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Estimating genomic relationships of metafounders across and within breeds using maximum likelihood, pseudo-expectation–maximization maximum likelihood and increase of relationships Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-05-02 Andres Legarra, Matias Bermann, Quanshun Mei, Ole F. Christensen
The theory of “metafounders” proposes a unified framework for relationships across base populations within breeds (e.g. unknown parent groups), and base populations across breeds (crosses) together with a sensible compatibility with genomic relationships. Considering metafounders might be advantageous in pedigree best linear unbiased prediction (BLUP) or single-step genomic BLUP. Existing methods to
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Redefining and interpreting genomic relationships of metafounders Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-05-02 Andres Legarra, Matias Bermann, Quanshun Mei, Ole F. Christensen
Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics—namely, heterozygosities
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Equivalence of variance components between standard and recursive genetic models using LDL′ transformations Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-05-02 Luis Varona, David López-Carbonell, Houssemeddine Srihi, Carlos Hervás-Rivero, Óscar González-Recio, Juan Altarriba
Recursive models are a category of structural equation models that propose a causal relationship between traits. These models are more parameterized than multiple trait models, and they require imposing restrictions on the parameter space to ensure statistical identification. Nevertheless, in certain situations, the likelihood of recursive models and multiple trait models are equivalent. Consequently
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Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-05-02 Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Fabio Pilla, Matteo Komjanc, Alessandro Achilli, Heidi Christine Hauffe, Paolo Ajmone Marsan
Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to
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Genomic prediction of blood biomarkers of metabolic disorders in Holstein cattle using parametric and nonparametric models Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-29 Lucio F. M. Mota, Diana Giannuzzi, Sara Pegolo, Enrico Sturaro, Daniel Gianola, Riccardo Negrini, Erminio Trevisi, Paolo Ajmone Marsan, Alessio Cecchinato
Metabolic disturbances adversely impact productive and reproductive performance of dairy cattle due to changes in endocrine status and immune function, which increase the risk of disease. This may occur in the post-partum phase, but also throughout lactation, with sub-clinical symptoms. Recently, increased attention has been directed towards improved health and resilience in dairy cattle, and genomic
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Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-17 Tristan Kistler, Evert W. Brascamp, Benjamin Basso, Piter Bijma, Florence Phocas
Breeding queens may be mated with drones that are produced by a single drone-producing queen (DPQ), or a group of sister-DPQs, but often only the dam of the DPQ(s) is reported in the pedigree. Furthermore, datasets may include colony phenotypes from DPQs that were open-mated at different locations, and thus to a heterogeneous drone population. Simulation was used to investigate the impact of the mating
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Estimating genetic parameters of digital behavior traits and their relationship with production traits in purebred pigs Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-16 Mary Kate Hollifield, Ching-Yi Chen, Eric Psota, Justin Holl, Daniela Lourenco, Ignacy Misztal
With the introduction of digital phenotyping and high-throughput data, traits that were previously difficult or impossible to measure directly have become easily accessible, offering the opportunity to enhance the efficiency and rate of genetic gain in animal production. It is of interest to assess how behavioral traits are indirectly related to the production traits during the performance testing
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Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-09 Chao Wang, Choulin Chen, Bowen Lei, Shenghua Qin, Yuanyuan Zhang, Kui Li, Song Zhang, Yuwen Liu
Enhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding epigenetic regulation mediated by eRNAs, research on the construction of eRNA-mediated gene regulatory networks (eGRN) and the identification of critical network components that influence complex traits is lacking. Here, employing the pig as a model, we conducted a comprehensive
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Mendelian randomization analysis of 34,497 German Holstein cows to infer causal associations between milk production and health traits Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-08 Helen Schneider, Valentin Haas, Ana-Marija Krizanac, Clemens Falker-Gieske, Johannes Heise, Jens Tetens, Georg Thaller, Jörn Bennewitz
Claw diseases and mastitis represent the most important health issues in dairy cattle with a frequently mentioned connection to milk production. Although many studies have aimed at investigating this connection in more detail by estimating genetic correlations, they do not provide information about causality. An alternative is to carry out Mendelian randomization (MR) studies using genetic variants
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Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-02 Meilin Jin, Huihua Wang, Gang Liu, Jian Lu, Zehu Yuan, Taotao Li, Engming Liu, Zengkui Lu, Lixin Du, Caihong Wei
Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions
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Microbiome composition as a potential predictor of longevity in rabbits Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-02 Iliyass Biada, Noelia Ibáñez-Escriche, Agustín Blasco, Cristina Casto-Rebollo, Maria A. Santacreu
Longevity and resilience are two fundamental traits for more sustainable livestock production. These traits are closely related, as resilient animals tend to have longer lifespans. An interesting criterion for increasing longevity in rabbit could be based on the information provided by its gut microbiome. The gut microbiome is essential for regulating health and plays crucial roles in the development
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Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-04-02 Ruifei Yang, Siqi Jin, Suyun Fang, Dawei Yan, Hao Zhang, Jingru Nie, Jinqiao Liu, Minjuan Lv, Bo Zhang, Xinxing Dong
Gene flow is crucial for enhancing economic traits of livestock. In China, breeders have used hybridization strategies for decades to improve livestock performance. Here, we performed whole-genome sequencing of a native Chinese Lijiang pig (LJP) breed. By integrating previously published data, we explored the genetic structure and introgression of genetic components from commercial European pigs (EP)
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Effect of temperature-humidity index on the evolution of trade-offs between fertility and production in dairy cattle Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-29 Aurélie Vinet, Sophie Mattalia, Roxane Vallée, Christine Bertrand, Anne Barbat, Julie Promp, Beatriz C. D. Cuyabano, Didier Boichard
In the current context of climate change, livestock production faces many challenges to improve the sustainability of systems. Dairy farming, in particular, must find ways to select animals that will be able to achieve sufficient overall production while maintaining their reproductive ability in environments with increasing temperatures. With future forecasted climate conditions in mind, this study
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A common regulatory haplotype doubles lactoferrin concentration in milk Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-28 Thomas J. Lopdell, Alexander J. Trevarton, Janelle Moody, Claire Prowse-Wilkins, Sarah Knowles, Kathryn Tiplady, Amanda J. Chamberlain, Michael E. Goddard, Richard J. Spelman, Klaus Lehnert, Russell G. Snell, Stephen R. Davis, Mathew D. Littlejohn
Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is economically valuable and has an extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence has also been previously observed to regulate lactoferrin content in milk
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Estimation of genetic parameters for the implementation of selective breeding in commercial insect production Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-25 Laura Skrubbeltrang Hansen, Stine Frey Laursen, Simon Bahrndorff, Morten Kargo, Jesper Givskov Sørensen, Goutam Sahana, Hanne Marie Nielsen, Torsten Nygaard Kristensen
There is a burgeoning interest in using insects as a sustainable source of food and feed, particularly by capitalising on various waste materials and by-products that are typically considered of low value. Enhancing the commercial production of insects can be achieved through two main approaches: optimising environmental conditions and implementing selective breeding strategies. In order to successfully
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The genetics of resilience and its relationships with egg production traits and antibody traits in chickens Genet. Sel. Evol. (IF 4.1) Pub Date : 2024-03-19 Tom V. L. Berghof, Nicolas Bedere, Katrijn Peeters, Marieke Poppe, Jeroen Visscher, Han A. Mulder
Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits. Recently, resilience indicators based on longitudinal data have
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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