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

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https://www.readbyqxmd.com/read/29178316/a-comparison-of-accuracy-validation-methods-for-genomic-and-pedigree-based-predictions-of-swine-litter-size-traits-using-large-white-and-simulated-data
#1
A M Putz, F Tiezzi, C Maltecca, K A Gray, M T Knauer
The objective of this study was to compare and determine the optimal validation method when comparing accuracy from single-step GBLUP (ssGBLUP) to traditional pedigree-based BLUP. Field data included six litter size traits. Simulated data included ten replicates designed to mimic the field data in order to determine the method that was closest to the true accuracy. Data were split into training and validation sets. The methods used were as follows: (i) theoretical accuracy derived from the prediction error variance (PEV) of the direct inverse (iLHS), (ii) approximated accuracies from the accf90(GS) program in the BLUPF90 family of programs (Approx), (iii) correlation between predictions and the single-step GEBVs from the full data set (GEBVFull ), (iv) correlation between predictions and the corrected phenotypes of females from the full data set (Yc ), (v) correlation from method iv divided by the square root of the heritability (Ych ) and (vi) correlation between sire predictions and the average of their daughters' corrected phenotypes (Ycs )...
November 27, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29164741/effects-of-breed-proportion-and-components-of-heterosis-for-semen-traits-in-a-composite-cattle-breed
#2
N Khayatzadeh, G Mészáros, Y T Utsunomiya, F Schmitz-Hsu, F Seefried, U Schnyder, M Ferenčaković, J F Garcia, I Curik, J Sölkner
The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds...
November 22, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29164684/bibi-bayesian-inference-of-breed-composition
#3
C A Martínez, K Khare, M A Elzo
The aim of this paper was to develop statistical models to estimate individual breed composition based on the previously proposed idea of regressing discrete random variables corresponding to counts of reference alleles of biallelic molecular markers located across the genome on the allele frequencies of each marker in the pure (base) breeds. Some of the existing regression-based methods do not guarantee that estimators of breed composition will lie in the appropriate parameter space, and none of them account for uncertainty about allele frequencies in the pure breeds, that is, uncertainty about the design matrix...
November 22, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29152841/adjusting-for-heterogeneity-of-experimental-data-in-genetic-evaluation-of-dry-matter-intake-in-dairy-cattle
#4
M E Uddin, T Meuwissen, R F Veerkamp
The objectives of the present study were (i) to find the best fitted model for repeatedly measured daily dry matter intake (DMI) data obtained from different herds and experiments across lactations and (ii) to get better estimates of the genetic parameters and better genetic evaluations. After editing, there were 572,512 daily DMI records of 3,495 animals (Holstein cows) from 11 different herds across 13 lactations and the animals were under 110 different nutritional experiments. The fitted model for this data set was a univariate repeated-measure animal model (called model 1) in which additive genetic and permanent environmental (within and across lactations) effects were fitted as random...
November 20, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28994157/genome-wide-association-study-and-annotating-candidate-gene-networks-affecting-age-at-first-calving-in-nellore-cattle
#5
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
#6
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
#7
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
#8
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/29164761/acknowledgements-to-referees
#9
(no author information available yet)
No abstract text is available yet for this article.
December 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29164760/can-we-make-genomic-selection-100-accurate
#10
G de Los Campos, M Á Toro
No abstract text is available yet for this article.
December 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29164759/it-is-unlikely-that-genomic-selection-will-ever-be-100-accurate
#11
Daniel Gianola
No abstract text is available yet for this article.
December 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29164758/is-gxe-a-burden-or-a-blessing-opportunities-for-genomic-selection-and-big-data
#12
EDITORIAL
H A Mulder
No abstract text is available yet for this article.
December 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
#13
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/28833593/implications-of-snp-weighting-on-single-step-genomic-predictions-for-different-reference-population-sizes
#14
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
#15
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
#16
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/28699266/can-we-make-genomic-selection-100-accurate
#17
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/28748554/estimation-of-inbreeding-depression-on-female-fertility-in-the-finnish-ayrshire-population
#18
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/28695620/correlated-response-in-litter-size-components-in-rabbits-selected-for-litter-size-variability
#19
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
#20
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
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