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Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-15 Marina Martínez-Álvaro, Jennifer Mattock, Óscar González-Recio, Alejandro Saborío-Montero, Ziqing Weng, Joana Lima, Carol-Anne Duthie, Richard Dewhurst, Matthew A. Cleveland, Mick Watson, Rainer Roehe
Growth rate is an important component of feed conversion efficiency in cattle and varies across the different stages of the finishing period. The metabolic effect of the rumen microbiome is essential for cattle growth, and investigating the genomic and microbial factors that underlie this temporal variation can help maximize feed conversion efficiency at each growth stage. By analysing longitudinal
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Confidence intervals for validation statistics with data truncation in genomic prediction Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-08 Matias Bermann, Andres Legarra, Alejandra Alvarez Munera, Ignacy Misztal, Daniela Lourenco
Validation by data truncation is a common practice in genetic evaluations because of the interest in predicting the genetic merit of a set of young selection candidates. Two of the most used validation methods in genetic evaluations use a single data partition: predictivity or predictive ability (correlation between pre-adjusted phenotypes and estimated breeding values (EBV) divided by the square root
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GWABLUP: genome-wide association assisted best linear unbiased prediction of genetic values Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-01 Theo Meuwissen, Leiv Sigbjorn Eikje, Arne B. Gjuvsland
Since the very beginning of genomic selection, researchers investigated methods that improved upon SNP-BLUP (single nucleotide polymorphism best linear unbiased prediction). SNP-BLUP gives equal weight to all SNPs, whereas it is expected that many SNPs are not near causal variants and thus do not have substantial effects. A recent approach to remedy this is to use genome-wide association study (GWAS)
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Searching for homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in the MMUT gene affecting newborn lamb viability Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-02-29 Maxime Ben Braiek, Carole Moreno-Romieux, Céline André, Jean-Michel Astruc, Philippe Bardou, Arnaud Bordes, Frédéric Debat, Francis Fidelle, Itsasne Granado-Tajada, Chris Hozé, Florence Plisson-Petit, François Rivemale, Julien Sarry, Némuel Tadi, Florent Woloszyn, Stéphane Fabre
Recessive deleterious variants are known to segregate in livestock populations, as in humans, and some may be lethal in the homozygous state. We used phased 50 k single nucleotide polymorphism (SNP) genotypes and pedigree data to scan the genome of 6845 Manech Tête Rousse dairy sheep to search for deficiency in homozygous haplotypes (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1
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Expected values for the accuracy of predicted breeding values accounting for genetic differences between reference and target populations Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-02-29 Beatriz C. D. Cuyabano, Didier Boichard, Cedric Gondro
Genetic merit, or breeding values as referred to in livestock and crop breeding programs, is one of the keys to the successful selection of animals in commercial farming systems. The developments in statistical methods during the twentieth century and single nucleotide polymorphism (SNP) chip technologies in the twenty-first century have revolutionized agricultural production, by allowing highly accurate
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Correction: Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-02-26 Jesús Valdés-Hernández, Josep M. Folch, Daniel Crespo-Piazuelo, Magí Passols, Cristina Sebastià, Lourdes Criado-Mesas, Anna Castelló, Armand Sánchez, Yuliaxis Ramayo-Caldas
Correction: Genetics Selection Evolution (2024) 56:12https://doi.org/10.1186/s12711-024-00882-x After publication of original article [1], we noticed that two errors were introduced during production: (1) In the Bioinformatic and statistical analyses section, the corresponding information on the X and Y matrices has been removed in three places: The part “A regularized canonical correlation analysis
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Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss) Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-02-22 Katy Paul, Gwendal Restoux, Florence Phocas
Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single
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Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-02-12 Jesús Valdés-Hernández, Josep M. Folch, Daniel Crespo-Piazuelo, Magí Passols, Cristina Sebastià, Lourdes Criado-Mesas, Anna Castelló, Armand Sánchez, Yuliaxis Ramayo-Caldas
Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and putative regulators involved in FA composition, we performed a multivariate integrative analysis between intramuscular FA and transcriptome profiles of porcine longissimus dorsi (LD) muscle. We also carried out
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Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-02-06 Jigme Dorji, Antonio Reverter, Pamela A. Alexandre, Amanda J. Chamberlain, Christy J. Vander-Jagt, James Kijas, Laercio R. Porto-Neto
The study of ancestral alleles provides insights into the evolutionary history, selection, and genetic structures of a population. In cattle, ancestral alleles are widely used in genetic analyses, including the detection of signatures of selection, determination of breed ancestry, and identification of admixture. Having a comprehensive list of ancestral alleles is expected to improve the accuracy of
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Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-31 Maulana Mughitz Naji, José Luis Gualdrón Duarte, Natalia Soledad Forneris, Tom Druet
Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding. We used data from 14,205 Belgian Blue beef cattle genotyped cows that
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Correction: Validation of reaction norm breeding values for robustness in Australian sheep Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-25 Dominic L. Waters, Sam A. Clark, Daniel J. Brown, Samuel F. Walkom, Julius H. J. van der Werf
Correction: Genetics Selection Evolution (2024) 56:4 https://doi.org/10.1186/s12711-023-00872-5 After publication of this original article [1], we noticed that an error was introduced in Eq. (2) page 3 which should be:$$\mathbf{y}=\mathbf{X}\mathbf{b}+{\mathbf{Z}}_{1}{\mathbf{a}}_{\mathbf{0}}+{\mathbf{Z}}_{\mathbf{2}}{\mathbf{a}}_{\mathbf{1}}+{\mathbf{Z}}_{\mathbf{3}}\mathbf{c}+\mathbf{Q}\mathbf{g}+{\mathbf{e}}
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The potential of microbiota information to better predict efficiency traits in growing pigs fed a conventional and a high-fiber diet Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-19 Vanille Déru, Francesco Tiezzi, Céline Carillier-Jacquin, Benoit Blanchet, Laurent Cauquil, Olivier Zemb, Alban Bouquet, Christian Maltecca, Hélène Gilbert
Improving pigs’ ability to digest diets with an increased dietary fiber content is a lever to improve feed efficiency and limit feed costs in pig production. The aim of this study was to determine whether information on the gut microbiota and host genetics can contribute to predict digestive efficiency (DE, i.e. digestibility coefficients of energy, organic matter, and nitrogen), feed efficiency (FE
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Simulation of dual-purpose chicken breeding programs implementing gene editing Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-17 Edward Y. S. Chuang, Robin Wellmann, Franck L. B. Meijboom, Jens Tetens, Jörn Bennewitz
In spite of being controversial and raising ethical concerns, the application of gene editing is more likely to be accepted when it contributes to improving animal welfare. One of the animal welfare and ethical issues in chicken breeding is chick culling, the killing of the male layer chicks after hatching due to the poor fattening performance. Although establishing dual-purpose chicken lines could
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A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-12 David Wragg, Wengang Zhang, Sarah Peterson, Murthy Yerramilli, Richard Mellanby, Jeffrey J. Schoenebeck, Dylan N. Clements
Low-pass whole-genome sequencing and imputation offer significant cost savings, enabling substantial increases in sample size and statistical power. This approach is particularly promising in livestock breeding, providing an affordable means of screening individuals for deleterious alleles or calculating genomic breeding values. Consequently, it may also be of value in companion animal genomics to
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Advances in understanding the genetic architecture of antibody response to paratuberculosis in sheep by heritability estimate and LDLA mapping analyses and investigation of candidate regions using sequence-based data Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-10 Mario Graziano Usai, Sara Casu, Tiziana Sechi, Sotero L. Salaris, Sabrina Miari, Giuliana Mulas, Maria Giovanna Cancedda, Ciriaco Ligios, Antonello Carta
Paratuberculosis is a contagious and incurable disease that is caused by Mycobacterium avium subsp. paratuberculosis (MAP) with significant negative effects on animal welfare and farm profitability. Based on a large naturally infected flock over 12 years, we analyzed repeated enzyme-linked immunosorbent assay tests (ELISA), OvineSNP50 BeadChip genotypes and whole-genome sequences imputed from 56 influential
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Validation of reaction norm breeding values for robustness in Australian sheep Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-05 Dominic L. Waters, Sam A. Clark, Daniel J. Brown, Samuel F. Walkom, Julius H. J. van der Werf
There can be variation between animals in how stable their genetic merit is across different environments due to genotype-by-environment (G×E) interactions. This variation could be used in breeding programs to select robust genotypes that combine high overall performance with stable genetic ranking across environments. There have been few attempts to validate breeding values for robustness in livestock
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Estimating the heritability of nitrogen and carbon isotopes in the tail hair of beef cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-03 Morteza Moradi, Christie L. Warburton, Laercio Ribeiro Porto-Neto, Luis F. P. Silva
The natural abundance of nitrogen (δ15N) and carbon (δ13C) isotopes in animal tissues are used to estimate an animal’s efficiency in nitrogen utilization, and their feed conversion efficiency, especially in tropical grazing systems with prolonged protein restriction. It is postulated that selection for improving these two characteristics (δ15N and δ13C) would assist the optimisation of the adaptation
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The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-03 Gabriele Senczuk, Martina Macrì, Marika Di Civita, Salvatore Mastrangelo, Maria del Rosario Fresno, Juan Capote, Fabio Pilla, Juan Vicente Delgado, Marcel Amills, Amparo Martínez
The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct
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Phenotype transition from wild mouflon to domestic sheep Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-01-02 Paolo Mereu, Monica Pirastru, Daria Sanna, Giovanni Bassu, Salvatore Naitana, Giovanni Giuseppe Leoni
The domestication of animals started around 12,000 years ago in the Near East region. This “endless process” is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of
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Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-21 Hui Wen, Jay S. Johnson, Pedro H. F. Freitas, Jacob M. Maskal, Leonardo S. Gloria, Andre C. Araujo, Victor B. Pedrosa, Francesco Tiezzi, Christian Maltecca, Yijian Huang, Allan P. Schinckel, Luiz F. Brito
Automatic and continuous recording of vaginal temperature (TV) using wearable sensors causes minimal disruptions to animal behavior and can generate data that enable the evaluation of temporal body temperature variation under heat stress (HS) conditions. However, the genetic basis of TV in lactating sows from a longitudinal perspective is still unknown. The objectives of this study were to define statistical
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Natural clines and human management impact the genetic structure of Algerian honey bee populations Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-19 Giovanna Salvatore, Amira Chibani Bahi Amar, Kamila Canale-Tabet, Riad Fridi, Nacera Tabet Aoul, Soumia Saci, Emmanuelle Labarthe, Valentino Palombo, Mariasilvia D’Andrea, Alain Vignal, Pierre Faux
The Algerian honey bee population is composed of two described subspecies A. m. intermissa and A. m. sahariensis, of which little is known regarding population genomics, both in terms of genetic differentiation and of possible contamination by exogenous stock. Moreover, the phenotypic differences between the two subspecies are expected to translate into genetic differences and possible adaptation to
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Genotype-by-environment interactions for feed efficiency traits in Nellore cattle based on bi-trait reaction norm models Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-14 João B. Silva Neto, Lucio F. M. Mota, Sabrina T. Amorim, Elisa Peripolli, Luiz F. Brito, Claudio U. Magnabosco, Fernando Baldi
Selecting animals for feed efficiency directly impacts the profitability of the beef cattle industry, which contributes to minimizing the environmental footprint of beef production. Genetic and environmental factors influence animal feed efficiency, leading to phenotypic variability when exposed to different environmental conditions (i.e., temperature and nutritional level). Thus, our aim was to assess
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Managing genomic diversity in conservation programs of Chinese domestic chickens Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-14 Mengmeng Zhang, Shiwei Wang, Ran Xu, Yijun Liu, Han Zhang, Mengxia Sun, Junyan Wang, Zhexi Liu, Keliang Wu
Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations. Three hundred
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Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-14 Juliane Friedrich, Richard I. Bailey, Andrea Talenti, Umer Chaudhry, Qasim Ali, Emmanuel F. Obishakin, Chukwunonso Ezeasor, Jessica Powell, Olivier Hanotte, Abdulfatai Tijjani, Karen Marshall, James Prendergast, Pamela Wiener
The genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this study, we analysed indigenous African cattle breeds as models of hybrid zones, considering taurine and indicine samples as ancestors. In a genomic cline analysis
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Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-12 Kyu-Sang Lim, Jian Cheng, Christopher Tuggle, Michael Dyck, PigGen Canada, Frederic Fortin, John Harding, Graham Plastow, Jack Dekkers
Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify potential genetic indicators for disease resilience that can be measured on selection candidates, we focused on the blood transcriptome
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The genetics of gaits in Icelandic horses goes beyond DMRT3, with RELN and STAU2 identified as two new candidate genes Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-11 Heiðrún Sigurðardóttir, Henrik Boije, Elsa Albertsdóttir, Thorvaldur Kristjansson, Marie Rhodin, Gabriella Lindgren, Susanne Eriksson
In domesticated animals, many important traits are complex and regulated by a large number of genes, genetic interactions, and environmental influences. The ability of Icelandic horses to perform the gait ‘pace’ is largely influenced by a single mutation in the DMRT3 gene, but genetic modifiers likely exist. The aim of this study was to identify novel genetic factors that influence pacing ability and
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A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-07 Klavdija Poklukar, Camille Mestre, Martin Škrlep, Marjeta Čandek-Potokar, Cristina Ovilo, Luca Fontanesi, Juliette Riquet, Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Maria Muñoz, Maurizio Gallo, Ricardo Bozzi, Rui Charneca, Raquel Quintanilla, Goran Kušec, Marie-José Mercat, Christoph Zimmer, Violeta Razmaite, Jose P. Araujo, Čedomir Radović, Radomir Savić, Danijel Karolyi, Bertrand Servin
Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically
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Genetic parameters, reciprocal cross differences, and age-related heterosis of egg-laying performance in chickens Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-07 Aixin Ni, Mario P. L. Calus, Henk Bovenhuis, Jingwei Yuan, Yuanmei Wang, Yanyan Sun, Jilan Chen
Egg-laying performance is economically important in poultry breeding programs. Crossbreeding between indigenous and elite commercial lines to exploit heterosis has been an upward trend in traditional layer breeding for niche markets. The objective of this study was to analyse the genetic background and to estimate the heterosis of longitudinal egg-laying traits in reciprocal crosses between an indigenous
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Impact of population structure in the estimation of recent historical effective population size by the software GONE Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-12-04 Irene Novo, Pilar Ordás, Natalia Moraga, Enrique Santiago, Humberto Quesada, Armando Caballero
Effective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration
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Micro-genetic environmental sensitivity across macro-environments of chickens reared in Burkina Faso and France Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-30 Mette Dam Madsen, Naomi Duijvesteijn, Julius van der Werf, Sam Clark
Commercial poultry production systems follow a pyramidal structure with a nucleus of purebred animals under controlled conditions at the top and crossbred animals under commercial production conditions at the bottom. Genetic correlations between the same phenotypes on nucleus and production animals can therefore be influenced by differences both in purebred-crossbred genotypes and in genotype-by-environment
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Genetic correlations of direct and indirect genetic components of social dominance with fitness and morphology traits in cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-30 Beniamino Tuliozi, Roberto Mantovani, Ivana Schoepf, Shogo Tsuruta, Enrico Mancin, Cristina Sartori
Within the same species, individuals show marked variation in their social dominance. Studies on a handful of populations have indicated heritable genetic variation for this trait, which is determined by both the genetic background of the individual (direct genetic effect) and of its opponent (indirect genetic effect). However, the evolutionary consequences of selection for this trait are largely speculative
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Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-28 José Luis Gualdrón Duarte, Can Yuan, Ann-Stephan Gori, Gabriel C. M. Moreira, Haruko Takeda, Wouter Coppieters, Carole Charlier, Michel Georges, Tom Druet
Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study for traits related to body size and muscular development in intensively selected beef cattle. We leveraged multiple trait information to refine and interpret the significant
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Heterogeneity in convergence behaviour of the single-step SNP-BLUP model across different effects and animal groups Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-23 Dawid Słomian, Kacper Żukowski, Joanna Szyda
The single-step model is becoming increasingly popular for national genetic evaluations of dairy cattle due to the benefits that it offers such as joint breeding value estimation for genotyped and ungenotyped animals. However, the complexity of the model due to a large number of correlated effects can lead to significant computational challenges, especially in terms of accuracy and efficiency of the
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Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-21 Gabriela Canabrava Gouveia, Virgínia Mara Pereira Ribeiro, Marina Rufino Salinas Fortes, Fernanda Santos Silva Raidan, Antonio Reverter, Laercio Ribeiro Porto-Neto, Mariana Mamedes de Moraes, Daniel Resende Gonçalves, Marcos Vinicius Gualberto Barbosa da Silva, Fabio Luiz Buranelo Toral
Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope
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Defining valid breeding goals for animal breeds Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-21 Robin Wellmann, Nicolas Gengler, Jörn Bennewitz, Jens Tetens
The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption. The generalized approach is based
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Correction: Sequence-based GWAS meta-analyses for beef production traits Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-13 Marie-Pierre Sanchez, Thierry Tribout, Naveen K. Kadri, Praveen K. Chitneedi, Steffen Maak, Chris Hozé, Mekki Boussaha, Pascal Croiseau, Romain Philippe, Mirjam Spengeler, Christa Kühn, Yining Wang, Changxi Li, Graham Plastow, Hubert Pausch, Didier Boichard
Correction: Genetics Selection Evolution (2023) 55:70 https://doi.org/10.1186/s12711-023-00848-5 Following publication of the original article [1], it has been reported that the incorrect copyright holder was used. The correct copyright holder is: © His Majesty the King in Right of Canada as represented by the Minister of Agriculture and Agri-Food Canada. The original article [1] has been corrected
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Exploring the potential of incremental feature selection to improve genomic prediction accuracy Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-09 Felix Heinrich, Thomas Martin Lange, Magdalena Kircher, Faisal Ramzan, Armin Otto Schmitt, Mehmet Gültas
The ever-increasing availability of high-density genomic markers in the form of single nucleotide polymorphisms (SNPs) enables genomic prediction, i.e. the inference of phenotypes based solely on genomic data, in the field of animal and plant breeding, where it has become an important tool. However, given the limited number of individuals, the abundance of variables (SNPs) can reduce the accuracy of
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Disentangling the dynamics of energy allocation to develop a proxy for robustness of fattening pigs Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-07 Guillaume Lenoir, Loïc Flatres-Grall, Rafael Muñoz-Tamayo, Ingrid David, Nicolas C. Friggens
There is a growing need to improve robustness of fattening pigs, but this trait is difficult to phenotype. Our first objective was to develop a proxy for robustness of fattening pigs by modelling the longitudinal energy allocation coefficient to growth, with the resulting environmental variance of this allocation coefficient considered as a proxy for robustness. The second objective was to estimate
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Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-11-02 Amanda B. Alvarenga, Kelli J. Retallick, Andre Garcia, Stephen P. Miller, Andrew Byrne, Hinayah R. Oliveira, Luiz F. Brito
Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and
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Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-25 Katherine D. Arias, Juan Pablo Gutiérrez, Iván Fernández, Isabel Álvarez, Félix Goyache
In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment
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Combined single-step evaluation of functional longevity of dairy cows including correlated traits Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-25 Laure-Hélène Maugan, Roberta Rostellato, Thierry Tribout, Sophie Mattalia, Vincent Ducrocq
For years, multiple trait genetic evaluations have been used to increase the accuracy of estimated breeding values (EBV) using information from correlated traits. In France, accurate approximations of multiple trait evaluations were implemented for traits that are described by different models by combining the results of univariate best linear unbiased prediction (BLUP) evaluations. Functional longevity
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Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-23 Zhang Wang, Weihua Tian, Dandan Wang, Yulong Guo, Zhimin Cheng, Yanyan Zhang, Xinyan Li, Yihao Zhi, Donghua Li, Zhuanjian Li, Ruirui Jiang, Guoxi Li, Yadong Tian, Xiangtao Kang, Hong Li, Ian C. Dunn, Xiaojun Liu
Modern breeding strategies have resulted in significant differences in muscle mass between indigenous chicken and specialized broiler. However, the molecular regulatory mechanisms that underlie these differences remain elusive. The aim of this study was to identify key genes and regulatory mechanisms underlying differences in breast muscle development between indigenous chicken and specialized broiler
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Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-18 Di Zhu, Yiqiang Zhao, Ran Zhang, Hanyu Wu, Gengyuan Cai, Zhenfang Wu, Yuzhe Wang, Xiaoxiang Hu
Although the accumulation of whole-genome sequencing (WGS) data has accelerated the identification of mutations underlying complex traits, its impact on the accuracy of genomic predictions is limited. Reliable genotyping data and pre-selected beneficial loci can be used to improve prediction accuracy. Previously, we reported a low-coverage sequencing genotyping method that yielded 11.3 million highly
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Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-16 Ben J. Hayes, James Copley, Elsie Dodd, Elizabeth M. Ross, Shannon Speight, Geoffry Fordyce
It has been challenging to implement genomic selection in multi-breed tropical beef cattle populations. If commercial (often crossbred) animals could be used in the reference population for these genomic evaluations, this could allow for very large reference populations. In tropical beef systems, such animals often have no pedigree information. Here we investigate potential models for such data, using
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Sequence-based GWAS meta-analyses for beef production traits Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-12 Marie-Pierre Sanchez, Thierry Tribout, Naveen K. Kadri, Praveen K. Chitneedi, Steffen Maak, Chris Hozé, Mekki Boussaha, Pascal Croiseau, Romain Philippe, Mirjam Spengeler, Christa Kühn, Yining Wang, Changxi Li, Graham Plastow, Hubert Pausch, Didier Boichard
Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed
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The mRNA-lncRNA landscape of multiple tissues uncovers key regulators and molecular pathways that underlie heterosis for feed intake and efficiency in laying chickens Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-06 Jingwei Yuan, Jinmeng Zhao, Yanyan Sun, Yuanmei Wang, Yunlei Li, Aixin Ni, Yunhe Zong, Hui Ma, Panlin Wang, Lei Shi, Jilan Chen
Heterosis is routinely exploited to improve animal performance. However, heterosis and its underlying molecular mechanism for feed intake and efficiency have been rarely explored in chickens. Feed efficiency continues to be an important breeding goal trait since feed accounts for 60 to 70% of the total production costs in poultry. Here, we profiled the mRNA-lncRNA landscape of 96 samples of the hypothalamus
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Interpreting single-step genomic evaluation as a neural network of three layers: pedigree, genotypes, and phenotypes Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-10-03 Tianjing Zhao, Hao Cheng
The single-step approach has become the most widely-used methodology for genomic evaluations when only a subset of phenotyped individuals in the pedigree are genotyped, where the genotypes for non-genotyped individuals are imputed based on gene contents (i.e., genotypes) of genotyped individuals through their pedigree relationships. We proposed a new method named single-step neural network with mixed
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Towards genetic improvement of social behaviours in livestock using large-scale sensor data: data simulation and genetic analysis Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-28 Zhuoshi Wang, Harmen Doekes, Piter Bijma
Harmful social behaviours, such as injurious feather pecking in poultry and tail biting in swine, reduce animal welfare and production efficiency. While these behaviours are heritable, selective breeding is still limited due to a lack of individual phenotyping methods for large groups and proper genetic models. In the near future, large-scale longitudinal data on social behaviours will become available
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An improved transmissibility model to detect transgenerational transmitted environmental effects Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-21 Ingrid David, Anne Ricard
Evolutionary studies have reported that non-genetic information can be inherited across generations (epigenetic marks, microbiota, cultural inheritance). Non-genetic information is considered to be a key element to explain the adaptation of wild species to environmental constraints because it lies at the root of the transgenerational transmission of environmental effects. The “transmissibility model”
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Genetic parameters for automatically-measured vaginal temperature, respiration efficiency, and other thermotolerance indicators measured on lactating sows under heat stress conditions Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-20 Pedro H. F. Freitas, Jay S. Johnson, Hui Wen, Jacob M. Maskal, Francesco Tiezzi, Christian Maltecca, Yijian Huang, Ashley E. DeDecker, Allan P. Schinckel, Luiz F. Brito
Genetic selection based on direct indicators of heat stress could capture additional mechanisms that are involved in heat stress response and enable more accurate selection for more heat-tolerant individuals. Therefore, the main objectives of this study were to estimate genetic parameters for various heat stress indicators in a commercial population of Landrace × Large White lactating sows measured
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Potential selection for lipid kinase activity and spermatogenesis in Henan native pig breeds and growth shaping by introgression of European genes Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-18 Ruimin Qiao, Xinjian Li, Ole Madsen, Martien A. M. Groenen, Pan Xu, Kejun Wang, Xuelei Han, Gaiying Li, Xiuling Li, Kui Li
China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and
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Genetic analysis of geometric morphometric 3D visuals of French jumping horses Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-18 Anne Ricard, Nathalie Crevier-Denoix, Philippe Pourcelot, Harmony Crichan, Margot Sabbagh, Bernard Dumont-Saint-Priest, Sophie Danvy
For centuries, morphology has been the most commonly selected trait in horses. A 3D video recording enabled us to obtain the coordinates of 43 anatomical landmarks of 2089 jumping horses. Generalized Procrustes analysis provided centered and scaled coordinates that were independent of volume, i.e., centroid size. Genetic analysis of these coordinates (mixed model; 17,994 horses in the pedigree) allowed
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Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-14 Caleb J. Grohmann, Caleb M. Shull, Tamar E. Crum, Clint Schwab, Timothy J. Safranski, Jared E. Decker
Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand
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Metabolomic-genomic prediction can improve prediction accuracy of breeding values for malting quality traits in barley Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-09-05 Xiangyu Guo, Pernille Sarup, Ahmed Jahoor, Just Jensen, Ole F. Christensen
Metabolomics measures an intermediate stage between genotype and phenotype, and may therefore be useful for breeding. Our objectives were to investigate genetic parameters and accuracies of predicted breeding values for malting quality (MQ) traits when integrating both genomic and metabolomic information. In total, 2430 plots of 562 malting spring barley lines from three years and two locations were
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Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-08-17 Victoria Lindsay-McGee, Enrique Sanchez-Molano, Georgios Banos, Emily L. Clark, Richard J. Piercy, Androniki Psifidi
The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism
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Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss) Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-08-14 Clémence Fraslin, Diego Robledo, Antti Kause, Ross D. Houston
Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that affects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of the host resistance. However, genomic selection is expensive partly because of the cost of genotyping large numbers of animals using high-density single nucleotide polymorphism
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Estimation and consequences of direct-maternal genetic and environmental covariances in models for genetic evaluation in broilers Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-08-07 Hélène Romé, Thinh T. Chu, Danye Marois, Chyong-Huoy Huang, Per Madsen, Just Jensen
Maternal effects influence juvenile traits such as body weight and early growth in broilers. Ignoring significant maternal effects leads to reduced accuracy and inflated predicted breeding values. Including genetic and environmental direct-maternal covariances into prediction models in broilers can increase the accuracy and limit inflation of predicted breeding values better than simply adding maternal
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Using residual regressions to quantify and map signal leakage in genomic prediction Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-08-07 Bruno D. Valente, Gustavo de los Campos, Alexander Grueneberg, Ching-Yi Chen, Roger Ros-Freixedes, William O. Herring
Most genomic prediction applications in animal breeding use genotypes with tens of thousands of single nucleotide polymorphisms (SNPs). However, modern sequencing technologies and imputation algorithms can generate ultra-high-density genotypes (including millions of SNPs) at an affordable cost. Empirical studies have not produced clear evidence that using ultra-high-density genotypes can significantly
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deepGBLUP: joint deep learning networks and GBLUP framework for accurate genomic prediction of complex traits in Korean native cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-07-31 Hyo-Jun Lee, Jun Heon Lee, Cedric Gondro, Yeong Jun Koh, Seung Hwan Lee
Genomic prediction has become widespread as a valuable tool to estimate genetic merit in animal and plant breeding. Here we develop a novel genomic prediction algorithm, called deepGBLUP, which integrates deep learning networks and a genomic best linear unbiased prediction (GBLUP) framework. The deep learning networks assign marker effects using locally-connected layers and subsequently use them to
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Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs Genet. Sel. Evol. (IF 4.1) Pub Date : 2023-07-26 Sungbong Jang, Roger Ros-Freixedes, John M. Hickey, Ching-Yi Chen, Justin Holl, William O. Herring, Ignacy Misztal, Daniela Lourenco
Whole-genome sequence (WGS) data harbor causative variants that may not be present in standard single nucleotide polymorphism (SNP) chip data. The objective of this study was to investigate the impact of using preselected variants from WGS for single-step genomic predictions in maternal and terminal pig lines with up to 1.8k sequenced and 104k sequence imputed animals per line. Two maternal and four