John Henshall
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View article: Classifying aneuploidy in genotype intensity data using deep learning
Classifying aneuploidy in genotype intensity data using deep learning Open
Aneuploidy is the loss or gain of one or more chromosomes. Although it is a rare phenomenon in liveborn individuals, it is observed in livestock breeding populations. These breeding populations are often routinely genotyped and the genotyp…
View article: 182. DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds
182. DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds Open
It is generally economically unviable to individually genotype large quantities of commercial crossbred broilers to predict purebred breeding values for crossbred performance. Pooling DNA of crossbreds with similar phenotypes, and genotypi…
View article: 435. Optimizing sampling strategies for sib test schemes in a broiler breeder program
435. Optimizing sampling strategies for sib test schemes in a broiler breeder program Open
In broiler breeding there is a known genotype by environment interaction for bodyweight measured in a bio-secure (BWB) or in a commercial environment (BWC), thus a sib test scheme to record and use BWC records is beneficial. This study est…
View article: Comparison of selective genotyping strategies in genomic selection programs for broilers using stochastic simulation
Comparison of selective genotyping strategies in genomic selection programs for broilers using stochastic simulation Open
Breeding programs using genomic information have become common in broilers. In broilers, the main traits for selection are body weight and feed efficiency. These traits are measured in both sexes and before sexual maturity. Thus, increases…
View article: Avian Primordial Germ Cells Are Bipotent for Male or Female Gametogenesis
Avian Primordial Germ Cells Are Bipotent for Male or Female Gametogenesis Open
In birds, males are the homogametic sex (ZZ) and females are the heterogametic sex (ZW). Here, we investigate the role of chromosomal sex and germ cell competition on avian germ cell differentiation. We recently developed genetically steri…
View article: Association analysis of loci implied in “buffering” epistasis
Association analysis of loci implied in “buffering” epistasis Open
The existence of buffering mechanisms is an emerging property of biological networks, and this results in the buildup of robustness through evolution. So far, there are no explicit methods to find loci implied in buffering mechanisms. Howe…
View article: Correction to: Validation of genomic predictions for body weight in broilers using crossbred information and considering breed-of-origin of alleles
Correction to: Validation of genomic predictions for body weight in broilers using crossbred information and considering breed-of-origin of alleles Open
Following publication of original article [1], we noticed that there was an error: Eq. (3) on page 5 is the genomic relationship matrix that
View article: Genetic parameters for body weight and different definitions of residual feed intake in broiler chickens
Genetic parameters for body weight and different definitions of residual feed intake in broiler chickens Open
Background The objectives of this study were to (1) simultaneously estimate genetic parameters for BW, feed intake (FI), and body weight gain (Gain) during a FI test in broiler chickens using multi-trait Bayesian analysis; (2) derive pheno…
View article: Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset Open
Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may incl…
View article: Association analysis of loci implied in “buffering” epistasis
Association analysis of loci implied in “buffering” epistasis Open
The existence of buffering mechanisms is an emerging property of biological networks, and this results in the possible existence of “buffering” loci, that would allow buildup of robustness through evolution. So far, there are no explicit m…
View article: MOESM2 of Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships
MOESM2 of Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships Open
Additional file 2. Estimates of variance components for CB performance of BW35 from models that either fit a single G matrix (GEN_CB), or that separately fit a genetic sire component and a genetic dam component with two BOA matrices.
View article: MOESM1 of Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships
MOESM1 of Estimating the purebred-crossbred genetic correlation of body weight in broiler chickens with pedigree or genomic relationships Open
Additional file 1. Estimates of variance components and purebred-crossbred genetic correlations of body weight around 7 (BW7) and 35Â days (BW35) for four models. Description: Estimates of variance components are presented for each purebre…
View article: Estimating the genetic merit of sires by using pooled DNA from progeny of undetermined pedigree
Estimating the genetic merit of sires by using pooled DNA from progeny of undetermined pedigree Open
Genotyping of DNA from pooled biological samples offers a cheap method to link phenotypic information from commercial production animals to the breeding population and can be turned into information on the genetic value of stud sires for t…
View article: Evaluation of non-additive genetic variation in feed-related traits of broiler chickens
Evaluation of non-additive genetic variation in feed-related traits of broiler chickens Open
Genome-wide association mapping and genomic predictions of phenotype of individuals in livestock are predominately based on the detection and estimation of additive genetic effects. Non-additive genetic effects are largely ignored. Studies…