Andres Legarra

Council on Dairy Cattle Breeding

Historical data collection for genetic evaluation purposes is a common practice in animal populations; however, the larger the dataset, the higher the computing power needed to perform the analyses. Also, fitting the same model to historical and recent data may be inappropriate. Data truncation can reduce the number of equations to solve, consequen...

Recently, high-dimensional omics data are becoming available in larger quantities, and models have been developed that integrate them with genomics to understand in finer detail the relationship between genotype and phenotype, and thus improve the performance of genetic evaluations. Our objectives are to quantify the effect of the inclusion of micr...

The genetic trend of milk yield for 4 French dairy sheep breeds (Lacaune, Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse) was partitioned in Mendelian sampling trends by categories of animals defined by sex and by selection pathways. Five categories were defined, as follows: (1) artificial insemination (AI) males (after progeny testing)...

The Lacaune dairy sheep breed split in 1972 into two subpopulations with no exchange of genetic material but a single genetic evaluation and same selection objectives. Previous work has shown that this led to the creation of two disconnected but genetically close subpopulations. Previous work also demonstrated that the currently performed combined...

Genomic selection was deployed in Lacaune dairy breed in 2015. Lacaune population split in 1972 into 2 breeding companies with associated flocks, and there have been very few exchanges of animals between the subpopulations, leading to divergence of the 2 subpopulations. In spite of that, there is a joint genomic prediction. The objective of this st...

Transmission ratio distortion (TRD), which is a deviation from Mendelian expectations, has been associated with basic mechanisms of life such as sperm and ova fertility and viability at developmental stages of the reproductive cycle. In this study different models including TRD regions were tested for different reproductive traits (days from first...

Interpopulation improvement for crosses of close populations in crops and livestock depends on the amount of heterosis and the amount of variance of dominance deviations in the hybrids. It has been intuited that the further the distance between populations, the lower the amount of dominance variation and the higher the heterosis. Although experienc...

National dairy evaluations use mostly multistep methods, where a nongenomic BLUP evaluation is followed by extraction of pseudo-phenotypes, genomic analyses, and merging nongenomic and genomic evaluations. With genomic preselection and many females genotyped, pseudo-phenotypes are biased, and it is hard to accommodate female genotypes fully. Such p...

This work aimed to develop single-step multibreed genomic predictions for US dairy population. About 45M yield phenotypes recorded between 2000 and 2020 in purebred Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey animals were analyzed. Genotypes at 79,294 SNPs were available for 3.9M animals. A 3-traits model with milk, fat, and protein yield...

Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, an...

Background Reliabilities of best linear unbiased predictions (BLUP) of breeding values are defined as the squared correlation between true and estimated breeding values and are helpful in assessing risk and genetic gain. Reliabilities can be computed from the prediction error variances for models with a single base population but are undefined for...

Background Single-step genomic predictions obtained from a breeding value model require calculating the inverse of the genomic relationship matrix $$({\mathbf{G}}^{-1})$$ ( G - 1 ) . The Algorithm for Proven and Young (APY) creates a sparse representation of $${\mathbf{G}}^{-1}$$ G - 1 with a low computational cost. APY consists of selecting a grou...

Gene expression is supposed to be an intermediate between DNA and the phenotype, and it can be measured. Thus, for a trait, we may have intermediate measures, which are in fact a series of genetically controlled traits. Similarly, several traits may be measured or predicted using infrared spectra, accelerometers, and similar high-throughput measure...

Background At the beginning of genomic selection, some Chinese companies genotyped pigs with different single nucleotide polymorphism (SNP) arrays. The obtained genomic data are then combined and to do this, several imputation strategies have been developed. Usually, only additive genetic effects are considered in genetic evaluations. However, domi...

Background Although single-step GBLUP (ssGBLUP) is an animal model, SNP effects can be backsolved from genomic estimated breeding values (GEBV). Predicted SNP effects allow to compute indirect prediction (IP) per individual as the sum of the SNP effects multiplied by its gene content, which is helpful when the number of genotyped animals is large,...

Single‐step genomic BLUP (ssGBLUP) relies on the combination of the genomic (G$$ \mathbf{G} $$) and pedigree relationship matrices for all (A$$ \mathbf{A} $$) and genotyped (A22$$ {\mathbf{A}}_{22} $$) animals. The procedure ensures G$$ \mathbf{G} $$ and A22$$ {\mathbf{A}}_{22} $$ are compatible so that both matrices refer to the same genetic base...

It is now widely accepted that animals' phenotypes are determined by the host genetic and the microbiome composition. For the genetic evaluation purpose, our objectives are to estimate the heritability and microbiability, and the additive metagenomic effect, assuming that these two components have additive effects. In this study were included, as d...

The objective of this work was to study long-term contributions to genetic gain in Basco-Béarnaise dairy sheep breed. From estimated breeding values, contributions from males and females and from five categories were analysed. The AlphaPart R package was used to partition the genetic gain into ancestral Mendelian samplings by sex and by category. T...

In the original version of this book, Chapter 8 was published with an incorrect author name. The correct name is Andres Legarra, instead of Andred Legarra. This has been rectified in the updated version of this book.

Joint genomic evaluation by combining data recordings and genomic information from different pig herds and populations is of interest for pig breeding companies because the efficiency of genomic selection (GS) could be further improved. In this work, an efficient strategy of joint genomic evaluation combining data from multiple pig populations is i...

Spanish Latxa and French Manech are dairy sheep breeds that split into Blond (Latxa Cara Rubia, LCR; Manech Tête Rousse, MTR) and Black (Latxa Cara Negra of Navarre, LCN; Manech Tête Noire, MTN) strains. Exchange of genetic material (artificial insemination doses) is becoming more and more frequent across these breeds, within color, to boost both g...

The use of genomic information for prediction of future phenotypes or breeding values for the candidates to selection has become a standard over the last decade. However, most procedures for genomic prediction only consider the additive (or substitution) effects associated with polymorphic markers. Nevertheless, the implementation of models that co...

Official multibreed genomic evaluations for dairy cattle in the United States are based on multibreed BLUP evaluation followed by single-breed estimation of SNP effects. Single-step genomic BLUP (ssGBLUP) allows the straight computation of genomic (G)EBV in a multibreed context. This work aimed to develop ssGBLUP multibreed genomic predictions for...

Background Multiple breed evaluation using genomic prediction includes the use of data from multiple populations, or from parental breeds and crosses, and is expected to lead to better genomic predictions. Increased complexity comes from the need to fit non-additive effects such as dominance and/or genotype-by-environment interactions. In these mod...

Background: Genetic selection has proven to be a successful strategy for the sustainable control of gastrointestinal parasitism in sheep. However, little is known on the relationship between resistance to parasites and production traits in dairy breeds. In this study, we estimated the heritabilities and genetic correlations for resistance to paras...

Bias in dairy genetic evaluations, when it exists, has to be understood and properly addressed. The origin of biases is not always clear. We analyzed 40 yr of records from the Lacaune dairy sheep breeding program to evaluate the extent of bias, assess possible corrections, and emit hypotheses on its origin. The data set included 7 traits (milk yiel...

Background Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on ped...

Single-step GBLUP (ssGBLUP) relies on the combination of genomic (G) and pedigree relationships for all (A) and genotyped animals (A22). The procedure implemented in the BLUPF90 software suite first involves combining a small percentage of A22 into G (blending) to avoid singularity problems, then an adjustment to account for the fact the genetic ba...

Allele substitution effects at quantitative trait loci (QTL) are part of the basis of quantitative genetics theory and applications such as association analysis and genomic prediction. In the presence of non-additive functional gene action, substitution effects are not constant across populations. We develop an original approach to model the differ...

Skip Nav Destination Article Navigation ACCEPTED MANUSCRIPT Genetic evaluation including intermediate omics features Ole F Christensen, Vinzent Börner, Luis Varona, Andres Legarra Genetics, iyab130, https://doi.org/10.1093/genetics/iyab130 Published: 07 August 2021 Article history Cite Permissions Icon Permissions Share Abstract In animal and plan...

Runs of homozygosity (ROH) are contiguous homozygous segments of the genome where the haplotypes inherited from each parent are identical. The occurrence of ROH is not randomly distributed across the genome, and ROH islands across many animals may be the result of selective pressure. The objective of this study was to demonstrate that the presence...

We revisited, in a genomic context, the theory of hybrid genetic evaluation models of hybrid crosses of pure lines, as the current practice is largely based on infinitesimal model assumptions. Expressions for covariances between hybrids due to additive substitution effects and dominance and epistatic deviations were analytically derived. Using dens...

Background Resilient animals can remain productive under different environmental conditions. Rearing in increasingly heterogeneous environmental conditions increases the need of selecting resilient animals. Detection of environmental challenges that affect an entire population can provide a unique opportunity to select animals that are more resilie...

Background: Bias has been reported in genetic or genomic evaluations of several species. Common biases are systematic differences between averages of estimated and true breeding values, and their over- or under-dispersion. In addition, comparing accuracies of pedigree versus genomic predictions is a difficult task. This work proposes to analyse bi...

Background: X-chromosomal loci present different inheritance patterns compared to autosomal loci and must be modeled accordingly. Sexual chromosomes are not systematically considered in whole-genome relationship matrices although rules based on genealogical or marker information have been derived. Loci on the X-chromosome could have a significant...

Decreases in genetic variance over generations reduce future genetic gain. We studied the evolution of genetic variance in the dairy sheep breed Manech Tête Rousse, which has been selected for increasingly complex objectives, including, in this order, milk yield, milk contents, scrapie resistance, and somatic cell score. We estimated base populatio...

Inbreeding depression is associated with a decrease in performance and fitness of the animals. The goal of this study was to evaluate pedigree-based and genomic methods to estimate the level of inbreeding and inbreeding depression for 3 semen traits (volume, concentration, and motility score) in the Basco-Béarnaise sheep breed. Data comprised 16,19...

With an ever-increasing number of genotyped animals, there is a question of whether to include all genotypes into single-step GBLUP (ssGBLUP) evaluations or to include only genotyped animals with phenotypes and use indirect predictions (IP) for the remaining young genotyped animals. Under ssGBLUP, SNP effects can be backsolved from GEBV, and IP can...

The objective of this study was to determine whether the linear regression (LR) method could be used to validate genomic threshold models used for analysis of categorical data. Statistics for the LR method were computed from estimated breeding values (EBVs) using the whole and truncated datasets. The method was tested using simulated and real chick...

Allele substitution effects at quantitative trait loci (QTL) are part of the basis of quantitative genetics theory and applications such as association analysis and genomic prediction. In presence of non-additive functional gene action, substitution effects are not constant across populations. We develop an original approach to model the difference...

The objective of this study was to determine whether the linear regression (LR) method could be used to validate genomic threshold models. Statistics for the LR method were computed from estimated breeding values (EBVs) using the whole and truncated data sets with variances from the reference and validation populations. The method was tested using...

Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collecte...

Single-step genomic evaluation became a standard procedure in livestock breeding, and the main reason is the ability to combine all pedigree, phenotypes, and genotypes available into one single evaluation, without the need of post-analysis processing. Therefore, the incorporation of data on genotyped and non-genotyped animals in this method is stra...

We investigated the effectiveness of mate allocation strategies accounting for non‑additive genetic effects to improve crossbred performance in a two-way crossbreeding scheme. We did this by computer simulation of 10 generations of evaluation and selection. QTL effects were simulated as correlated across purebreds and crossbreds, and (positive) het...

(1) Background: Ranking traits are used commonly for breeding purposes in several equine populations; however, implementation is complex, because the position of a horse in a competition event is discontinuous and is influenced by the performance of its competitors. One approach to overcoming these limitations is to assume an underlying Gaussian li...

Early application of genomic selection relied on SNP estimation with phenotypes or de-regressed proofs (DRP). Chips of 50k SNP seemed sufficient for an accurate estimation of SNP effects. Genomic estimated breeding values (GEBV) were composed by an index with parent average, direct genomic value, and deduction of a parental index to eliminate doubl...

Traditionally, breeding programs have estimated and managed inbreeding based on pedigree information. The availability of genomic marker panels has made possible new alternatives to achieve more precise estimates, for example in case of missing pedigree. The objective of the present study was to assess and compare, different estimation methods (ped...

The availability of genomic marker panels has made possible more precise estimates of breeding values. Sheep breeding programs are implementing genomic selection. In Latxa dairy sheep breed, a previous study using pre-corrected data and a small number of genotyped animals did not show a clear advantage of genomic selection. The objective of the pre...

Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two plac...

The existence of buffering mechanisms is an emerging property of biological networks, and this results in the build-up of robustness through evolution. So far, there are no explicit methods to find loci implied in buffering mechanisms. However, buffering can be seen as interaction with genetic background. Here we develop this idea into a tractable...

The genomic measure of inbreeding is closer to the actual inbreeding than the pedigree-based measure. However, it cannot be computed for ungenotyped animals. An estimate of genomic inbreeding comes from the diagonal of matrix H used in single-step methods. This matrix projects genomic relationships to all ungenotyped members of the pedigree. The di...

In large genotyped populations, the value of adding all genotyped animals into the single-step GBLUP (ssGBLUP) evaluation is unclear. Indirect predictions (IP) are useful to compute genomic predictions for genotyped animals not included in the evaluations. IP can be calculated as the sum of SNP effects weighted by the gene content. Having IP is ben...

Quality control and consistency tests on genotypes and historical pedigree data are applied in a routine genomic evaluation and academic research. The quality control takes more time to finish as more genotypes become available, and this step is a bottleneck in a pipeline of routine evaluation. For the efficient quality control, we have developed s...

Abstract Background Single-step genomic best linear unbiased prediction (SSGBLUP) is a comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for genome-wide association studies (GWAS) without a formal framework of hypothesis testing. Our objective was to implement p-values for single-marker GWAS...

After publication of original article [1], the authors noticed that there was an error.

Bias in genetic evaluations has been a constant concern in animal genetics. The interest in this topic has increased in the last years, since many studies have detected overestimation (bias) in estimated breeding values (EBV). Detecting the existence of bias, and the realized accuracy of predictions, is therefore of importance, yet this is difficul...

La raza Latxa es una raza de ovino lechero autóctona del País Vasco y Navarra en la que se distinguen tres poblaciones: Latxa Cara Rubia (LCR), Latxa Cara Negra de Euskadi (LCNEUS) y Latxa Cara Negra de Navarra (LCNNAF). El programa de mejora comenzó en 1984 y actualmente tiene resultados consolidados, con una ganancia genética anual para producció...

Las razas ovinas del Pirineo Latxa, Manech y Basco-Bearnesa son razas autóctonas de la Comunidad Autónoma Vasca (CAPV) y Navarra (NA) la primera, y del País Vasco francés y Béarn, la segunda y tercera.

Causal variants inferred from sequence data analysis are expected to increase accuracy of genomic selection. In this work we evaluated the gain in reliability of genomic predictions, for stature in US Holsteins, when adding selected sequence variants to a pre-existent SNP chip. Two prediction methods were tested: de-regressed proofs assuming hetero...

Traditionally, inbreeding estimates have been estimated based on pedigree information. However, in sheep there is a considerable proportion of unknown pedigree due to natural mating and limited use of paternity analysis. Therefore, there is an under estimation of inbreeding coefficients based on pedigree. In the genomics era, genomic information ca...

Inbreeding depression is caused by increased homozygosity of individuals and it is involved in the decrease of performance and fitness of the animals. The goal of this study is to estimate inbreeding depression for semen traits in Basco-Béarnaise rams. Genomic (e.g. using SNP-by-SNP approach) or pedigree-based inbreeding can be used to obtain inbre...

Traditionally, inbreeding estimates have been estimated based on pedigree information. However, in sheep there is a considerable proportion of unknown pedigree due to natural mating and limited use of paternity analysis. Therefore, there is an under estimation of inbreeding coefficients based on pedigree. In the genomics era, genomic information ca...

The recently presented method Linear Regression (LR), was proposed to benchmark models in genetic selection schemes. The principle of the method is to estimate biases and accuracies comparing estimated breeding values (EBVs) obtained from a partial data set (with old records, EBVp) and from a whole data set (with the addition of new records, EBVw)....

Runs of homozygosity (ROH) are contiguous homozygous segments of the genome where the haplotypes inherited from each parent are identical. Currently, inbreeding estimated from ROH is considered a powerful approach to distinguish between recent,potentially harmful, from ancient inbreeding, potentially beneficial. Accordingly, inbreeding based on ROH...

Indirect predictions (IP) can be obtained for young animals that are not yet included or will never make up to an official genomic evaluation. Additionally, if lots of animals are genotyped but they do not contribute to the evaluation, having IP for them would reduce computing cost. This is beneficial if accuracy levels are maintained. If single-st...

The partition of the total genetic variance into its additive and non-additive components can differ from trait to trait, and between purebred and crossbred populations. A quantification of these genetic variance components will determine the extent to which it would be of interest to account for dominance in genomic evaluations or to establish mat...

The existence of buffering mechanisms is an emerging property of biological networks, and this results in the possible existence of 'buffering' loci, that would allow buildup of robustness through evolution. So far, there are no explicit methods to find loci implied in buffering mechanisms. However, buffering can be seen as interaction with genetic...