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A method for partitioning trends in genetic mean and variance to understand breeding practices Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-06-02 Thiago P. Oliveira, Jana Obšteter, Ivan Pocrnic, Nicolas Heslot, Gregor Gorjanc
In breeding programmes, the observed genetic change is a sum of the contributions of different selection paths represented by groups of individuals. Quantifying these sources of genetic change is essential for identifying the key breeding actions and optimizing breeding programmes. However, it is difficult to disentangle the contribution of individual paths due to the inherent complexity of breeding
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Genetic analysis of protein efficiency and its association with performance and meat quality traits under a protein-restricted diet Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-06-02 Esther Oluwada Ewaoluwagbemiga, Giuseppe Bee, Claudia Kasper
An essential component in the development of sustainable pig production is the reduction of nitrogen excretion in fattening pigs. Pig feeds typically contain high levels of dietary crude protein, and due to incomplete conversion to muscle tissue, excess nitrogen is excreted, resulting in environmental problems such as nitrate pollution and greenhouse gas emissions. Therefore, improving protein efficiency
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A breed-of-origin of alleles model that includes crossbred data improves predictive ability for crossbred animals in a multi-breed population Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-05-15 Ana Guillenea, Mogens Sandø Lund, Ross Evans, Vinzent Boerner, Emre Karaman
Recently, crossbred animals have begun to be used as parents in the next generations of dairy and beef cattle systems, which has increased the interest in predicting the genetic merit of those animals. The primary objective of this study was to investigate three available methods for genomic prediction of crossbred animals. In the first two methods, SNP effects from within-breed evaluations are used
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The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-05-11 Audald Lloret-Villas, Hubert Pausch, Alexander S. Leonard
Low-pass sequencing followed by sequence variant genotype imputation is an alternative to the routine microarray-based genotyping in cattle. However, the impact of haplotype reference panels and their interplay with the coverage of low-pass whole-genome sequencing data have not been sufficiently explored in typical livestock settings where only a small number of reference samples is available. Sequence
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Characterization of the genetic pool of the Canadienne dairy cattle breed Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-05-09 Alexandra Carrier, Isabelle Gilbert, Pierre Leclerc, Mario Duchesne, Claude Robert
Canadienne cattle are the oldest breed of dairy cattle in North America. The Canadienne breed originates from cattle that were brought to America by the mid-seventeenth century French settlers. The herd book was established in 1886 and the current breed characteristics include dark coat color, small size compared to the modern Holstein breed, and overall rusticity shaped by the harsh environmental
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SIMplyBee: an R package to simulate honeybee populations and breeding programs Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-05-09 Jana Obšteter, Laura K. Strachan, Jernej Bubnič, Janez Prešern, Gregor Gorjanc
The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator
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Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-05-04 Emilie Delpuech, Marc Vandeputte, Romain Morvezen, Anastasia Bestin, Mathieu Besson, Joseph Brunier, Aline Bajek, Boudjema Imarazene, Yoannah François, Olivier Bouchez, Xavier Cousin, Charles Poncet, Thierry Morin, Jean-Sébastien Bruant, Béatrice Chatain, Pierrick Haffray, Florence Phocas, François Allal
Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. We generated a dataset of 838,451 single nucleotide
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On the holobiont ‘predictome’ of immunocompetence in pigs Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-05-01 Joan Calle-García, Yuliaxis Ramayo-Caldas, Laura M. Zingaretti, Raquel Quintanilla, María Ballester, Miguel Pérez-Enciso
Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence
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Reintroducing genetic diversity in populations from cryopreserved material: the case of Abondance, a French local dairy cattle breed Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-19 Alicia Jacques, Grégoire Leroy, Xavier Rognon, Etienne Verrier, Michèle Tixier-Boichard, Gwendal Restoux
Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit
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Variation in the proportion of the segregating genome shared between full-sibling cattle and sheep Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-18 David Kenny, Donagh P. Berry, Thierry Pabiou, Pierce Rafter
The construction of covariance matrices that account for the genetic relationships among individuals, using pedigree or genotype data, is integral to genetic evaluations, which are now routinely used in the field of animal breeding. The objective of the present study was to estimate the standard deviation in the proportion of the segregating genome that is shared between pairs of full-sibling cattle
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Correction: Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-17 Andre Garcia, Ignacio Aguilar, Andres Legarra, Shogo Tsuruta, Ignacy Misztal, Daniela Lourenco
Correction: Genetics Selection Evolution (2022) 54:66 https://doi.org/10.1186/s12711-022-00752-4 After publication of this work [1], we noticed that there was an error in Eqs. (14) to (19) presented on page 4 of the paper, where we refer to the term \(\mathrm{var}(\widehat{\mathbf{a}})\) as the prediction error covariance (PEC) of SNP effects which is not correct. The correct equations should be:$
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Correction: In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-11 Tuan V. Nguyen, Christy J. Vander Jagt, Jianghui Wang, Hans D. Daetwyler, Ruidong Xiang, Michael E. Goddard, Loan T. Nguyen, Elizabeth M. Ross, Ben J. Hayes, Amanda J. Chamberlain, Iona M. MacLeod
Correction: Genetic Selection Evolution (2023) 55:9 https://doi.org/10.1186/s12711-023-00783-5 After publication of original article [1], the authors identified two errors in the paper. 1. Under the heading Building long‑read reference populations for SV discovery, phasing and imputation, point number 2, “Existing short read databases with many sequenced individuals would continue to be invaluable
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A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-03 Simone Ceccobelli, Vincenzo Landi, Gabriele Senczuk, Salvatore Mastrangelo, Maria Teresa Sardina, Slim Ben-Jemaa, Christian Persichilli, Taki Karsli, Valentin-Adrian Bâlteanu, María Agustina Raschia, Mario Andrés Poli, Gabriel Ciappesoni, Farai Catherine Muchadeyi, Edgar Farai Dzomba, Nokuthula Winfred Kunene, Gesine Lühken, Tatiana Evgenievna Deniskova, Arsen Vladimirovich Dotsev, Natalia Anatolievna
To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations)
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Integrating on-farm and genomic information improves the predictive ability of milk infrared prediction of blood indicators of metabolic disorders in dairy cows Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-03 Lucio F. M. Mota, Diana Giannuzzi, Sara Pegolo, Erminio Trevisi, Paolo Ajmone-Marsan, Alessio Cecchinato
Blood metabolic profiles can be used to assess metabolic disorders and to evaluate the health status of dairy cows. Given that these analyses are time-consuming, expensive, and stressful for the cows, there has been increased interest in Fourier transform infrared (FTIR) spectroscopy of milk samples as a rapid, cost-effective alternative for predicting metabolic disturbances. The integration of FTIR
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Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-04-03 Sara Faggion, Paolo Carnier, Rafaella Franch, Massimiliano Babbucci, Francesco Pascoli, Giulia Dalla Rovere, Massimo Caggiano, Hervé Chavanne, Anna Toffan, Luca Bargelloni
The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV might be a preventive action. In this study, 972 sea bream larvae were subjected to a NNV challenge test and the symptomatology
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Genomic prediction in pigs using data from a commercial crossbred population: insights from the Duroc x (Landrace x Yorkshire) three-way crossbreeding system Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-28 Siyi Liu, Tianxiong Yao, Dong Chen, Shijun Xiao, Liqing Chen, Zhiyan Zhang
Genomic selection is widely applied for genetic improvement in livestock crossbreeding systems to select excellent nucleus purebred (PB) animals and to improve the performance of commercial crossbred (CB) animals. Most current predictions are based solely on PB performance. Our objective was to explore the potential application of genomic selection of PB animals using genotypes of CB animals with extreme
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Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-23 Salvatore Mastrangelo, Slim Ben-Jemaa, Francesco Perini, Filippo Cendron, Filippo Biscarini, Emiliano Lasagna, Mauro Penasa, Martino Cassandro
Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative
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Validation with single-step SNPBLUP shows that evaluations can continue using a single mean of genotyped individuals, even with multiple breeds Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-22 Michael Aldridge, Jeremie Vandenplas, Pascal Duenk, John Henshall, Rachel Hawken, Mario Calus
In genomic prediction, it is common to centre the genotypes of single nucleotide polymorphisms based on the allele frequencies in the current population, rather than those in the base generation. The mean breeding value of non-genotyped animals is conditional on the mean performance of genotyped relatives, but can be corrected by fitting the mean performance of genotyped individuals as a fixed regression
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A web tool for the global identification of pig breeds Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-21 Jian Miao, Zitao Chen, Zhenyang Zhang, Zhen Wang, Qishan Wang, Zhe Zhang, Yuchun Pan
Natural and artificial selection for more than 9000 years have led to a variety of domestic pig breeds. Accurate identification of pig breeds is important for breed conservation, sustainable breeding, pork traceability, and local resource registration. We evaluated the performance of four selectors and six classifiers for breed identification using a wide range of pig breeds (N = 91). The internal
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Genomic evaluation for two-way crossbred performance in cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-17 Quanshun Mei, Huiming Liu, Shuhong Zhao, Tao Xiang, Ole F Christensen
Dairy cattle production systems are mostly based on purebreds, but recently the use of crossbreeding has received increased interest. For genetic evaluations including crossbreds, several methods based on single-step genomic best linear unbiased prediction (ssGBLUP) have been proposed, including metafounder ssGBLUP (MF-ssGBLUP) and breed-specific ssGBLUP (BS-ssGBLUP). Ideally, models that account for
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Single-step genome-wide association analyses of claw horn lesions in Holstein cattle using linear and threshold models Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-10 Bingjie Li, Matthew Barden, Vanessa Kapsona, Enrique Sánchez-Molano, Alkiviadis Anagnostopoulos, Bethany Eloise Griffiths, Cherril Bedford, Xiaoxia Dai, Mike Coffey, Androniki Psifidi, Georgios Oikonomou, Georgios Banos
Lameness in dairy cattle is primarily caused by foot lesions including the claw horn lesions (CHL) of sole haemorrhage (SH), sole ulcers (SU), and white line disease (WL). This study investigated the genetic architecture of the three CHL based on detailed animal phenotypes of CHL susceptibility and severity. Estimation of genetic parameters and breeding values, single-step genome-wide association analyses
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Effect of environmental variance-based resilience selection on the gut metabolome of rabbits Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-09 Cristina Casto-Rebollo, María José Argente, María Luz García, Agustín Blasco, Noelia Ibáñez-Escriche
Gut metabolites are key actors in host-microbiota crosstalk with effect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its effect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal
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Selective genotyping strategies for a sib test scheme of a broiler breeder program Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-07 Charlie A. de Hollander, Vivian P. Breen, John Henshall, Fernando B. Lopes, Mario PL. Calus
In broiler breeding, genotype-by-environment interaction is known to result in a genetic correlation between body weight measured in bio-secure and commercial environments that is substantially less than 1. Thus, measuring body weights on sibs of selection candidates in a commercial environment and genotyping them could increase genetic progress. Using real data, the aim of this study was to evaluate
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Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-03-02 Simon Boitard, Laurence Liaubet, Cyriel Paris, Katia Fève, Patrice Dehais, Alban Bouquet, Juliette Riquet, Marie-José Mercat
Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent
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Adjusted fence height: an improved phenotype for the genetic evaluation of show jumping performance in Warmblood horses Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-02-23 Léa Chapard, Anna Van Thillo, Roel Meyermans, Wim Gorssen, Nadine Buys, Steven Janssens
Show jumping is one of the most popular disciplines in the horse sector, which makes success in show jumping competitions an important breeding goal for many studbooks. Therefore, the genetic evaluation of show jumping performance is of major interest and this is the case for two Belgian Warmblood studbooks: the Belgian Warmblood horse and Zangersheide. In this study, first an improved phenotype for
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Genomic selection models substantially improve the accuracy of genetic merit predictions for fillet yield and body weight in rainbow trout using a multi-trait model and multi-generation progeny testing Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-02-09 Andre Garcia, Shogo Tsuruta, Guangtu Gao, Yniv Palti, Daniela Lourenco, Tim Leeds
In aquaculture, the proportion of edible meat (FY = fillet yield) is of major economic importance, and breeding animals of superior genetic merit for this trait can improve efficiency and profitability. Achieving genetic gains for fillet yield is possible using a pedigree-based best linear unbiased prediction (PBLUP) model with direct and indirect selection. To investigate the feasibility of using
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Selection index theory for populations under directional and stabilizing selection Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-02-03 Robin Wellmann
The purpose of a selection index is that its use to select animals for breeding maximizes the profit of a breed in future generations. The profit of a breed is in general a quantity that predicts the satisfaction of future owners with their breed, and the satisfaction of the consumers with the products that are produced by the breed. Many traits, such as conformation traits and product quality traits
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In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-31 Tuan V. Nguyen, Christy J. Vander Jagt, Jianghui Wang, Hans D. Daetwyler, Ruidong Xiang, Michael E. Goddard, Loan T. Nguyen, Elizabeth M. Ross, Ben J. Hayes, Amanda J. Chamberlain, Iona M. MacLeod
Studies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in the genome. However, unlike small variants (< 50 bp), it has been challenging to accurately identify and genotype SV at the population scale using short-read sequencing. Long-read sequencing technologies are becoming competitively priced and can address
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Nest preference and laying duration traits to select against floor eggs in laying hens Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-25 Lorry Bécot, Nicolas Bédère, Jenna Coton, Thierry Burlot, Pascale Le Roy
Floor eggs, which are defined as eggs that hens lay off-nest, are a major issue in cage-free layer poultry systems. They create additional work for farmers because they must be collected by hand. They are also usually soiled or broken, which results in economic losses. Nonetheless, knowledge about the genetics of nesting behavior is limited. The aim of this study was to estimate genetic parameters
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Reducing computational demands of restricted maximum likelihood estimation with genomic relationship matrices Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-25 Karin Meyer
Restricted maximum likelihood estimation of genetic parameters accounting for genomic relationships has been reported to impose computational burdens which typically are many times higher than those of corresponding analyses considering pedigree based relationships only. This can be attributed to the dense nature of genomic relationship matrices and their inverses. We outline a reparameterisation of
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Reliabilities of estimated breeding values in models with metafounders Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-23 Matias Bermann, Ignacio Aguilar, Daniela Lourenco, Ignacy Misztal, Andres Legarra
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 models that include several base populations and when unknown
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Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-20 Zhou Wu, Mirte Bosse, Christina M. Rochus, Martien A. M. Groenen, Richard P. M. A. Crooijmans
In poultry, the population structure of local breeds is usually complex mainly due to unrecorded breeding. Local chicken breeds offer an interesting proxy to understand the complexity of population structure in the context of human-mediated development of diverse morphologies and varieties. We studied 37 traditional Dutch chicken breeds to investigate population structure and the corresponding genomic
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Estimation of genotype by temperature-humidity index interactions on milk production and udder health traits in Montbeliarde cows Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-19 Aurélie Vinet, Sophie Mattalia, Roxane Vallée, Christine Bertrand, Beatriz C. D. Cuyabano, Didier Boichard
Heat stress negatively influences cattle welfare, health and productivity. To cope with the forecasted increases in temperature and heat waves frequency, identifying high-producing animals that are tolerant to heat is of capital importance to maintain milk production. This study, based on the joint analysis of on-farm performance and weather data, had two objectives: (1) to determine the response in
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Unraveling the phenotypic and genomic background of behavioral plasticity and temperament in North American Angus cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-19 Amanda B. Alvarenga, Hinayah R. Oliveira, Simon P. Turner, Andre Garcia, Kelli J. Retallick, Stephen P. Miller, Luiz F. Brito
Longitudinal records of temperament can be used for assessing behavioral plasticity, such as aptness to learn, memorize, or change behavioral responses based on affective state. In this study, we evaluated the phenotypic and genomic background of North American Angus cow temperament measured throughout their lifetime around the weaning season, including the development of a new indicator trait termed
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Predicting the impact of genotype-by-genotype interaction on the purebred–crossbred genetic correlation from phenotype and genotype marker data of parental lines Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-13 Duenk, Pascal, Wientjes, Yvonne C. J., Bijma, Piter, Iversen, Maja W., Lopes, Marcos S., Calus, Mario P. L.
The genetic correlation between purebred (PB) and crossbred (CB) performances ( $${r}_{pc}$$ ) partially determines the response in CB when selection is on PB performance in the parental lines. An earlier study has derived expressions for an upper and lower bound of $${r}_{pc}$$ , using the variance components of the parental purebred lines, including e.g. the additive genetic variance in the sire
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A computationally efficient method for approximating reliabilities in large-scale single-step genomic prediction Genet. Sel. Evol. (IF 5.1) Pub Date : 2023-01-05 Gao, Hongding, Kudinov, Andrei A., Taskinen, Matti, Pitkänen, Timo J., Lidauer, Martin H., Mäntysaari, Esa A., Strandén, Ismo
In this study, computationally efficient methods to approximate the reliabilities of genomic estimated breeding values (GEBV) in a single-step genomic prediction model including a residual polygenic (RPG) effect are described. In order to calculate the reliabilities of the genotyped animals, a single nucleotide polymorphism best linear unbiased prediction (SNPBLUP) or a genomic BLUP (GBLUP), was used
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A comparison of marker-based estimators of inbreeding and inbreeding depression Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-12-27 Caballero, Armando, Fernández, Almudena, Villanueva, Beatriz, Toro, Miguel A.
The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization
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Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-12-19 Mora, Mónica, Velasco-Galilea, María, Sánchez, Juan Pablo, Ramayo-Caldas, Yuliaxis, Piles, Miriam
The effect of the cecal microbiome on growth of rabbits that were fed under different regimes has been studied previously. However, the term “effect” carries a causal meaning that can be confounded because of potential genetic associations between the microbiome and production traits. Structural equation models (SEM) can help disentangle such a complex interplay by decomposing the effect on a production
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Application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-12-16 Kotlarz, Krzysztof, Kosinska-Selbi, Barbara, Cai, Zexi, Sahana, Goutam, Szyda, Joanna
Genome-wide association studies (GWAS) help identify polymorphic sites or genes linked to phenotypic variance, but a few identified genes and/or single nucleotide polymorphisms (SNPs) are unlikely to explain a large part of the phenotypic variability of complex traits. In this study, the focus was moved from single loci to functional units, expressed by the metabolic pathways as defined in the Kyoto
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Genetic characteristics of colostrum refractive index and its use as a proxy for the concentration of immunoglobulins in Holstein cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-12-02 Costa, Angela, Visentin, Giulio, Goi, Arianna, De Marchi, Massimo, Penasa, Mauro
Colostral concentration of immunoglobulins (Ig) is crucial for the passive transfer of antibodies from the cow to the new-born calf. Direct determination of Ig by the gold standard radial immunodiffusion method is demanding in terms of time and costs. For this reason, a refractometer is commonly used at the farm level for an indirect estimation of colostrum quality, which is given as the Ig concentration
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Inference about quantitative traits under selection: a Bayesian revisitation for the post-genomic era Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-12-02 Gianola, Daniel, Fernando, Rohan L., Schön, Chris C.
Selection schemes distort inference when estimating differences between treatments or genetic associations between traits, and may degrade prediction of outcomes, e.g., the expected performance of the progeny of an individual with a certain genotype. If input and output measurements are not collected on random samples, inferences and predictions must be biased to some degree. Our paper revisits inference
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Host genetic control on rumen microbiota and its impact on dairy traits in sheep Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-11-24 Martinez Boggio, Guillermo, Meynadier, Annabelle, Buitenhuis, Albert Johannes, Marie-Etancelin, Christel
Milk yield and fine composition in sheep depend on the volatile and long-chain fatty acids, microbial proteins, vitamins produced through feedstuff digestion by the rumen microbiota. In cattle, the host genome has been shown to have a low to moderate genetic control on rumen microbiota abundance but a high control on dairy traits with heritabilities higher than 0.30. There is little information on
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Optimisation of the core subset for the APY approximation of genomic relationships Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-11-22 Pocrnic, Ivan, Lindgren, Finn, Tolhurst, Daniel, Herring, William O., Gorjanc, Gregor
By entering the era of mega-scale genomics, we are facing many computational issues with standard genomic evaluation models due to their dense data structure and cubic computational complexity. Several scalable approaches have been proposed to address this challenge, such as the Algorithm for Proven and Young (APY). In APY, genotyped animals are partitioned into core and non-core subsets, which induces
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Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-11-18 Wang, Dan, Xie, Kerui, Wang, Yanyan, Hu, Jiaqing, Li, Wenqiang, Yang, Aiguo, Zhang, Qin, Ning, Chao, Fan, Xinzhong
Rabbit wool traits are important in fiber production and for model organism research on hair growth, but their genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a breed well-known for the quality of its wool. Considering the cost to generate population-scale sequence data and the biased detection of variants using chip data, developing an effective
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Failing the four-gamete test enables exact phasing: the Corners’ Algorithm Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-11-14 Gomez-Raya, Luis, Rauw, Wendy M.
Failing the four-gamete test for two polymorphic DNA markers is an indication that two or three rather than four haplotypes segregate in the population. The objective of this paper is to show that when just three haplotypes are segregating, all three haplotypes can be fully and unambiguously phase-resolved. The Corners’ Algorithm tests the four corners in a 3 × 3 table of two-locus genotypes. If one
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Can breeders prevent pathogen adaptation when selecting for increased resistance to infectious diseases? Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-11-08 Hulst, Andries D., Bijma, Piter, De Jong, Mart C. M.
Recent research shows that genetic selection has high potential to reduce the prevalence of infectious diseases in livestock. However, like all interventions that target infectious diseases, genetic selection of livestock can exert selection pressure on pathogen populations. Such selection on the pathogen may lead to escape strategies and reduce the effect of selection of livestock for disease resistance
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A method to obtain exact single-step GBLUP for non-genotyped descendants when the genomic relationship matrix of ancestors is not available Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-10-31 Garrick, Dorian J., Fernando, Rohan L.
Single-step genomic best linear unbiased prediction (GBLUP) involves a joint analysis of individuals with genotype information, and their ancestors, descendants, or contemporaries, without recorded genotypes. Livestock applications typically represent populations with fewer individuals with genotypes relative to the number not genotyped. Most breeding programmes are structured, consisting of a nucleus
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Mutation of the MYH3 gene causes recessive cleft palate in Limousine cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-10-29 Vaiman, Anne, Fritz, Sébastien, Beauvallet, Christian, Boussaha, Mekki, Grohs, Cécile, Daniel-Carlier, Nathalie, Relun, Anne, Boichard, Didier, Vilotte, Jean-Luc, Duchesne, Amandine
The palate is a structure separating the oral and nasal cavities and its integrity is essential for feeding and breathing. The total or partial opening of the palate is called a cleft palate and is a common malformation in mammals with environmental or hereditary aetiologies. Generally, it compromises life expectancy in the absence of surgical repair. A new form of non-syndromic cleft palate arose
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Inbreeding and pedigree analysis of the European red dairy cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-10-23 Nyman, Sofia, Johansson, Anna M., Palucci, Valentina, Schönherz, Anna A., Guldbrandtsen, Bernt, Hinrichs, Dirk, de Koning, Dirk-Jan
Red dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals
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Impacts of additive, dominance, and inbreeding depression effects on genomic evaluation by combining two SNP chips in Canadian Yorkshire pigs bred in China Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-10-22 Mei, Quanshun, Vitezica, Zulma G., Li, Jielin, Zhao, Shuhong, Legarra, Andres, Xiang, Tao
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, dominance effects that may be important for some traits can be fitted
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Genetic parameters of colostrum and calf serum antibodies in Swedish dairy cattle Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-10-22 Cordero-Solorzano, Juan, de Koning, Dirk-Jan, Tråvén, Madeleine, de Haan, Therese, Jouffroy, Mathilde, Larsson, Andrea, Myrthe, Aline, Arts, Joop A. J., Parmentier, Henk K., Bovenhuis, Henk, Wensman, Jonas Johansson
A sufficient IgG content in the colostrum is essential for the newborn calf, as it provides passive immunity which substantially affects the probability of survival during rearing. Failure of passive transfer (FPT) occurs when a calf does not absorb enough antibodies from the colostrum and is defined by an IgG concentration in calf serum lower than 10 g/L. Apart from delayed access to colostrum, FPT
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New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-10-15 Sanchez, Marie-Pierre, Tribout, Thierry, Fritz, Sébastien, Guatteo, Raphaël, Fourichon, Christine, Schibler, Laurent, Delafosse, Arnaud, Boichard, Didier
Bovine paratuberculosis, or Johne’s disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences. An important line of defense to this disease is host genetic resistance to MAP, which, when it will be more fully understood, could be
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Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-27 Garcia, Andre, Aguilar, Ignacio, Legarra, Andres, Tsuruta, Shogo, Misztal, Ignacy, Lourenco, Daniela
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, for genotyped animals not in the official evaluations, and when
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Genomic prediction with whole-genome sequence data in intensely selected pig lines Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-24 Ros-Freixedes, Roger, Johnsson, Martin, Whalen, Andrew, Chen, Ching-Yi, Valente, Bruno D., Herring, William O., Gorjanc, Gregor, Hickey, John M.
Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. However, empirical results have been ambiguous so far. Large datasets that capture most of the genomic diversity in a population must be assembled so that allele substitution effects are estimated with high accuracy. The objectives of this study were to use a
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Causal inference for the covariance between breeding values under identity disequilibrium Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-23 Cantet, Rodolfo J. C., Angarita-Barajas, Belcy K., Forneris, Natalia S., Munilla, Sebastián
The covariance matrix of breeding values is at the heart of prediction methods. Prediction of breeding values can be formulated using either an “observed” or a theoretical covariance matrix, and a major argument for choosing one or the other is the reduction of the computational burden for inverting such a matrix. In this regard, covariance matrices that are derived from Markov causal models possess
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Optimization of alternative breeding schemes for the genetic improvement of common Tigray highland sheep in northern Ethiopia Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-16 Haileselassie, Kiflay Welday, Kebede, Solomon Abgaz, Letta, Mengistu Ugre, GebreMichael, Solomon Gizaw
Genetic improvement is one of the major means to enhance the productivity of livestock, and well-designed animal genetic improvement schemes are necessary to achieve genetic gains. The objective of the current study was to design an alternative breeding program to improve the productivity of common Tigray highland sheep. Two village- and two central nucleus-based breeding schemes were simulated and
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Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-14 Liu, Yuwen, Fu, Yang, Yang, Yalan, Yi, Guoqiang, Lian, Jinmin, Xie, Bingkun, Yao, Yilong, Chen, Muya, Niu, Yongchao, Liu, Lei, Wang, Liyuan, Zhang, Yongsheng, Fan, Xinhao, Tang, Yijie, Yuan, Pengxiang, Zhu, Min, Li, Qiaowei, Zhang, Song, Chen, Yun, Wang, Binhu, He, Jieyu, Lu, Dan, Liachko, Ivan, Sullivan, Shawn T., Pang, Bin, Chen, Yaoqing, He, Xin, Li, Kui, Tang, Zhonglin
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology
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Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-09 Kalds, Peter, Zhou, Shiwei, Gao, Yawei, Cai, Bei, Huang, Shuhong, Chen, Yulin, Wang, Xiaolong
After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order
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Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-06 Bolormaa, Sunduimijid, MacLeod, Iona M., Khansefid, Majid, Marett, Leah C., Wales, William J., Miglior, Filippo, Baes, Christine F., Schenkel, Flavio S., Connor, Erin E., Manzanilla-Pech, Coralia I. V., Stothard, Paul, Herman, Emily, Nieuwhof, Gert J., Goddard, Michael E., Pryce, Jennie E.
Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international
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Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission Genet. Sel. Evol. (IF 5.1) Pub Date : 2022-09-05 Pooley, Christopher, Marion, Glenn, Bishop, Stephen, Doeschl-Wilson, Andrea
The spread of infectious diseases in populations is controlled by the susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection), and recoverability (propensity to recover/die) of individuals. Estimating genetic risk factors for these three underlying host epidemiological traits can help reduce disease spread through genetic control strategies. Previous studies