sought after for luxury fabrics, but some key wool quality attributes are unfavourably correlated with the characteristic skin wrinkle of Merinos.

THI Modulation of Genetic and Non-genetic Variance Components for Carcass Traits in Hanwoo Cattle.

The phenotype of carcass traits in beef cattle are affected by random genetic and non-genetic effects, which both can be modulated by an environmental variable such as Temperature-Humidity Index (THI), a key environmental factor in cattle production. In this study, a multivariate reaction norm model (MRNM) was used to assess if the random genetic and non-genetic (i.e.

Differential Gene Expression in Longissimus Dorsi Muscle of Hanwoo Steers-New Insight in Genes Involved in Marbling Development at Younger Ages.

The Korean Hanwoo breed possesses a high capacity to accumulate intramuscular fat, which is measured as a marbling score in the beef industry. Unfortunately, the development of marbling is not completely understood and the identification of differentially expressed genes at an early age is required to better understand this trait. In this study, we took muscle samples from 12 Hanwoo steers at the age of 18 and 30 months.