Prediction Accuracy of Pedigree and Genomic Estimated Breeding Values over Generations in Layer Chickens

This study investigated the accuracy of estimated breeding values (EBV) over different training generations in layer chickens using pedigree and marker-based models. On average, the accuracy of EBV based on markers was higher than that based on pedigree. The accuracy of all methods increased with an increase in the number of generations in training data, but slightly dropped or remained even after including training generations far apart from validation

Evaluation of Egg Production in Layers Using Random Regression Models

The objectives of this study were to estimate genetic parameters for egg production over the age trajectory in three commercial layer breeding lines, which represent different biotypes for egg production, and to validate the use of breeding values for slope as a measure of persistency to be used in the selection program. Egg production data of over 26,000 layers per line from six consecutive generations were analyzed. Daily records were cumulated into biweekly periods. Data were analyzed with a random regression model with linear polynomials on period for random additive genetic and permanent environmental effects. In all lines, a nonzero genetic variance for mean and slope and a positive genetic correlation between mean and slope were estimated. Breeding values for slope well reflected the shape of the egg production curve and can be used to select for persistency of egg production. The model proposed in this study appealing for implementation in large and multiple populations under commercial conditions by breeding companies or other breeding organizations

Comparison of analyses of the QTLMAS XIV common dataset. I: genomic selection

Background - For the XIV QTLMAS workshop, a dataset for traits with complex genetic architecture has been simulated and released for analyses by participants. One of the tasks was to estimate direct genomic values for individuals without phenotypes. The aim of this paper was to compare results of different approaches used by the participants to calculate direct genomic values for quantitative trait (QT) and binary trait (BT). Results - Participants applied 26 approaches for QT and 15 approaches for BT. Accuracy for QT was between 0.26 and 0.89 for males and between 0.31 and 0.89 for females, and for BT ranged from 0.27 to 0.85. For QT, percentage of lost response to selection varied from 8% to 83%, whereas for BT the loss was between 15% and 71%. Conclusions - Bayesian model averaging methods predicted breeding values slightly better than GBLUP in a simulated data set. The methods utilizing genomic information performed better than traditional pedigree based BLUP analyses. Bivariate analyses was slightly advantageous over single trait for the same method. None of the methods estimated the non-additivity of QTL affecting the QT, which may be one of the constrains in accuracy observed in real data. -------------------------------------------------------------------------------

Egg Shell Quality Assessment–Do We Need Multiple Records?

The objective of this study was to estimate repeatability within and between ages for dynamic stiffnessin two lines of layer chickens in order to verify if multiple records are necessary to adequately describe a bird’s genetic merit for egg shell quality.Repeatability was low across ages to moderate within age,which suggests that for accurate evaluation eggs should be collected at different stages of laying cycle,with additional benefit from analyzing more than one egg within age

Genetics and Genomic Regions Affecting Response to Newcastle Disease Virus Infection under Heat Stress in Layer Chickens.

Newcastle disease virus (NDV) is a highly contagious avian pathogen that poses a tremendous threat to poultry producers in endemic zones due to its epidemic potential. To investigate host genetic resistance to NDV while under the effects of heat stress, a genome-wide association study (GWAS) was performed on Hy-Line Brown layer chickens that were challenged with NDV while under high ambient temperature to identify regions associated with host viral titer, circulating anti-NDV antibody titer, and body weight change. A single nucleotide polymorphism (SNP) on chromosome 1 was associated with viral titer at two days post-infection (dpi), while 30 SNPs spanning a quantitative trait loci (QTL) on chromosome 24 were associated with viral titer at 6 dpi. Immune related genes, such as CAMK1d and CCDC3 on chromosome 1, associated with viral titer at 2 dpi, and TIRAP, ETS1, and KIRREL3, associated with viral titer at 6 dpi, were located in two QTL regions for viral titer that were identified in this study. This study identified genomic regions and candidate genes that are associated with response to NDV during heat stress in Hy-Line Brown layer chickens. Regions identified for viral titer on chromosome 1 and 24, at 2 and 6 dpi, respectively, included several genes that have key roles in regulating the immune response

Juvenile IGF-I: An Early Bio-marker for Feed Efficiency in Pigs

At Iowa State University, purebred Yorkshire pigs have been divergently selected for increased and decreased feed efficiency based on residual feed intake for ten generations. In this study, juvenile IGF-I serum concentrations were measured in these divergently selected lines, with the goal of validating juvenile IGF-I as an early blood bio-marker to help select young piglets for later feed efficiency performance. Previous findings (Bunter et al., 2002, 2005, 2010) and this validation study support that lower juvenile IGF-I concentration in piglets is genetically correlated with increased grow-finish feed efficiency. IGF-I concentration is a moderately heritable trait that is more cost and time effective to measure than feed intake and feed efficiency. These characteristics make IGF-I a useful bio-marker for feed efficiency in swine

Genetic relationships among time of egg formation, clutch traits and traditional selection traits in laying hens

In a population of Rhode Island White hens heritability of egg formation, clutch characters and traditional selection traits as well as the genetic and phenotypic correlations between them were estimated via multitrait animal model. Over 1300 birds and about 4000 birds were recorded in two consecutive generations for oviposition time and traditional traits, respectively. The heritability estimates obtained for classical selection criteria: age at first egg (h2=0.42), egg weight (h2=0.50) and body weight (h2=0.42) were considerably higher than those for egg production traits: initial egg production (h2=0.22), clutch traits (h2 between 0.11 and 0.23) and oviposition time (h2 between 0.13 and 0.19). Both genetic and phenotypic correlations between clutch traits and traditional selection traits were low, except for initial egg production and maximal clutch length (rg=0.40 and rp=0.38). As expected, negative correlations were registered for number of clutches and average clutch length. It indicates an opportunity of selection aimed at improvement of egg production persistence by an increase in the average clutch size. Oviposition time was favourably correlated with traditional selection criteria

Cathepsin mRNA level in bovine cumulus cells fails to be a good marker of oocyte quality

Cathepsins (CTS) are lysosomal cysteine proteinases, of which elevated transcript content is attributed to the reduced quality of oocytes. The aim of this study was to investigate whether transcript content of three CTS genes in cumulus cells (CC) may be related to oocyte quality. The relationships between mRNA content of CTS genes in CC, the fatty acids profile in follicular fluid (FF) and selected quality traits of the corresponding oocyte (COC morphology, follicle diameter, mtDNA copy number) were investigated. Although an increased RA of the CTSB and the CTSK genes was accompanied by inferior COC morphology, it was also correlated with a higher mtDNA copy number in the oocyte and an increased content of C18.3n3 and n3 in FF. The last two traits were attributed to better quality oocytes, which contrasts with the high RA of the CTS genes. In conclusion, elevated transcript levels of CTS genes within CC are of limited value as an indicator of reduced quality in bovine oocytes. We suggest that the possible reason for the ambiguity of the obtained data could be the origin of cumulus cells within the COC, which may prove to be crucial for this type of studies

A biphasic curve for modeling, classifying, and predicting egg production in single cycle and molted flocks

Egg production on a flock level can be summarized into several phases determined by biology of individual birds: rapid increase in production reflecting achieving sexual maturity, peak production related to maximum laying potential, followed by gradual decrease in the rate of lay as the birds age. In 1989 Yang et al. proposed a mathematical model (modified compartmental model) to describe this process. In this study a biphasic modified compartmental model was proposed for modeling, classifying, and predicting egg production in single cycle and molted flocks. Goodness-of-fit was high for both single cycle (average R2 = 0.99) and molted flocks (average R2 = 0.97), suggesting that the model could be used for benchmarking molted flocks. The difference in R2 between the biphasic model and the model used by Yang et al in 1989 can be used to differentiate between single cycle and molted flocks. The biphasic model was shown to predict future records well up to 8 wk in advance, but as with any regression model, caution is recommended when predicting records outside of the observed age range