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Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie

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https://www.readbyqxmd.com/read/28994157/genome-wide-association-study-and-annotating-candidate-gene-networks-affecting-age-at-first-calving-in-nellore-cattle
#1
R R Mota, S E F Guimarães, M R S Fortes, B Hayes, F F Silva, L L Verardo, M J Kelly, C F de Campos, J D Guimarães, R R Wenceslau, J M Penitente-Filho, J F Garcia, S Moore
We performed a genome-wide mapping for the age at first calving (AFC) with the goal of annotating candidate genes that regulate fertility in Nellore cattle. Phenotypic data from 762 cows and 777k SNP genotypes from 2,992 bulls and cows were used. Single nucleotide polymorphism (SNP) effects based on the single-step GBLUP methodology were blocked into adjacent windows of 1 Megabase (Mb) to explain the genetic variance. SNP windows explaining more than 0.40% of the AFC genetic variance were identified on chromosomes 2, 8, 9, 14, 16 and 17...
October 9, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28960562/direct-and-maternal-additive-effects-are-not-the-main-determinants-of-iberian-piglet-perinatal-mortality
#2
M Muñoz, M C Rodríguez, L A García-Cortes, A González, J M García-Casco, L Silió
Data of 127,800 Iberian piglets were used to study genetic parameters of mortality at birth at the piglet level. These records proceed from three data sets: 4,987 litter of 2,156 sows of a dam line, 2,768 litter of 817 sows of a complete diallel cross between four Iberian strains and 7,153 litter of 2,113 sows of the Torbiscal composite line. Perinatal mortality was considered as a binary trait, and Bayesian threshold animal models were fitted to separately analyse the three data sets. The posterior means of direct heritability were 0...
September 28, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28940847/genetic-mapping-using-1-4m-snp-array-refined-loci-for-fatty-acid-composition-traits-in-chinese-erhualian-and-bamaxiang-pigs
#3
J Zhang, Y Zhang, H Gong, L Cui, T Huang, H Ai, J Ren, L Huang, B Yang
Chinese indigenous pigs display marked genetic and phenotypic differences compared with western commercial pigs. In this study, we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian (n = 331) and Bamaxiang (n = 315) pigs based on a customized 1.4 million SNP array. We identified a total of 64 significant associations for 20 fatty acid composition traits at the p-value threshold of 1 × 10(-6) among which 42 associations in low linkage disequilibrium (r(2 ) < ...
September 20, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28940585/correction-for-adipocyte-size-and-number-in-the-analysis-of-differences-in-gene-expression-in-fat-tissues
#4
L Alfonso
In gene expression studies of candidate genes related to fat deposition, accounting for differences in cell number using reference genes could be not sufficient when cell transcriptional levels are related to cell size, or the tissues are constituted by different types of cells where candidate genes could be differentially expressed. In these situations, mixed model can be applied giving the possibility to take into account the effects of adipocyte size and number on gene expression. The inclusion in the models of analysis of adipocyte size and number, previously estimated taking into account the possible bimodality of size distribution, reduces the rate of false positives in the expression of candidate genes, although, as expected, more powerful designs are needed to detect true differences...
September 20, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28833593/implications-of-snp-weighting-on-single-step-genomic-predictions-for-different-reference-population-sizes
#5
D A L Lourenco, B O Fragomeni, H L Bradford, I R Menezes, J B S Ferraz, I Aguilar, S Tsuruta, I Misztal
We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single-step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G)...
August 22, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28833716/genomic-estimation-of-additive-and-dominance-effects-and-impact-of-accounting-for-dominance-on-accuracy-of-genomic-evaluation-in-sheep-populations
#6
N Moghaddar, J H J van der Werf
The objectives of this study were to estimate the additive and dominance variance component of several weight and ultrasound scanned body composition traits in purebred and combined cross-bred sheep populations based on single nucleotide polymorphism (SNP) marker genotypes and then to investigate the effect of fitting additive and dominance effects on accuracy of genomic evaluation. Additive and dominance variance components were estimated in a mixed model equation based on "average information restricted maximum likelihood" using additive and dominance (co)variances between animals calculated from 48,599 SNP marker genotypes...
August 17, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28804930/gaussian-covariance-graph-models-accounting-for-correlated-marker-effects-in-genome-wide-prediction
#7
C A Martínez, K Khare, S Rahman, M A Elzo
Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G...
August 13, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28748554/estimation-of-inbreeding-depression-on-female-fertility-in-the-finnish-ayrshire-population
#8
K Martikainen, A M Tyrisevä, K Matilainen, J Pösö, P Uimari
Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (FPH ), runs of homozygosity (FROH ) and pedigree (FPED ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows...
July 27, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28876507/revolutionary-leaps-in-the-development-of-agriculture
#9
EDITORIAL
J J Lauvergne
No abstract text is available yet for this article.
October 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28699266/can-we-make-genomic-selection-100-accurate
#10
EDITORIAL
M E Goddard
No abstract text is available yet for this article.
August 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28695620/correlated-response-in-litter-size-components-in-rabbits-selected-for-litter-size-variability
#11
M J Argente, E W Calle, M L García, A Blasco
A divergent selection experiment for the environmental variability of litter size (Ve) over seven generations was carried out in rabbits at the University Miguel Hernández of Elche. The Ve was estimated as the phenotypic variance within the female, after correcting for year-season and parity-lactation status. The aim of this study was to analyse the correlated responses to selection in litter size components. The ovulation rate (OR) and number of implanted embryos (IE) in females were measured by laparoscopy at 12 day of the second gestation...
July 11, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28691230/contemporary-group-estimates-adjusted-for-climatic-effects-provide-a-finer-definition-of-the-unknown-environmental-challenges-experienced-by-growing-pigs
#12
S Z Y Guy, L Li, P C Thomson, S Hermesch
Environmental descriptors derived from mean performances of contemporary groups (CGs) are assumed to capture any known and unknown environmental challenges. The objective of this paper was to obtain a finer definition of the unknown challenges, by adjusting CG estimates for the known climatic effects of monthly maximum air temperature (MaxT), minimum air temperature (MinT) and monthly rainfall (Rain). As the unknown component could include infection challenges, these refined descriptors may help to better model varying responses of sire progeny to environmental infection challenges for the definition of disease resilience...
July 10, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28685498/role-of-inbreeding-depression-non-inbred-dominance-deviations-and-random-year-season-effect-in-genetic-trends-for-prolificacy-in-closed-rabbit-lines
#13
E N Fernández, J P Sánchez, R Martínez, A Legarra, M Baselga
In closed rabbit lines selected for prolificacy at the Polytechnic University of Valencia, genetic responses are predicted using BLUP. With a standard additive BLUP model and year-season (YS) effects fitted as fixed, genetic trends were overestimated compared to responses estimated using control populations obtained from frozen embryos. In these lines, there is a confounding between genetic trend, YS effects and inbreeding, and the role of dominance is uncertain. This is a common situation in data from reproductively closed selection lines...
July 6, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508489/prediction-of-whole-genome-risk-for-selection-and-management-of-hyperketonemia-in-holstein-dairy-cattle
#14
K A Weigel, R S Pralle, H Adams, K Cho, C Do, H M White
Hyperketonemia (HYK), a common early postpartum health disorder characterized by elevated blood concentrations of β-hydroxybutyrate (BHB), affects millions of dairy cows worldwide and leads to significant economic losses and animal welfare concerns. In this study, blood concentrations of BHB were assessed for 1,453 Holstein cows using electronic handheld meters at four time points between 5 and 18 days postpartum. Incidence rates of subclinical (1.2 ≤ maximum BHB ≤ 2.9 mmol/L) and clinical ketosis (maximum BHB ≥ 3...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508488/modelling-female-fertility-traits-in-beef-cattle-using-linear-and-non-linear-models
#15
H Naya, F Peñagaricano, J I Urioste
Female fertility traits are key components of the profitability of beef cattle production. However, these traits are difficult and expensive to measure, particularly under extensive pastoral conditions, and consequently, fertility records are in general scarce and somehow incomplete. Moreover, fertility traits are usually dominated by the effects of herd-year environment, and it is generally assumed that relatively small margins are kept for genetic improvement. New ways of modelling genetic variation in these traits are needed...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508487/accuracy-of-genomic-breeding-values-revisited-assessment-of-two-established-approaches-and-a-novel-one-to-determine-the-accuracy-in-two-step-genomic-prediction
#16
G Ni, S Kipp, H Simianer, M Erbe
Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality. In previous studies, several methods were proposed to assess the accuracy of GBV including methods using population parameters or parameters inferred from mixed-model equations...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508486/pedigree-based-estimation-of-covariance-between-dominance-deviations-and-additive-genetic-effects-in-closed-rabbit-lines-considering-inbreeding-and-using-a-computationally-simpler-equivalent-model
#17
E N Fernández, A Legarra, R Martínez, J P Sánchez, M Baselga
Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508485/-conversion-of-epistatic-into-additive-genetic-variance-in-finite-populations-and-possible-impact-on-long-term-selection-response
#18
W G Hill
The role of epistasis in understanding the genetic architecture and variation of quantitative traits and its role, if any, in artificial selection and livestock improvement more generally has a long and sometimes controversial history. Its presence has been clearly demonstrated in, for example, laboratory experiments, but the amount of variation it contributes is likely to be small in outbred populations. In a finite population, although additive x additive epistatic variance is lost by genetic drift, it also contributes by conversion to additive variance through drift sampling and therefore has a potential indirect role in medium and long-term selection response, with superficial similarity to and hard to distinguish from mutation...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508484/special-issue-quantitative-and-statistical-genetics-papers-in-honour-of-daniel-gianola
#19
EDITORIAL
H Simianer, G J M Rosa, A Mäki-Tanila
No abstract text is available yet for this article.
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508483/genomic-variance-estimates-with-or-without-disequilibrium-covariances
#20
C Lehermeier, G de Los Campos, V Wimmer, C-C Schön
Whole-genome regression methods are often used for estimating genomic heritability: the proportion of phenotypic variance that can be explained by regression on marker genotypes. Recently, there has been an intensive debate on whether and how to account for the contribution of linkage disequilibrium (LD) to genomic variance. Here, we investigate two different methods for genomic variance estimation that differ in their ability to account for LD. By analysing flowering time in a data set on 1,057 fully sequenced Arabidopsis lines with strong evidence for diversifying selection, we observed a large contribution of covariances between quantitative trait loci (QTL) to the genomic variance...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
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