Abstract Background A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a method may need to be adjusted because marker-based pedigree-based matrices not on same scale. The apply when GBLUP model includes both breeding values residual polygenic effects. objective this study was compare methods with without adjustment for 16 traits Nordic Holstein population. Methods...

This study compared genomic predictions based on imputed high-density markers (~777,000) in the Nordic Holstein population using a BLUP (GBLUP) model, 4 Bayesian exponential power models with different shape parameters (0.3, 0.5, 0.8, and 1.0) for distribution, mixture model (a of normal distributions). Direct values (DGV) were estimated milk yield, fat protein fertility, mastitis, deregressed proofs (DRP) as response variable. The validation animals split into groups according to their...

Abstract Fat‐tailed sheep have a unique characteristic of depositing fat in their tails. In the present study, we conducted genome‐wide association studies (GWAS) on traits related to tail deposition and body size Hulun Buir sheep. A total number 300 individuals belonging two fat‐tailed lines breed genotyped with Ovine Infinium HD SNP BeadChip were included current study. Two mixed models, one for continuous binary phenotypic traits, employed analyse ten that is, length (BL), height (BH),...

Summary Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts runs homozygosity ( ROH ) along genomes. Recently, decreasing performance on reproductive traits, might have resulted from inbreeding, been observed in Chinese pigs. In this study, 830 individuals Western pig breeds were genotyped using the reduced‐representation sequencing method. After imputation quality control, 60 850 high‐confidence SNP...

This study investigated the efficiency of genomic prediction using an admixed reference population comprising 3 Yorkshire populations with different genetic backgrounds. In total, 2,084 and 1,388 individuals growth reproduction records, respectively, were genotyped a PorcineSNP80 marker panel. The corrected phenotypic values derived from conventional EBV each taken as response variables. Three approaches, that is, linear BLUP (GBLUP) model, Bayesian mixture model (BayesR), single-step GBLUP...

The random regression test-day model has become the most commonly adopted for routine genetic evaluations in dairy populations, which allows accurately accounting and environmental effects over lactation. objective of this study was to explore appropriate models evaluation milk yield a Holstein population with relatively small size, is common situation regional or independent breeding companies preform evaluation. Data included 419,567 records from 54,417 cows first Variance components...

The number of teats is related to the nursing ability sows. In present study, we conducted genome-wide association studies (GWAS) for traits teat in Duroc pig population. Two mixed models, one counted and another binary phenotypic traits, were employed analyze seven traits: right (RTN), left (LTN), total (TTN) numbers; maximum on a side (MAX); minus (LR); absolute value LR (ALR); presence symmetry between numbers (SLR). We identified 11, 1, 4, 13, 9 significant SNPs associated with RTN, LTN,...

Summary Breeding animals can be accurately evaluated using appropriate genomic prediction models, based on marker data and phenotype information. In this study, direct values (DGV) were estimated for 16 traits of Nordic Total Merit (NTM) Index in Red cattle population three models two different response variables. The as follows: a linear mixed model (GBLUP), Bayesian variable selection similar to BayesA (BayesA*) least absolute shrinkage operator (Bayesian Lasso). variables deregressed...

Including genotyped females in a reference population (RP) is an obvious way to increase the RP genomic selection, especially for dairy breeds of limited size. However, incorporation these must be conducted cautiously because potential preferential treatment cows and lower reliabilities phenotypes compared with proven pseudo-phenotypes bulls. Breeding organizations Denmark, Finland, Sweden have implemented female-genotyping project possibility genotyping entire herds using low-density (LD)...

Single-step genomic prediction models utilizing both genotyped and nongenotyped animals are likely to become the prevailing tool in genetic evaluations of livestock. Various single-step have been proposed, based either on estimation individual marker effects or direct via a relationship matrix. In this study, classical pedigree-based animal model, regular BLUP (ssGBLUP) algorithm for proven young (APY) with 2 strategies choosing core animals, Bayesian regression (ssBR) model were compared...

Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism fat deposition in tails, we firstly evaluated morphology transcription level differences between these lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) phenotypic extremes sizes. Five comparisons performed taking account factors, sex type. We screened out 373 DEGs big-tailed small-tailed sheep, 775...

Abstract Background After the extensive implementation of genomic selection (GS), choice statistical model and data used to estimate variance components (VCs) remains unclear. A primary concern is that VCs estimated from a traditional pedigree-based animal (P-AM) will be biased due ignoring impact GS. The objectives this study were examine effects GS on estimates VC in analysis different sets phenotypes investigate estimation using methods. Data simulated resemble Danish Jersey population....

Genotype imputation from BeadChip to whole-genome sequencing (WGS) data is a cost-effective method of obtaining genotypes WGS variants. Beagle, one the most popular software programs, has been widely used for genotype inference in humans and non-human species. A few studies have systematically comprehensively compared performance beagle versions parameter settings farm animals. Here, we investigated three representative Beagle (Beagle 4.1, 5.0, 5.4), effective population size (Ne) setting...

Abstract Background Methods for estimating variance components (VC) using restricted maximum likelihood (REML) typically require elements from the inverse of coefficient matrix mixed model equations (MME). As genomic information becomes more prevalent, MME denser, presenting a challenge analyzing large datasets. Thus, computational algorithms based on iterative solving and Monte Carlo approximation become appealing. While standard average REML (AI-REML) is known its rapid convergence,...

Abstract Background In this study, computationally efficient methods to approximate the reliabilities of genomic estimated breeding values (GEBV) in a single-step prediction model including residual polygenic (RPG) effect are described. order calculate genotyped animals, single nucleotide polymorphism best linear unbiased (SNPBLUP) or BLUP (GBLUP), was used, where two alternatives account for RPG were tested. direct approach, included effect, while blended method, it did not but an index...

Abstract Records on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy genetic evaluation quantitative traits with individual records. Here, we investigated value group Besides, group-recorded including correlated The study was based simulated pig population, three scenarios structure size. results...

Abstract Background In breeding programs, recording large-scale feed intake (FI) data routinely at the individual level is costly and difficult compared with other production traits. An alternative approach could be to record FI group since animals such as pigs are normally housed in groups fed by a shared feeder. However, date there have been few investigations about difference between group- individual-level recorded different environments. We hypothesized that genetically correlated but...

In genomic selection, prediction accuracy is highly driven by the size of animals in reference population (RP). Combining related populations from different countries and regions or using a with large RP has been considered to be viable strategies cattle breeding. The genetic relationship between important for improving predictive ability. this study, we used 122 French bulls as test individuals. estimated breeding values (GEBVs) evaluated RP, America Chinese were compared. results showed...

The efficiency of feed utilization plays an important role in animal breeding. However, measuring intake (FI) is costly on individual basis under practical conditions. Using group measurements to model FI could be practically feasible and cost-effective. objectives this study were develop a random regression based repeated with consideration missing phenotypes caused by drop out animals. Focus variance components (VC) estimation genetic evaluation, investigate the effect composition VC...

Efficient computational solutions are a continuing concern for genomic predictions in animal and plant breeding. MiX99 was developed fast solving of large-scale mixed model equations by preconditioned conjugate gradient with iteration on data. offers stand-alone tools pruning pedigree, computing inbreeding coefficients allele frequencies, constructing inverting various covariance matrices, calculating reliabilities, etc. In this paper, we describe workflow manner the most important programs...

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