Journal of Animal Breeding and Genetics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

The biodiversity and genetic structure of Balearic sheep breeds
Summary The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was foun...
Source: Journal of Animal Breeding and Genetics - March 31, 2015 Category: Genetics & Stem Cells Authors: A.L. Pons, V. Landi, A. Martinez, J.V. Delgado Tags: Original Article Source Type: research

Quantitative genetics of disease traits
Summary John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James’ most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this r...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: N.R. Wray, P.M. Visscher Tags: Invited Review Source Type: research

Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits
Summary Linkage disequilibrium (LD) influences the genetic variation in a quantitative trait contributed by two or more loci, with positive LD increasing the variance. The magnitude of LD also affects the relative magnitude of dominance and epistatic variation. We quantify the extent of the non‐additive variance expected within populations, deriving analytical expressions for simple models and using numerical simulation in finite population more generally. As LD generates non‐independence among loci, a simple partition into additive, dominance and epistatic components is not possible, so we merely distinguish between a...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: W.G. Hill, A. Mäki‐Tanila Tags: Original Article Source Type: research

Some aspects of design and analysis of selection programmes in aquaculture species
In this study, we focus on a few aspects of aquaculture genetics to which Professor James made substantial contributions. His outstanding ability to comprehend, clarify and simplify complex problems with easy‐to‐understand mathematical derivations is clearly demonstrated in the areas of large‐scale strain comparisons, genotype‐by‐environment interactions (GxE), transformations and interpretation of selection response, as well as in the treatment of economic aspects of designing breeding programmes. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: Y. Li, R.W. Ponzoni Tags: Invited Review Source Type: research

Community‐based livestock breeding programmes: essentials and examples
Summary Breeding programmes described as community‐based (CBBP) typically relate to low‐input systems with farmers having a common interest to improve and share their genetic resources. CBBPs are more frequent with keepers of small ruminants, in particular smallholders of local breeds, than with cattle, pigs or chickens with which farmers may have easier access to alternative programmes. Constraints that limit the adoption of conventional breeding technologies in low‐input systems cover a range of organizational and technical aspects. The analysis of 8 CBBPs located in countries of Latin‐America, Africa and Asia hi...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: J.P. Mueller, B. Rischkowsky, A. Haile, J. Philipsson, O. Mwai, B. Besbes, A. Valle Zárate, M. Tibbo, T. Mirkena, G. Duguma, J. Sölkner, M. Wurzinger Tags: Invited Review Source Type: research

Comparison of breeding objectives across countries with application to sheep indexes in New Zealand and Ireland
The objective of this study was to describe the methodology to calculate correlations between national selection indexes and gain a deeper understanding of the factors influencing responses in economically important traits in both the New Zealand and Irish sheep industries. Moderate to strong correlations were calculated among indexes within and between countries, with the strongest correlation (0.86) between the New Zealand and Irish maternal indexes. In both countries, responses to selection in the maternal indexes are largely driven by growth traits; each index, however, has a different balance of traits. Ewe mature wei...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: B.F.S. Santos, N. McHugh, T.J. Byrne, D.P. Berry, P.R. Amer Tags: Original Article Source Type: research

How old are quantitative trait loci and how widely do they segregate?
Summary The mutations that cause genetic variation in quantitative traits could be old and segregate across many breeds or they could be young and segregate only within one breed. This has implications for our understanding of the evolution of quantitative traits and for genomic prediction to improve livestock. We investigated the age of quantitative trait loci (QTL) for milk production traits identified as segregating in Holstein dairy cattle. We use a multitrait method and found that six of 11 QTL also segregate in Jerseys. Variants identified as Holstein‐only QTL were fixed or rare [minor allele frequency (MAF) <�...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: K.E. Kemper, B.J. Hayes, H.D. Daetwyler, M.E. Goddard Tags: Original Article Source Type: research

Managing the rate of increase in average co‐ancestry in a rolling front tree breeding strategy
Summary In breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long‐ and short‐term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by ...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: R.J. Kerr, T.A. McRae, G.W. Dutkowski, B. Tier Tags: Invited Review Source Type: research

grain: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach
Summary GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the ‘classical’ inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC), defined here for the first time. AHC is defined as the numbe...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: R. Baumung, J. Farkas, D. Boichard, G. Mészáros, J. Sölkner, I. Curik Tags: Original Article Source Type: research

Genetic contributions and their optimization
Summary Genetic contributions were first formalized in 1958 by James and McBride (Journal of Genetics, 56, 55–62) and have since been shown to provide a unifying framework for theories of gain and inbreeding. As such they have underpinned the development of methods that provide the most effective combination of maximizing gain whilst managing inbreeding and loss of genetic variation. It is shown how this optimum contribution technology can be developed from theory and adapted to provide practical selection protocols for a wide variety of situations including overlapping generations and multistage selection. The natural d...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: J.A. Woolliams, P. Berg, B.S. Dagnachew, T.H.E. Meuwissen Tags: Invited Review Source Type: research

Quantitative genetics, spread of genes and genetic improvement: papers in honour of John James
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: F.W. Nicholas, C.M. Wade, L. Ollivier, J. Sölkner Tags: Introduction Source Type: research

A 57‐bp deletion in the ovine KAP6‐1 gene affects wool fibre diameter
In this study, we used polymerase chain reaction – single‐strand conformational polymorphism (PCR‐SSCP) analysis to screen for variation in a gene encoding the ovine HGT‐KAP6‐1 protein. We identified three gene variants (A, B and C). Variants A and B were similar to each other, with only three nucleotide differences occurring downstream of the coding sequence. However, variant C had a 57‐bp deletion that would notionally result in a loss of 19 amino acids in the protein. The presence of C was found to be associated with an increase in mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), coeffici...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: H. Zhou, H. Gong, S. Li, Y. Luo, J.G.H. Hickford Tags: Original Article Source Type: research

The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs
Summary The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotype...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: T. Aasmundstad, I. Andersen‐Ranberg, Ø. Nordbø, T. Meuwissen, O. Vangen, E. Grindflek Tags: Original Article Source Type: research

Combined use of principal component analysis and random forests identify population‐informative single nucleotide polymorphisms: application in cattle breeds
In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out‐of‐bag (OOB) error rate for both ranking met...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: F. Bertolini, G. Galimberti, D.G. Calò, G. Schiavo, D. Matassino, L. Fontanesi Tags: Original Article Source Type: research

Y‐chromosomal variation of local goat breeds of Turkey close to the domestication centre
In this study, the male‐specific region markers, sex‐determining region‐Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honamlı, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illus...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: B. Cinar Kul, N. Bilgen, J.A. Lenstra, O. Korkmaz Agaoglu, B. Akyuz, O. Ertugrul Tags: Original Article Source Type: research