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BIBI: Bayesian inference of breed composition
Summary 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...
Source: Journal of Animal Breeding and Genetics - November 22, 2017 Category: Genetics & Stem Cells Authors: C. A. Mart ínez, K. Khare, M. A. Elzo Tags: ORIGINAL ARTICLE Source Type: research

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Journal of Animal Breeding and Genetics,Volume 135, Issue 1, Page 28-36, February 2018. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 20, 2017 Category: Genetics & Stem Cells Source Type: research

Adjusting for heterogeneity of experimental data in genetic evaluation of dry matter intake in dairy cattle
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 envi...
Source: Journal of Animal Breeding and Genetics - October 1, 2017 Category: Genetics & Stem Cells Authors: M. E. Uddin, T. Meuwissen, R. F. Veerkamp Tags: ORIGINAL ARTICLE Source Type: research

Genome ‐wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle
Summary 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. From these windows, we identified 123 coding protein genes that were used ...
Source: Journal of Animal Breeding and Genetics - October 1, 2017 Category: Genetics & Stem Cells Authors: R.R. Mota, S.E.F. Guimar ães, M.R.S. Fortes, B. Hayes, F.F. Silva, L.L. Verardo, M.J. Kelly, C.F. Campos, J.D. Guimarães, R.R. Wenceslau, J.M. Penitente‐Filho, J.F. Garcia, S. Moore Tags: ORIGINAL ARTICLE Source Type: research

Direct and maternal additive effects are not the main determinants of Iberian piglet perinatal mortality
Summary 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 0.010, 0.004 and 0.003, and those of maternal heritability were 0.034, 0.011 and...
Source: Journal of Animal Breeding and Genetics - September 28, 2017 Category: Genetics & Stem Cells Authors: M. Mu ñoz, M.C. Rodríguez, L.A. García‐Cortes, A. González, J.M. García‐Casco, L. Silió Tags: ORIGINAL ARTICLE Source Type: research

Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang 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 (r2 < .2) with previously reported loci were considered novel. We substantially improved the strength and precision of the associations at four previously detected loci near FADS2, ELOVL7, ELOVL6 and FASN genes, ...
Source: Journal of Animal Breeding and Genetics - September 21, 2017 Category: Genetics & Stem Cells Authors: J. Zhang, Y. Zhang, H. Gong, L. Cui, T. Huang, H. Ai, J. Ren, L. Huang, B. Yang Tags: ORIGINAL ARTICLE Source Type: research

Correction for adipocyte size and number in the analysis of differences in gene expression in fat tissues
Summary 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 bimodalit...
Source: Journal of Animal Breeding and Genetics - September 20, 2017 Category: Genetics & Stem Cells Authors: L. Alfonso Tags: ORIGINAL ARTICLE Source Type: research

Revolutionary leaps in the development of agriculture
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - September 6, 2017 Category: Genetics & Stem Cells Authors: J.J. Lauvergne Tags: EDITORIAL Source Type: research

Implications of SNP weighting on single ‐step genomic predictions for different reference population sizes
Summary 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). The WssGBLUP performed better in small genotyped populations; however, any advantage...
Source: Journal of Animal Breeding and Genetics - August 1, 2017 Category: Genetics & Stem Cells Authors: D. A. L. Lourenco, B. O. Fragomeni, H. L. Bradford, I. R. Menezes, J. B. S. Ferraz, I. Aguilar, S. Tsuruta, I. Misztal Tags: ORIGINAL ARTICLE Source Type: research

Genomic estimation of additive and dominance effects and impact of accounting for dominance on accuracy of genomic evaluation in sheep populations
This study showed a substantial dominance genetic variance for weight and ultrasound scanned body composition traits particularly in cross‐bred population; however, improvement in the accuracy of genomic breeding values was small and statistically not significant. Dominance variance estimates in combined cross‐bred population could be overestimated if heterosis is not fitted in the model. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - August 1, 2017 Category: Genetics & Stem Cells Authors: N. Moghaddar, J. H. J. Werf Tags: ORIGINAL ARTICLE Source Type: research

Gaussian covariance graph models accounting for correlated marker effects in genome ‐wide prediction
In this study, methods adapting the theory of GCovGM to genome‐wide prediction were developed (Bayes GCov, Bayes GCov‐KR and Bayes GCov‐H). In simulated data sets, improvements in correlation between phenotypes and predicted breeding values and accuracies of predicted breeding values were found. Our models account for correlation of marker effects and permit to accommodate general structures as opposed to models proposed in previous studies, which consider spatial correlation only. In addition, they allow incorporation of biological information in the prediction process through its use when constructing graph G, and ...
Source: Journal of Animal Breeding and Genetics - August 1, 2017 Category: Genetics & Stem Cells Authors: C.A. Mart ínez, K. Khare, S. Rahman, M.A. Elzo Tags: ORIGINAL ARTICLE Source Type: research

Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population
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 ...
Source: Journal of Animal Breeding and Genetics - July 27, 2017 Category: Genetics & Stem Cells Authors: K. Martikainen, A. M. Tyrisev ä, K. Matilainen, J. Pösö, P. Uimari Tags: ORIGINAL ARTICLE Source Type: research

Can we make genomic selection 100% accurate?
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 11, 2017 Category: Genetics & Stem Cells Authors: M.E. Goddard Tags: EDITORIAL Source Type: research

Correlated response in litter size components in rabbits selected for litter size variability
In conclusion, a decrease in litter size variability showed a favourable effect on ES and led to a higher litter size at birth. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - June 1, 2017 Category: Genetics & Stem Cells Authors: M.J. Argente, E.W. Calle, M.L. Garc ía, A. Blasco Tags: ORIGINAL ARTICLE Source Type: research

Contemporary group estimates adjusted for climatic effects provide a finer definition of the unknown environmental challenges experienced by growing pigs
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. Data were recorded from 1999 to 2013 at a piggery in south‐east Queensland, Australia (n = 31,230). Firstly, CG estimates of average daily gain (ADG) an...
Source: Journal of Animal Breeding and Genetics - June 1, 2017 Category: Genetics & Stem Cells Authors: S.Z.Y. Guy, L. Li, P.C. Thomson, S. Hermesch Tags: ORIGINAL ARTICLE Source Type: research