Estimation of individual animal SNP-BLUP reliability using full Monte Carlo sampling

Calculation of individual animal reliability of estimated genomic breeding value by SNP-BLUP requires inversion of the mixed model equations (MME). When the SNP-BLUP model includes a residual polygenic (RPG) effect, the size of the MME will be at least the number of genotyped animals (n) plus the number of SNP markers (m). Inversion of the MME in SNP-BLUP involves computations proportional to the cube of the MME size; that is, (n + m)3, which can present a considerable computational burden. We introduce a full Monte Carlo (MC) sampling-based method for approximating reliability in the SNP-BLUP model and compare its performance to the genomic BLUP (GBLUP) model. The performance of the full MC approach was evaluated using 2 data sets, including 19,757 and 222,619 genotyped animals selected from populations with 231,186 and 13.35 million pedigree animals, respectively. Genotypes were available in the data sets for 11,729 and 50,240 SNP markers. An advantage of the full MC approximation method was its low computational demand. A drawback was its tendency to overestimate reliability for animals with low reliability, especially when the weight of the RPG effect was high. The overestimation can be lessened by increasing the number of MC samples

Genealogical data of Boer and Nubian goats in Mexico

The pedigree file of the Boer and Nubian goat breeds in Mexico was constructed using the national database provided by the Asociación Mexicana de Criadores de Ganado Caprino de Registro. Field technicians routinely updated the goat national database by recording information from flocks participating in the performance-recording system. Information on animal identification number, parents, birth date, sex, breed, and farm of origin were used to undertake pedigree analyses using the ENDOG program (version 4.8). This paper presents a pedigree data file, tables and figures of characteristics of pedigree data, pedigree analyses, pedigree integrity, effective population size and genetic conservation index. The data can be used to estimate other population parameters, to monitor the genetic diversity of the Boer and Nubian goat breeds in Mexico, and also to design balanced breeding programs, maintaining genetic variation at reasonable levels and maximizing genetic progress in these populations.202

Invited review: Reliability computation from the animal model era to the single-step genomic model era

The calculation of exact reliabilities involving the inversion of mixed model equations poses a heavy computational challenge when the system of equations is large. This has prompted the development of different approximation methods. We give an overview of the various methods and computational approaches in calculating reliability from the era before the animal model to the era of single-step genomic models. The different methods are discussed in terms of modeling, development, and applicability in large dairy cattle populations. The paper also describes the problems faced in reliability computation. Many details dispersed throughout the literature are presented in this paper. It is clear that a universal solution applicable to every model and input data may not be possible, but we point out several efficient and accurate algorithms developed recently for a variety of very large genomic evaluations

Using Monte Carlo method to include polygenic effects in calculation of SNP-BLUP model reliability

202

Genetic parameters of reproductive traits in Tunisian Holsteins

Multi-trait Bayesian procedure was used to estimate genetic parameters for reproductive traits in Tunisian Holstein cows. A total of 31 348 lactations of the calving years 2005 to 2012 were analyzed. Fertility traits were the calving interval (CI), days open (DO), days to first insemination (DFI), days from first insemination to conception (FIC), and number of inseminations per conception (NI). Posterior means of heritabilities of CI, DO, DFI, FIC, and NI were 0.047, 0.03, 0.025, 0.024, and 0.069, respectively. Posterior means of repeatabilities of the same respective traits were 0.106, 0.094, 0.051, 0.036, and 0.17. Genetic correlations among female fertility traits were also computed. Calving interval and DO had the highest genetic correlation estimate (0.85) because they have overlapping genetic meanings. The lowest genetic correlation estimate (−0.25) was found between DFI and NI. Genetic parameter estimates are low and are even lower than those reported in most literature, implying that more focus should be put upon improving the management of reproduction in dairy cattle herds in Tunisia

Genetic diversity and population structure of Boer and Nubian goats in Mexico

202

Invited review : Reliability computation from the animal model era to the single-step genomic model era

The calculation of exact reliabilities involving the inversion of mixed model equations poses a heavy computational challenge when the system of equations is large. This has prompted the development of different approximation methods. We give an overview of the various methods and computational approaches in calculating reliability from the era before the animal model to the era of single-step genomic models. The different methods are discussed in terms of modeling, development, and applicability in large dairy cattle populations. The paper also describes the problems faced in reliability computation. Many details dispersed throughout the literature are presented in this paper. It is clear that a universal solution applicable to every model and input data may not be possible, but we point out several efficient and accurate algorithms developed recently for a variety of very large genomic evaluations