Genetic Analysis of the Impact of Heat Stress on Fertility Traits in Dairy Cows in the Netherlands.

This study aimed to use Temperature-Humidity Index (THI) as an indicator for assessing heat stress conditions for fertility traits in the Holstein dairy cattle breed in the Netherlands. Data from artificial insemination and calving events of 416,814 first-parity cows from the Netherlands were used, considering different THI definitions based on different numbers of days before and after artificial insemination events. To achieve our aim, we investigated first, at population level, the relationship between different THI definitions and 4 fertility traits: conception rate, interval calving to first insemination, interval first to last insemination, and calving interval.

Breeding for resilience in finishing pigs can decrease tail biting, lameness and mortality.

Background: Previous research showed that deviations in longitudinal data are heritable and can be used as a proxy for pigs' general resilience. However, only a few studies investigated the relationship between these resilience traits and other traits related to resilience and welfare. Therefore, this study investigated the relationship between resilience traits derived from deviations in longitudinal data and traits related to animal resilience, health and welfare, such as tail and ear biting wounds, lameness and mortality.

The genetics of resilience and its relationships with egg production traits and antibody traits in chickens.

Background: Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits.

Multienvironment genomic prediction in tetraploid potato.

Multienvironment genomic prediction was applied to tetraploid potato using 147 potato varieties, tested for 2 years, in 3 locations representative of 3 distinct regions in Europe. Different prediction scenarios were investigated to help breeders predict genotypic performance in the regions from one year to the next, for genotypes that were tested this year (scenario 1), as well as new genotypes (scenario 3). In scenario 2, we predicted new genotypes for any one of the 6 trials, using all the information that is available.

A promising resilience parameter for breeding: the use of weight and feed trajectories in growing pigs.

Background: Increasing resilience is a priority in modern pig breeding. Recent research shows that general resilience can be quantified via variability in longitudinal data. The collection of such longitudinal data on weight, feed intake and feeding behaviour in pigs has been facilitated by the development of technologies such as automated feeding stations.

Predicting nitrogen use efficiency, nitrogen loss and dry matter intake of individual dairy cows in late lactation by including mid-infrared spectra of milk samples.

Background: Nitrate leaching to groundwater and surface water and ammonia volatilization from dairy farms have negative impacts on the environment. Meanwhile, the increasing demand for dairy products will result in more pollution if N losses are not controlled. Therefore, a more efficient, and environmentally friendly production system is needed, in which nitrogen use efficiency (NUE) of dairy cows plays a key role.

Research Note: Genome-wide association study for natural antibodies and resilience in a purebred layer chicken line.

Resilience is the capacity of an animal to be minimally affected by disturbances or rapidly return to the state pertained before exposure to a disturbance. Resilience indicators can be estimated from longitudinal production data, using deviations of observed from expected production levels. One component of resilience is disease resilience, which includes general disease resistance.

Capturing indirect genetic effects on phenotypic variability: Competition meets canalization.

Phenotypic variability of a genotype is relevant both in natural and domestic populations. In the past two decades, variability has been studied as a heritable quantitative genetic trait in its own right, often referred to as inherited variability or environmental canalization. So far, studies on inherited variability have only considered genetic effects of the focal individual, that is, direct genetic effects on inherited variability.

Using egg production longitudinal recording to study the genetic background of resilience in purebred and crossbred laying hens.

Background: There is growing interest in using genetic selection to obtain more resilient farm animals (i.e. that are minimally affected by disturbances or rapidly recover from them).

Development of resilience indicator traits based on daily step count data for dairy cattle breeding.

Background: Resilient animals are minimally affected by disturbances, such as diseases and heat stress, and quickly recover. Daily activity data can potentially indicate resilience, because resilient animals likely keep variations due to disturbances that threat animal homeostasis at a low magnitude. We used daily step count of cows to define resilience indicators based on theory, exploratory analysis and literature, and then investigated if they can be used to genetically improve resilience by estimating heritability and repeatability, and genetic associations with other resilience-related traits, i.

Training Set Construction for Genomic Prediction in Auto-Tetraploids: An Example in Potato.

Training set construction is an important prerequisite to Genomic Prediction (GP), and while this has been studied in diploids, polyploids have not received the same attention. Polyploidy is a common feature in many crop plants, like for example banana and blueberry, but also potato which is the third most important crop in the world in terms of food consumption, after rice and wheat. The aim of this study was to investigate the impact of different training set construction methods using a publicly available diversity panel of tetraploid potatoes.

Understanding the Effectiveness of Genomic Prediction in Tetraploid Potato.

Use of genomic prediction (GP) in tetraploid is becoming more common. Therefore, we think it is the right time for a comparison of GP models for tetraploid potato. GP models were compared that contrasted shrinkage with variable selection, parametric vs.

Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus).

Background: Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia).

Heritable variation in swimming performance in Nile tilapia (Oreochromis niloticus) and negative genetic correlations with growth and harvest weight.

Nile tilapia is predominantly produced in smallholder ponds without aeration. We hypothesize that Nile tilapia with high oxygen uptake efficiency (OUE) may perform better under these conditions than Nile tilapia with low OUE. Critical swimming speed (U, in cm s) is a potential indicator for OUE.

Genomic Breeding Programs Realize Larger Benefits by Cooperation in the Presence of Genotype × Environment Interaction Than Conventional Breeding Programs.

Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment.

Optimizing design to estimate genetic correlations between environments with common environmental effects.

Breeding programs for different species aim to improve performance by testing members of full-sib (FS) and half-sib (HS) families in different environments. When genotypes respond differently to changes in the environment, this is defined as genotype by environment (G × E) interaction. The presence of common environmental effects within families generates covariance between siblings, and these effects should be taken into account when estimating a genetic correlation.

Estimation of litter size variability phenotypes in Large White sows.

The objective of this study was to obtain new phenotypes of phenotypic variability for the total number born (TNB) in pigs using the residual variance of TNB. The analysis was based on 246,799 Large White litter observations provided by Topigs Norsvin. Three animal models were used to obtain estimates of residual variance for TNB: the basic model (BM) containing fixed effects of farm-year and season and random effects of animal and permanent environmental sow, the basic model with an additional fixed effect of parity (BMP) and a random regression model (RRM).

Body Weight Deviations as Indicator for Resilience in Layer Chickens.

Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to the state pertained before exposure to a disturbance. Less resilient animals are expected to be more susceptible to environmental perturbations, such as diseases, and will consequently show more and/or greater fluctuations in production than more resilient animals. Natural antibodies (NAb) are antibodies recognizing antigens without previous exposure to these, and are hypothesized to be an indication of general disease resistance.

Opportunities to Improve Resilience in Animal Breeding Programs.

Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to the state pertained before exposure to a disturbance. However, indicators for general resilience to environmental disturbances have not yet been defined, and perhaps therefore resilience is not yet included in breeding goals. The current developments on big data collection give opportunities to determine new resilience indicators based on longitudinal data, which can aid to incorporate resilience in animal breeding goals.

Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection.

Background: High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits.

Relationship Between the Estimated Breeding Values for Litter Traits at Birth and Ovarian and Embryonic Traits and Their Additive Genetic Variance in Gilts at 35 Days of Pregnancy.

We investigated (1) the relationship between the estimated breeding values (EBVs) for litter traits at birth and ovulation rate (OR), average corpora luteal weight, uterine length and embryonic survival and development traits in gilts at 35 days of pregnancy by linear regression, (2) the genetic variance of OR, average corpora lutea (CL) weight, uterine length and embryonic survival and development traits at 35 days of pregnancy, and (3) the genetic correlations between these traits. Landrace ( = 86) and Yorkshire × Landrace ( = 304) gilts were inseminated and slaughtered at 35 days of pregnancy. OR was assessed by dissection of the CL on both ovaries.

The impact of genome editing on the introduction of monogenic traits in livestock.

Background: Genome editing technologies provide new tools for genetic improvement and have the potential to become the next game changer in animal and plant breeding. The aim of this study was to investigate how genome editing in combination with genomic selection can accelerate the introduction of a monogenic trait in a livestock population as compared to genomic selection alone.

Methods: A breeding population was simulated under genomic selection for a polygenic trait.

Modelling the co-evolution of indirect genetic effects and inherited variability.

When individuals interact, their phenotypes may be affected not only by their own genes but also by genes in their social partners. This phenomenon is known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, however, competition not only affects trait levels of individuals, but also inflates variability of trait values among individuals.

Use of multi-trait and random regression models to identify genetic variation in tolerance to porcine reproductive and respiratory syndrome virus.

Background: A host can adopt two response strategies to infection: resistance (reduce pathogen load) and tolerance (minimize impact of infection on performance). Both strategies may be under genetic control and could thus be targeted for genetic improvement. Although there is evidence that supports a genetic basis for resistance to porcine reproductive and respiratory syndrome (PRRS), it is not known whether pigs also differ genetically in tolerance.