Defining a breeding objective for Nile tilapia that takes into account the diversity of smallholder production systems
Summary In general, livestock and fish farming systems in developing countries tend to be highly diverse in terms of agro‐ecological conditions and market orientation. There are no studies that have investigated if and how this diversity translates to varying preferences for breeding objective traits. This is particularly important for breeding programmes that are organized on a national level (e.g. government‐supported nucleus breeding programmes). The aim of this study was to investigate whether Nile tilapia farmers with diverse production systems and economic constraints have different preferences for breeding objec...
Source: Journal of Animal Breeding and Genetics - March 21, 2016 Category: Genetics & Stem Cells Authors: S.K. Omasaki, J.A.M Arendonk, A.K. Kahi, H. Komen Tags: Original Article Source Type: research

The use of coancestry based on shared segments for maintaining genetic diversity
This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 17, 2016 Category: Genetics & Stem Cells Authors: F. Gómez‐Romano, B. Villanueva, J. Sölkner, M.A.R. Cara, G. Mészáros, A.M. Pérez O'Brien, J. Fernández Tags: Original Article Source Type: research

Variation in the prion protein sequence in Dutch goat breeds
In this study, frequencies of the allelic variants of the PrP gene are determined for six goat breeds in the Netherlands. Overall frequencies in Dutch goats were determined from 768 brain tissue samples in 2005, 766 in 2008 and 300 in 2012, derived from random sampling for the national scrapie surveillance without knowledge of the breed. Breed specific frequencies were determined in the winter 2013/2014 by sampling 300 breeding animals from the main breeders of the different breeds. Detailed analysis of the scrapie‐resistant K222 haplotype was carried out in 2014 for 220 Dutch Toggenburger goats and in 2015 for 942 goats...
Source: Journal of Animal Breeding and Genetics - March 16, 2016 Category: Genetics & Stem Cells Authors: J.J. Windig, R.A.H. Hoving, J. Priem, A. Bossers, L.J.M. Keulen, J.P.M. Langeveld Tags: Original Article Source Type: research

Quantitative analysis of short‐ and long‐distance racing performance in young and adult horses and association analysis with functional candidate genes in Spanish Trotter horses
Summary The association of five candidate genes with sporting performance in young and adult Spanish Trotter horses (STHs) was performed according to a previous selection based on quantitative analysis of the trait time per kilometre (TPK). A total of 334 516 records of TPK from 5958 STHs were used to estimate the estimated breeding values (EBVs) at different age groups (young and adults horses) throughout the range of distances (1600–2700 m) using a bicharacter random regression model. The heritability estimated by distance ranged from 0.16 to 0.40, with a different range for the two age groups. Considering the animal...
Source: Journal of Animal Breeding and Genetics - March 16, 2016 Category: Genetics & Stem Cells Authors: S. Negro Rama, M. Valera, A. Membrillo, M.D. Gómez, M. Solé, A. Menendez‐Buxadera, G. Anaya, A. Molina Tags: Original Article Source Type: research

Promotion of alleles by genome editing in livestock breeding programmes
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 16, 2016 Category: Genetics & Stem Cells Authors: J.M. Hickey, C. Bruce, A. Whitelaw, G. Gorjanc Tags: Editorial Source Type: research

Is genomic selection now a mature technology?
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 16, 2016 Category: Genetics & Stem Cells Authors: I. Misztal Tags: Editorial Source Type: research

Quantitative analysis of short ‐ and long‐distance racing performance in young and adult horses and association analysis with functional candidate genes in Spanish Trotter horses
Summary The association of five candidate genes with sporting performance in young and adult Spanish Trotter horses (STHs) was performed according to a previous selection based on quantitative analysis of the trait time per kilometre (TPK). A total of 334 516 records of TPK from 5958 STHs were used to estimate the estimated breeding values (EBVs) at different age groups (young and adults horses) throughout the range of distances (1600–2700 m) using a bicharacter random regression model. The heritability estimated by distance ranged from 0.16 to 0.40, with a different range for the two age groups. Considering the animal...
Source: Journal of Animal Breeding and Genetics - March 15, 2016 Category: Genetics & Stem Cells Authors: S. Negro Rama, M. Valera, A. Membrillo, M.D. G ómez, M. Solé, A. Menendez‐Buxadera, G. Anaya, A. Molina Tags: Original Article Source Type: research

Evaluation of sire by environment interactions for growth rate and backfat depth using reaction norm models in pigs
Summary Reaction norm models for sires were used to evaluate genotype by environment interactions for lifetime average daily gain (ADG) and backfat depth (BF) in pigs recorded at 143 days. Data for ADG and BF were available for 265 103 pigs recorded in Australia between 2000 and 2010 in nine herds. The full data set and two subsets based on minimum numbers of progeny per sire of 50 and 100 were analysed. The environmental descriptor was quantified as least square means of herd‐by‐birth month (HBM) contemporary groups which varied from 540 to 738 g/day for ADG and from 8.2 to 13.8 mm for BF. Several models were eval...
Source: Journal of Animal Breeding and Genetics - March 14, 2016 Category: Genetics & Stem Cells Authors: L. Li, S. Hermesch Tags: Original Article Source Type: research

Genetic parameters for milk fatty acids, milk yield and quality traits of a Holstein cattle population reared under tropical conditions
Summary Information about genetic parameters is essential for selection decisions and genetic evaluation. These estimates are population specific; however, there are few studies with dairy cattle populations reared under tropical and sub‐tropical conditions. Thus, the aim was to obtain estimates of heritability and genetic correlations for milk yield and quality traits using pedigree and genomic information from a Holstein population maintained in a tropical environment. Phenotypic records (n = 36 457) of 4203 cows as well as the genotypes for 57 368 single nucleotide polymorphisms from 755 of these cows were used. C...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: J. Petrini, L.H.S. Iung, M.A.P. Rodriguez, M. Salvian, F. Pértille, G.A. Rovadoscki, L.D. Cassoli, L.L. Coutinho, P.F. Machado, G.R. Wiggans, G.B. Mourão Tags: Original Article Source Type: research

Selection against abdominal fat percentage may increase intramuscular fat content in broilers
Summary Excessive abdominal fat content (AFC) has negative impacts on feed efficiency and carcass quality. Unlike AFC, intramuscular fat content (IMFC) could be a favourable trait, which has a positive impact on meat quality. To meet consumers' needs, a long‐term goal of broiler breeders is to decrease AFC and improve the IMFC simultaneously. The current study was designed to investigate the relationship between AFC and IMFC and to compare IMFC, including the pectoral major muscle fat content (PIMFC) and intramuscular fat content of leg muscle (LIMFC), between two broiler lines divergently selected for abdominal fat perc...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: L. Leng, H. Zhang, J.Q. Dong, Z.P. Wang, X.Y. Zhang, S.Z. Wang, Z.P. Cao, Y.M. Li, H. Li Tags: Original Article Source Type: research

Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis
Summary The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed het...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: K. Wijnrocx, L. François, A. Stinckens, S. Janssens, N. Buys Tags: Original Article Source Type: research

Genomewide association study of immune traits in chicken F2 resource population
In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10−6) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10−5) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10−5) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven su...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: Y. Sun, Q. Li, Y. Hu, Y. Sun, R. Liu, M. Zheng, J. Wen, P. Li, L. Liu, G. Zhao Tags: Original Article Source Type: research

Accounting for genetic architecture in single‐ and multipopulation genomic prediction using weights from genomewide association studies in pigs
Summary We studied the effect of including GWAS results on the accuracy of single‐ and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: R. Veroneze, P.S. Lopes, M.S. Lopes, A.M. Hidalgo, S.E.F. Guimarães, B. Harlizius, E.F. Knol, J.A.M. Arendonk, F.F. Silva, J.W.M. Bastiaansen Tags: Original Article Source Type: research

Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers
Summary There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian ...
Source: Journal of Animal Breeding and Genetics - January 18, 2016 Category: Genetics & Stem Cells Authors: M. Heidaritabar, M.P.L. Calus, H‐J. Megens, A. Vereijken, M.A.M. Groenen, J.W.M. Bastiaansen Tags: Original Article Source Type: research

On genetic canalization, infinitesimal model and whole‐genome sequence data
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - January 14, 2016 Category: Genetics & Stem Cells Authors: J. Ødegård, T. Meuwissen Tags: Editorial Source Type: research