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Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account
This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions...
Source: Journal of Animal Breeding and Genetics - July 27, 2016 Category: Genetics & Stem Cells Authors: B. Hulsegge, M.P.L. Calus, J.K. Oldenbroek, J.J. Windig Tags: Original Article Source Type: research

Risk aversion affects economic values of blue fox breeding scheme
Summary The profit and production of an average Finnish blue fox farm was simulated using a deterministic bio‐economic farm model. Risk was included using Arrow‐Prat absolute risk aversion coefficient and profit variance. Risk‐rated economic values were calculated for pregnancy rate, litter loss, litter size, pelt size, pelt quality, pelt colour clarity, feed efficiency and eye infection. With high absolute risk aversion, economic values were lower than with low absolute risk aversion. Economic values were highest for litter loss (18.16 and 26.42 EUR), litter size (13.27 and 19.40 EUR), pregnancy (11.99 and 18.39 EUR...
Source: Journal of Animal Breeding and Genetics - July 19, 2016 Category: Genetics & Stem Cells Authors: J. Peura, R. Kempe, I. Strandén, L. Rydhmer Tags: Original Article Source Type: research

Kalle Maijala 1927 –2016
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 14, 2016 Category: Genetics & Stem Cells Authors: Asko M äki‐Tanila Tags: Obituary Source Type: research

Double ‐decker ark of animal breeds
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 14, 2016 Category: Genetics & Stem Cells Authors: D. Martin ‐Collado Tags: Book Review Source Type: research

Kalle Maijala 1927–2016
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 14, 2016 Category: Genetics & Stem Cells Authors: Asko Mäki‐Tanila Tags: Obituary Source Type: research

Double‐decker ark of animal breeds
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 14, 2016 Category: Genetics & Stem Cells Authors: D. Martin‐Collado Tags: Book Review Source Type: research

ICQG 5 on Madison's Isthmus links genomics and statistics of complex traits
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 14, 2016 Category: Genetics & Stem Cells Authors: Henner Simianer, Peter Sørensen Tags: Editorial Source Type: research

Use of high ‐density SNP data to identify patterns of diversity and signatures of selection in broiler chickens
Summary The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high‐density SNP data from a broiler chicken line to detect low‐diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity i...
Source: Journal of Animal Breeding and Genetics - June 28, 2016 Category: Genetics & Stem Cells Authors: J.J. Stainton, B. Charlesworth, C.S. Haley, A. Kranis, K. Watson, P. Wiener Tags: Original Article Source Type: research

An evaluation of alternative selection indexes for a non ‐linear profit trait approaching its economic optimum
This study used simulation to evaluate the performance of alternative selection index configurations in the context of a breeding programme where a trait with a non‐linear economic value is approaching an economic optimum. The simulation used a simple population structure that approximately mimics selection in dual purpose sheep flocks in New Zealand (NZ). In the NZ dual purpose sheep population, number of lambs born is a genetic trait that is approaching an economic optimum, while genetically correlated growth traits have linear economic values and are not approaching any optimum. The predominant view among theoretical ...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: D. Martin ‐Collado, T.J. Byrne, B. Visser, P.R. Amer Tags: Original Article Source Type: research

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers
In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: M. Heidaritabar, A. Wolc, J. Arango, J. Zeng, P. Settar, J.E. Fulton, N.P. O'Sullivan, J.W.M. Bastiaansen, R.L. Fernando, D.J. Garrick, J.C.M. Dekkers Tags: Original Article Source Type: research

Use of high‐density SNP data to identify patterns of diversity and signatures of selection in broiler chickens
Summary The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high‐density SNP data from a broiler chicken line to detect low‐diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity i...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: J.J. Stainton, B. Charlesworth, C.S. Haley, A. Kranis, K. Watson, P. Wiener Tags: Original Article Source Type: research

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?
Summary In the last decades, several endangered breeds of livestock species have been re‐established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO‐recommended microsatellites of these landraces and three phenotypically similar Nordic‐type landraces and compared these breeds with central European, Mediterranean and south‐west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south‐west Asian...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: J.A. Lenstra, J. Tigchelaar, I. Biebach, , J.H. Hallsson, J. Kantanen, V.H. Nielsen, F. Pompanon, S. Naderi, H.‐R. Rezaei, N. Sæther, O. Ertugrul, C. Grossen, G. Camenisch, M. Vos‐Loohuis, M. Straten, E.A. Poel, J. Windig, K. Oldenbroek Tags: Original Article Source Type: research

Genome wide association study on beef production traits in Marchigiana cattle breed
Summary A genomewide association study was carried out on a sample of Marchigiana breed cattle to detect markers significantly associated with carcass and meat traits. Four hundred and nine young bulls from 117 commercial herds were genotyped by Illumina 50K BeadChip assay. Eight growth and carcass traits (average daily gain, carcass weight, dressing percentage, body weight, skin weight, shank circumference, head weight and carcass conformation) and two meat quality traits (pH at slaughter and pH 24 h after slaughter) were measured. Data were analysed with a linear mixed model that included fixed effects of herd, slaughte...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: S. Sorbolini, S. Bongiorni, M. Cellesi, G. Gaspa, C. Dimauro, A. Valentini, N.P.P. Macciotta Tags: Original Article Source Type: research

Traditional livestock breeding practices of men and women Somali pastoralists: trait preferences and selection of breeding animals
Summary Somalia, one of the world's poorest countries, has livestock as the mainstay of the economy, with an estimated 65% of the population engaged in the livestock sector. This paper presents a gendered study on the traditional livestock breeding practices of Somali pastoralists for camels, cattle, sheep and goats, with a focus on documenting livestock traits of importance, the criteria used to select male breeding animals and the criteria used to cull female breeding animals. Data for the study were obtained by performing participatory rural appraisals (PRAs) with separate male and female pastoral groups from 20 settlem...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: K. Marshall, N. Mtimet, F. Wanyoike, N. Ndiwa, H. Ghebremariam, L. Mugunieri, R. Costagli Tags: Original Article Source Type: research

Prediction of genetic gain in finite populations with heterogeneous predicted breeding values accuracies
Summary The algebraic expression of the genetic selection differential (expected genetic superiority of breeders after a selection on their Predicted Breeding Values) was derived when a limited number of individuals were selected from a limited sample of candidates on the basis of their predicted genetic value, with heterogeneous reliabilities. A formula is proposed for situations in which these reliabilities can be clustered in a few classes. We show that the expected genetic selection differential increases with the number of classes, the mean reliability being constant. In the panel of cases simulated, this increase rea...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: J.‐M. Elsen Tags: Original Article Source Type: research

An evaluation of alternative selection indexes for a non‐linear profit trait approaching its economic optimum
This study used simulation to evaluate the performance of alternative selection index configurations in the context of a breeding programme where a trait with a non‐linear economic value is approaching an economic optimum. The simulation used a simple population structure that approximately mimics selection in dual purpose sheep flocks in New Zealand (NZ). In the NZ dual purpose sheep population, number of lambs born is a genetic trait that is approaching an economic optimum, while genetically correlated growth traits have linear economic values and are not approaching any optimum. The predominant view among theoretical ...
Source: Journal of Animal Breeding and Genetics - June 1, 2016 Category: Genetics & Stem Cells Authors: D. Martin‐Collado, T.J. Byrne, B. Visser, P.R. Amer Tags: Original Article Source Type: research

Analysis of competition performance in dressage and show jumping of Dutch Warmblood horses
Summary Most Warmblood horse studbooks aim to improve the performance in dressage and show jumping. The Dutch Royal Warmblood Studbook (KWPN) includes the highest score achieved in competition by a horse to evaluate its genetic ability of performance. However, the records collected during competition are associated with some aspects that might affect the quality of the genetic evaluation based on these records. These aspects include the influence of rider, censoring and preselection of the data. The aim of this study was to quantify the impact of rider effect, censoring and preselection on the genetic analysis of competiti...
Source: Journal of Animal Breeding and Genetics - May 30, 2016 Category: Genetics & Stem Cells Authors: G. Rovere, B.J. Ducro, J.A.M. Arendonk, E. Norberg, P. Madsen Tags: Original Article Source Type: research

Inbreeding depression in Zebu cattle traits
Summary The productivity of herds may be negatively affected by inbreeding depression, and it is important to know how intense is this effect on the livestock performance. We performed a comprehensive analysis involving five Zebu breeds reared in Brazil to estimate inbreeding depression in productive and reproductive traits. Inbreeding depression was estimated for 13 traits by including the individual inbreeding rate as a linear covariate in the standard genetic evaluation models. For all breeds and for almost all traits (no effect was observed on gestation length), the performance of the animals was compromised by an incr...
Source: Journal of Animal Breeding and Genetics - May 19, 2016 Category: Genetics & Stem Cells Authors: R.J. Pereira, M.L. Santana, D.R. Ayres, A.B. Bignardi, G.R.O. Menezes, L.O.C. Silva, C.H.C. Machado, L.A. Josahkian, L.G. Albuquerque Tags: Original Article Source Type: research

Genomic data and breeding value estimation in dairy cattle: theory, practice, problems
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 12, 2016 Category: Genetics & Stem Cells Authors: E.A. Mäntysaari, I. Strandén Tags: Editorial Source Type: research

Estimating heritability of wool shedding in a cross ‐bred ewe population
Summary Low wool prices and high production costs in sheep systems have resulted in the introduction of genotypes that shed wool into flocks to reduce shearing costs. Wool shedding occurs naturally in a few breeds and can be incorporated by cross‐breeding. The opportunity to enhance shedding through selection depends on the extent of genetic variability present. Genetic and environmental parameters for wool shedding for ewes from a three‐breed composite population were estimated using Bayesian inference. Data on 2025 cross‐bred ewes, including 3345 wool shedding scores (WS) and 1647 breeding weight (BW) records, were...
Source: Journal of Animal Breeding and Genetics - May 4, 2016 Category: Genetics & Stem Cells Authors: N. Vargas Jurado, K.A. Leymaster, L.A. Kuehn, R.M. Lewis Tags: Original Article Source Type: research

Polymorphism in exon 2 encoding the putative ligand binding pocket of the bovine insulin ‐like growth factor 1 receptor affects milk traits in four different cattle breeds
Summary As a member of the somatotropic axis, insulin‐like growth factor I receptor (IGF1R) seems to be a promising candidate gene. Two silent polymorphisms, identified by MspI and TaqI restriction enzymes, were selected within exon 2, encoding the majority of the putative ligand binding pocket. A total of 1169 cows of four pure breeds (Polish Holstein Friesian, Montbeliarde, Jersey and Holstein Friesian) were genotyped. The T (IGF1R/e2/MspI) and G (IGF1R/e2/TaqI) alleles were found to be prevalent. Three combinations of genotypes (TT/GG, TT/AG and CT/GG) were associated with the highest productivity (milk, protein and f...
Source: Journal of Animal Breeding and Genetics - April 26, 2016 Category: Genetics & Stem Cells Authors: M. Szewczuk Tags: Original Article Source Type: research

Relationship between calving difficulty and fertility traits in first ‐parity Iranian Holsteins under standard and recursive models
Summary The main objective of this study was to estimate the genetic and phenotypic relationships between calving difficulty (CD) and fertility traits, including success at first service (SF), number of inseminations to conception (INS), interval from calving to first service (CTFS), interval between first and last service (IFL) and days open (DO), in first‐parity Iranian Holsteins under standard (SMMs) and recursive (RMMs) mixed models. The data analysed in this paper included 29 950 records on CD and fertility traits, collected in the time period from 1995 to 2014 by the Animal Breeding and Improvement Center of Iran....
Source: Journal of Animal Breeding and Genetics - April 17, 2016 Category: Genetics & Stem Cells Authors: M.S. Mokhtari, M. Moradi Shahrbabak, A. Nejati Javaremi, G.J.M. Rosa Tags: Original Article Source Type: research

Relationship between calving difficulty and fertility traits in first‐parity Iranian Holsteins under standard and recursive models
Summary The main objective of this study was to estimate the genetic and phenotypic relationships between calving difficulty (CD) and fertility traits, including success at first service (SF), number of inseminations to conception (INS), interval from calving to first service (CTFS), interval between first and last service (IFL) and days open (DO), in first‐parity Iranian Holsteins under standard (SMMs) and recursive (RMMs) mixed models. The data analysed in this paper included 29 950 records on CD and fertility traits, collected in the time period from 1995 to 2014 by the Animal Breeding and Improvement Center of Iran....
Source: Journal of Animal Breeding and Genetics - April 17, 2016 Category: Genetics & Stem Cells Authors: M.S. Mokhtari, M. Moradi Shahrbabak, A. Nejati Javaremi, G.J.M. Rosa Tags: Original Article Source Type: research

Estimating heritability of wool shedding in a cross‐bred ewe population
Summary Low wool prices and high production costs in sheep systems have resulted in the introduction of genotypes that shed wool into flocks to reduce shearing costs. Wool shedding occurs naturally in a few breeds and can be incorporated by cross‐breeding. The opportunity to enhance shedding through selection depends on the extent of genetic variability present. Genetic and environmental parameters for wool shedding for ewes from a three‐breed composite population were estimated using Bayesian inference. Data on 2025 cross‐bred ewes, including 3345 wool shedding scores (WS) and 1647 breeding weight (BW) records, were...
Source: Journal of Animal Breeding and Genetics - April 1, 2016 Category: Genetics & Stem Cells Authors: N. Vargas Jurado, K.A. Leymaster, L.A. Kuehn, R.M. Lewis Tags: Original Article Source Type: research

A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
Summary Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR‐O) or the base population (GVR‐B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD‐L). Estimators were evaluated for...
Source: Journal of Animal Breeding and Genetics - April 1, 2016 Category: Genetics & Stem Cells Authors: N.S. Forneris, J.P. Steibel, A. Legarra, Z.G. Vitezica, R.O. Bates, C.W. Ernst, A.L. Basso, R.J.C. Cantet Tags: Original Article Source Type: research

Polymorphism in exon 2 encoding the putative ligand binding pocket of the bovine insulin‐like growth factor 1 receptor affects milk traits in four different cattle breeds
Summary As a member of the somatotropic axis, insulin‐like growth factor I receptor (IGF1R) seems to be a promising candidate gene. Two silent polymorphisms, identified by MspI and TaqI restriction enzymes, were selected within exon 2, encoding the majority of the putative ligand binding pocket. A total of 1169 cows of four pure breeds (Polish Holstein Friesian, Montbeliarde, Jersey and Holstein Friesian) were genotyped. The T (IGF1R/e2/MspI) and G (IGF1R/e2/TaqI) alleles were found to be prevalent. Three combinations of genotypes (TT/GG, TT/AG and CT/GG) were associated with the highest productivity (milk, protein and f...
Source: Journal of Animal Breeding and Genetics - April 1, 2016 Category: Genetics & Stem Cells Authors: M. Szewczuk Tags: Original Article Source Type: research

Accuracy of genomic prediction of purebreds for cross bred performance in pigs
The objective of our study was to assess empirically the predictive ability (accuracy) of direct genomic values of PB for CB performance across two traits using CB and PB genomic and phenotypic data. We studied three scenarios in which genetic merit was predicted within each population, and four scenarios where PB genetic merit for CB performance was predicted based on either CB or a PB training data. Accuracy of prediction of PB genetic merit for CB performance based on CB training data ranged from 0.23 to 0.27 for gestation length (GLE), whereas it ranged from 0.11 to 0.22 for total number of piglets born (TNB). When bas...
Source: Journal of Animal Breeding and Genetics - April 1, 2016 Category: Genetics & Stem Cells Authors: A.M. Hidalgo, J.W.M. Bastiaansen, M.S. Lopes, M.P.L. Calus, D.J. Koning Tags: Original Article Source Type: research

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 16, 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

Genomic prediction of growth in pigs based on a model including additive and dominance effects
Summary Independent of whether prediction is based on pedigree or genomic information, the focus of animal breeders has been on additive genetic effects or ‘breeding values’. However, when predicting phenotypes rather than breeding values of an animal, models that account for both additive and dominance effects might be more accurate. Our aim with this study was to compare the accuracy of predicting phenotypes using a model that accounts for only additive effects (MA) and a model that accounts for both additive and dominance effects simultaneously (MAD). Lifetime daily gain (DG) was evaluated in three pig populations (...
Source: Journal of Animal Breeding and Genetics - December 16, 2015 Category: Genetics & Stem Cells Authors: M.S. Lopes, J.W.M. Bastiaansen, L. Janss, E.F. Knol, H. Bovenhuis Tags: Original Article Source Type: research

Growth traits of four maternal lines of rabbits founded on different criteria: comparisons at foundation and at last periods after selection
The objective was to compare growth traits in four maternal lines of rabbits (A, V, H and LP), with the aim of understanding the consequence of the different foundation and selection processes on the growth performance of the lines. The lines are currently in the 43th, 38th, 22th and 8th generations, respectively. Two comparisons were performed. One compared the values of the lines at their foundation, using the complete data set, the full pedigree and a two‐trait analysis, including data on the selection criteria, litter size. The other comparisons were done during the last period when all the lines were housed together...
Source: Journal of Animal Breeding and Genetics - December 16, 2015 Category: Genetics & Stem Cells Authors: C. Mínguez, J.P. Sanchez, A.G. EL Nagar, M. Ragab, M. Baselga Tags: Original Article Source Type: research

A combined coalescence gene‐dropping tool for evaluating genomic selection in complex scenarios (ms2gs)
We present ms2gs, a combined coalescence – gene dropping (i.e. backward–forward) simulator for complex traits. It therefore aims at combining the advantages of both approaches. It is primarily conceived for very short term, recent scenarios such as those that are of interest in animal and plant breeding. It is very flexible in terms of defining QTL architecture and SNP ascertainment bias, and it allows for easy modelling of alternative markers such as RADs. It can use real sequence or chip data or generate molecular polymorphisms via the coalescence. It can generate QTL conditional on extant molecular information, such...
Source: Journal of Animal Breeding and Genetics - December 1, 2015 Category: Genetics & Stem Cells Authors: M. Pérez‐Enciso, A. Legarra Tags: Original Article Source Type: research

Behavioural linear standardized scoring system of the Lidia cattle breed by testing in herd: estimation of genetic parameters
Summary Docility is very important for cattle production, and many behavioural tests to measure this trait have been developed. However, very few objective behavioural tests to measure the opposite approach ‘aggressive behaviour’ have been described. Therefore, the aim of this work was to validate in the Lidia cattle breed a behavioural linear standardized scoring system that measure the aggressiveness and enable genetic analysis of behavioural traits expressing fearless and fighting ability. Reproducibility and repeatability measures were calculated for the 12 linear traits of this scoring system to assess its accurac...
Source: Journal of Animal Breeding and Genetics - December 1, 2015 Category: Genetics & Stem Cells Authors: R. Pelayo, M. Solé, M.J. Sánchez, A. Molina, M. Valera Tags: Original Article Source Type: research

Identification of genome‐wide selection signatures in the Limousin beef cattle breed
Summary The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth (GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation (CAPN1 and CAPN5) were annotated. Noticeable clusters of selection foo...
Source: Journal of Animal Breeding and Genetics - November 27, 2015 Category: Genetics & Stem Cells Authors: A. Gurgul, T. Szmatoła, K. Ropka‐Molik, I. Jasielczuk, K. Pawlina, E. Semik, M. Bugno‐Poniewierska Tags: Original Article Source Type: research

Identification of genome ‐wide selection signatures in the Limousin beef cattle breed
Summary The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth (GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation (CAPN1 and CAPN5) were annotated. Noticeable clusters of selection foo...
Source: Journal of Animal Breeding and Genetics - November 26, 2015 Category: Genetics & Stem Cells Authors: A. Gurgul, T. Szmato ła, K. Ropka‐Molik, I. Jasielczuk, K. Pawlina, E. Semik, M. Bugno‐Poniewierska Tags: Original Article Source Type: research

An efficient empirical Bayes method for genomewide association studies
Summary Linear mixed model (LMM) is one of the most popular methods for genomewide association studies (GWAS). Numerous forms of LMM have been developed; however, there are two major issues in GWAS that have not been fully addressed before. The two issues are (i) the genomic background noise and (ii) low statistical power after Bonferroni correction. We proposed an empirical Bayes (EB) method by assigning each marker effect a normal prior distribution, resulting in shrinkage estimates of marker effects. We found that such a shrinkage approach can selectively shrink marker effects and reduce the noise level to zero for majo...
Source: Journal of Animal Breeding and Genetics - November 19, 2015 Category: Genetics & Stem Cells Authors: Q. Wang, J. Wei, Y. Pan, S. Xu Tags: Original Article Source Type: research

Modelling repeated competition records in genetic evaluations of Danish sport horses
Summary Genetic evaluations of sport performance typically consider competition records of ranking points in each competition, accumulated lifetime points or annual earnings. Repeated observations have the advantage of allowing for adjustment of effects associated with each competition such as rider experience, judge and competing horses, but also demands more computer capacity than single‐trait records, which could prohibit multiple‐trait evaluations. The aim of the study was to compare CPU times, estimated breeding values (EBVs), reliabilities and model prediction abilities when modelling repeated competition ranking...
Source: Journal of Animal Breeding and Genetics - November 18, 2015 Category: Genetics & Stem Cells Authors: L. Jönsson, P. Madsen, T. Mark Tags: Original Article Source Type: research