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Genetic parameters for different types of medullated fibre in Alpacas J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-26 Alan Cruz, Yanin Murillo, Alonso Burgos, Alex Yucra, Renzo Morante, Max Quispe, Christian Quispe, Edgar Quispe, Juan Pablo Gutiérrez
The quality of alpaca textile fibre has great potential, especially if objectionable fibres (coarse and medullated fibres) that cause itching are reduced, considering that objectionable fibres can be identified by diameter and medullation types. The objective of this study was to estimate genetic parameters for medullar types and their respective diameters to evaluate the possibility of incorporating
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Characterization of runs of homozygosity islands in American mink using whole‐genome sequencing data J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-23 Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Younes Miar
The genome‐wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome‐wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole‐genome
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Identification of genomic regions and pathways associated with traits related to rumen acidosis in feedlot Nellore cattle J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-20 Daniela D. Estevam, Johnny M. Souza, Fernando S. B. Rey, Cyntia L. Martins, Nedenia B. Stafuzza, Rafael Espigolan, Danilo D. Millen, Mario D. B. Arrigoni
There may be an increased risk of metabolic disorders, such as rumen acidosis, in cattle fed high‐concentrate diets, particularly those from Bos taurus indicus genotypes, which have shown to be more sensitive to ruminal acidification. Therefore, this study aimed to estimate (co)variance components and identify genomic regions and pathways associated with ruminal acidosis in feedlot Nellore cattle fed
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Correction to Impact of multi-output and stacking methods on feed efficiency prediction from genotype using machine learning algorithms J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-12
Mora M, González P, Quevedo JR, Montañés E, Tusell L, Bergsma R, Piles M. Impact of multi-output and stacking methods on feed efficiency prediction from genotype using machine learning algorithms. J Anim Breed Genet. 2023 Nov;140(6):638–652. doi: 10.1111/jbg.12815. PMID: 37403756. The text in the funding section in the published article is incorrect; the correct text is shown below. This work received
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Estimation of genetic parameters for reproductive indices in sheep J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-10 Beatriz Bastos Senes, Valdecy Aparecida Rocha da Cruz, Hymerson Costa Azevedo, Raphael Bermal Costa, Gregório Miguel Ferreira de Camargo
This study aimed to estimate two reproductive efficiency indices in sheep based on the ratio between litter weight (at birth and weaning) and dam weight, as well as their genetic parameters. Phenotypic and pedigree data comprising the period from 1990 to 2018 were obtained from the Santa Inês sheep database of Embrapa Tabuleiros Costeiros. For estimation of the genetic parameters of the indices, a
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Genetic analysis of body weight and growth curve parameters in Muzaffarnagari sheep of India J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-30 Ajoy Mandal, Indrajit Gayari, Hasan Baneh, David R. Notter
The objective of this study was to estimate genetic effects on parameters of the Brody and Richards growth curves using body weight records from birth to 12 months of age on 2287 Muzaffarnagari lamb for a period of 29 years (1976–2004). Estimated growth curve parameters were analysed using six univariate animal models, and genetic correlations among and between the parameters of each function and between
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Sex-specific genetic parameter estimates of body weight in Mazandaran indigenous chickens J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-03 Mohammad Esmaeili, Mohsen Gholizadeh, Hasan Hafezian, Ayoub Farhadi
Body weight is an economically important trait in poultry that shows sexual dimorphism (SD). In the present study, variation in SD in Mazandaran native chickens was investigated in terms of the (Co) variance components and genetic parameters of body weight between males and females. Studied traits were body weights at hatch (BW1), 8 weeks (BW8) and 12 weeks of age (BW12). Also, for weight at sexual
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Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-01 Nora Laseca, Chiraz Ziadi, Davinia I. Perdomo-Gonzalez, Mercedes Valera, Sebastián Demyda-Peyras, Antonio Molina
Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level
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Inbreeding depression and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-02-01 Oscar Cortes, Javier Cañon, Sara Andrino, María Fernanadez, Carlos Carleos
Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree-based inbreeding coefficients. However, with the development of single-nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding
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Estimation of additive and maternal covariance of production traits in Murrah buffalo J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-29 Smriti Sharma, Surender Singh Dhaka, Chandrashekhar Santosh Patil
The study was done to determine additive, maternal and common permanent environmental effects and best-suited model for some production traits using six univariate animal models that differed in the (co)variance components fitted to assess the importance of maternal effect using likelihood ratio test in Murrah buffaloes. Data from 614 Murrah buffaloes related to production traits were collected from
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Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-21 Guoyan Qiao, Pan Xu, Tingting Guo, Xue He, Yaojing Yue, Bohui Yang
Genomic structural variants (SVs) constitute a significant proportion of genetic variation in the genome. The rapid development of long-reads sequencing has facilitated the detection of long-fragment SVs. There is no published study to detect SVs using long-read data from sheep. We applied a long-read mapping approach to detect SVs and characterized a total of 30,771 insertions, deletions, inversions
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Defining desired genetic gains for Pacific white shrimp (Litopenaeus vannamei) breeding objective using participatory approaches J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-19 Mina Rahbar, Roghieh Safari, Carlos I. Perez-Rostro
The objective of this study was to define desired genetic gains from economically important traits of Pacific white shrimp (Litopenaeus vannamei) using participatory approaches. Two questionnaires were sent out to 100 Pacific white shrimp farmers in all five Iranian shrimp farming provinces. Questionnaire A (Q-A) includes management factors and farming environments. Moreover, in this questionnaire
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Evidence of additive genetic variation for major milk proteins in dairy cows: A meta-analysis J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-17 Navid Ghavi Hossein-Zadeh
In the past, there have been reports of genetic parameters for milk proteins in various dairy cattle populations. The high variability among genetic parameter estimates has been caused by this. This study aimed to use a random-effects meta-analysis model to compile published estimates of genetic parameter for major milk proteins of α-lactalbumin, β-lactoglobulin, sum of whey proteins, casein, αs1-casein
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Modelling the lactation curve in Alpine × Beetal crossbred dairy goats using random regression models fitted with Legendre polynomial and B-spline functions J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-12 Amritanshu Upadhyay, Rani Alex, Mahesh Shivanand Dige, Shweta Sahoo, Kashif Dawood Khan, Pradyut Das, Vikas Vohra, Gopal Ramdasji Gowane
The current study sought to genetically assess the lactation curve of Alpine × Beetal crossbred goats through the application of random regression models (RRM). The objective was to estimate genetic parameters of the first lactation test-day milk yield (TDMY) for devising a practical breeding strategy within the nucleus breeding programme. In order to model variations in lactation curves, 25,998 TDMY
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Characteristics of restricted selection indices and geometrical interpretation of restricted breeding values J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-11 Masahiro Satoh
Restricted selection is used to control genetic changes in one or more characters. Three main selection indices are adopted for this purpose. First, Kempthorne's index is used to maximize aggregate breeding value (BV) with changes in some traits restricted to zero; second, Harville's index is used to maximize aggregate BV with proportional changes for some traits; and third, Yamada's index is mathematically
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Longevity in South African Afrikaner cows as assessed through survival analysis J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2024-01-10 Allison M. Bot Steffl, Michael D. MacNeil, Michiel M. Scholtz, Leticia P. Sanglard, Tiago Passafaro, Michael G. Gonda
The Afrikaner breed of cattle is indigenous to South Africa and, due to their hardiness, was once the most popular breed amongst South African farmers, although in recent years their numbers have decreased. The goal of this study was to assess factors affecting length of productive life, defined as the interval between production of the first and last calf, in Afrikaner cattle using survival analysis
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Genome-wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-12-28 Samuele Bovo, Anisa Ribani, Giuseppina Schiavo, Valeria Taurisano, Francesca Bertolini, Daniela Fornasini, Andrea Frabetti, Luca Fontanesi
Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from
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Investigation of phenotypic, genetic and genomic background of Milk spectra in Sarda dairy sheep J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-12-26 Michele Congiu, Laura Falchi, Silvia Carta, Alberto Cesarani, Corrado Dimauro, Fabio Correddu, Nicolò Pietro Paolo Macciotta
Aim of this study was to analyse the genetic background of milk Fourier transform infrared (FTIR) spectra in dairy sheep. Individual milk FTIR spectra, with 1060 wavenumbers each, were available for 793 adult Sarda breed ewes genotyped at 45,813 SNP. The absorbance values of each wavenumber was analysed using a linear mixed model that included dim class, parity and lambing month as fixed effects and
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A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-12-25 Belete Kuraz Abebe, Hongbao Wang, Anning Li, Linsen Zan
In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle
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Pedigree diversity and implications for genetic selection of Katahdin sheep J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-12-18 Sara M. Nilson, Joan M. Burke, Brenda M. Murdoch, James L. M. Morgan, Ronald M. Lewis
The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement
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Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-12-06 Michela Ablondi, Giorgia Stocco, Matteo Cortellari, Antonello Carta, Andrea Summer, Alessio Negro, Silverio Grande, Paola Crepaldi, Claudio Cipolat-Gotet, Stefano Biffani
Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single-nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels
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Genomic analysis of feed efficiency traits in beef cattle using random regression models J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-12-07 Pedro Vital Brasil Ramos, Gilberto Romeiro de Oliveira Menezes, Delvan Alves da Silva, Daniela Lourenco, Gustavo Garcia Santiago, Roberto A. A. Torres Júnior, Fabyano Fonseca e Silva, Paulo Sávio Lopes, Renata Veroneze
Feed efficiency plays a major role in the overall profitability and sustainability of the beef cattle industry, as it is directly related to the reduction of the animal demand for input and methane emissions. Traditionally, the average daily feed intake and weight gain are used to calculate feed efficiency traits. However, feed efficiency traits can be analysed longitudinally using random regression
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Genomic predictions and GWAS for heat tolerance in pigs based on reaction norm models with performance records and data from public weather stations considering alternative temperature thresholds J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-11-27 Pedro Henrique F. Freitas, Jay S. Johnson, Francesco Tiezzi, Yijian Huang, Allan P. Schinckel, Luiz F. Brito
Genetic improvement of livestock productivity has resulted in greater production of metabolic heat and potentially greater susceptibility to heat stress. Various studies have demonstrated that there is genetic variability for heat tolerance and genetic selection for more heat tolerant individuals is possible. The rate of genetic progress tends to be greater when genomic information is incorporated
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Should performance at different race lengths be treated as genetically distinct traits in Coldblooded trotters? J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-11-27 Paulina Berglund, Sreten Andonov, Erling Strandberg, Susanne Eriksson
Speed, in the form of racing time per kilometre (km), is a performance trait of the Swedish–Norwegian Coldblooded trotter included in the joint Swedish–Norwegian genetic evaluation. A few popular stallions have dominated Coldblooded trotter breeding, which has led to an increasing average relationship between individuals in the population. This study investigated the scope for broadening the breeding
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Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-11-27 E. R. Carrara, P. S. Lopes, R. Veroneze, R. J. Pereira, L. E. F. Zadra, M. G. C. D. Peixoto
For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained
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Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-11-22 Candela Ojeda-Marín, Juan Pablo Gutiérrez, Nora Formoso-Rafferty, Félix Goyache, Isabel Cervantes
Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently
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Candidate genes for longitudinal traits under sequential sampling in beef cattle J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-11-02 Virgínia Mara Pereira Ribeiro, Gabriela Canabrava Gouveia, Fabio Luiz Buranelo Toral
Both the measurement age of a longitudinal trait and the common pre-sampling procedures used in beef cattle herds may affect the identification of a functional candidate gene (FCG) that is potentially associated with a trait. To identify the FCG that takes part in the genetic control of body weight at five different ages in a beef cattle population with and without sequential sampling, the animals
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Genomic background of biotypes related to growth, carcass and meat quality traits in Duroc pigs based on principal component analysis J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-30 Hannah E. Green, Hinayah Rojas de Oliveira, Amanda Botelho Alvarenga, Stacy Scramlin-Zuelly, Daniela Grossi, Allan P. Schinckel, Luiz F. Brito
As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes
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A multivariate gametic model for the analysis of purebred and crossbred data. An example between two populations of Iberian pigs J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-27 Houssemeddine Srihi, David López-Carbonell, Noelia Ibáñez-Escriche, Joaquim Casellas, Pilar Hernández, Sara Negro, Luis Varona
Crossbreeding plays a pivotal role within pig breeding programmes, aiming to maximize heterosis and improve reproductive traits in crossbred maternal lines. Nevertheless, there is evidence indicating that the performance of reciprocal crosses between two genetic lines might exhibit variability. These variations in performance can be attributed to differences in the correlations between gametic effects
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Early life jumping traits: Are they good proxies for success in show jumping competitions in Belgian warmblood horses? J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-26 Léa Chapard, Roel Meyermans, Wim Gorssen, Katrijn Hooyberghs, Inge Meurrens, Stefaan De Smet, Nadine Buys, Steven Janssens
The main goal of the Belgian Warmblood horse studbook (BWP) is to breed successful competition horses, with emphasis on show jumping. However, competition results are only available later in life and competition traits are lowly heritable. Hence, the use of phenotypes that record performance-related traits at an early life stage could help increase genetic progress. In this study, we evaluated the
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Genomic prediction and genome-wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high-density SNP genotypes in Yunong-black pigs J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-12 Ziyi Wu, Tengfei Dou, Liyao Bai, Jinyi Han, Feng Yang, Kejun Wang, Xuelei Han, Ruimin Qiao, Xiu-Ling Li, Xin-Jian Li
Body composition traits are complex traits controlled by minor genes and, in hybrid populations, are impacted by additive and nonadditive effects. We aimed to identify candidate genes and increase the accuracy of genomic prediction of body composition traits in crossbred pigs by including dominance genetic effects. Genomic selection (GS) and genome-wide association studies were performed on seven body
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Genetic evaluation of gestation length in Italian Holstein breed J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-11 Ferdinando Galluzzo, Giulio Visentin, Johannes B. C. H. M. van Kaam, Raffaella Finocchiaro, Stefano Biffani, Angela Costa, Maurizio Marusi, Martino Cassandro
Gestation length (GL) can potentially affect health and performance of both the dam and the newborn calf, and it is controlled by two genetic components, direct and maternal. This means that both the calf (direct effect) and the cow (maternal effect) genotypes contribute to determine GL and its variability. The aims of the present study were to estimate direct and maternal variance components of GL
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Ascertaining the genetic background of the Celtic-Iberian pig strain: A signatures of selection approach J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-09 Katherine D. Arias, Hanboreum Lee, Riccardo Bozzi, Isabel Álvarez, Juan Pablo Gutiérrez, Iván Fernandez, Juan Menéndez, Albano Beja-Pereira, Félix Goyache
Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of
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Genetic associations between stayability to consecutive calvings and traits of economic interest in taurine and zebu breeds J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-03 Débora da Silva Morales, Diogo Osmar Silva, Denise Rocha Ayres, Mário Luiz Santana Junior, Annaiza Braga Bignardi, Ricardo Vieira Ventura, Gilberto Romeiro de Oliveira Menezes, Roberto Carvalheiro, Mário Luiz Piccoli, Vanerlei Mozaquatro Roso, Rodrigo Junqueira Pereira
Stayability (STAY) is a way to evaluate the productive longevity of females. Measuring the STAY at each cow calving allows earlier indicators of longevity to be obtained. Our objective with this study was to verify the association between STAY and consecutive calvings and traits potentially used as selection criteria in beef cattle, such as age at first calving (AFC), days to calving (DC), weaning
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Including genomic information in the genetic evaluation of production and reproduction traits in South African Merino sheep J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-10-03 Cornelius Nel, Phillip Gurman, Andrew Swan, Julius van der Werf, Margaretha Snyman, Kennedy Dzama, Willem Olivier, Anna Scholtz, Schalk Cloete
Genomic selection (GS) has become common in sheep breeding programmes in Australia, New Zealand, France and Ireland but requires validation in South Africa (SA). This study aimed to compare the predictive ability, bias and dispersion of pedigree BLUP (ABLUP) and single-step genomic BLUP (ssGBLUP) for production and reproduction traits in South African Merinos. Animals in this study originated from
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Genetic parameters for health traits and their association with fertility and milk production in Chinese Holsteins J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-09-25 Junxing Zhang, Liyun Han, Hailiang Zhang, Honghong Hu, Hui Sheng, Tongtong Yang, Yi Zhang, Wan Wen, Liqin Ma, Yun Ma, Yachun Wang
Herd health is one of the key problems influencing the efficiency of the dairy industry. Genetic selection, with a focus on animal health, is important for herd improvement. This study aimed to estimate genetic parameters for health traits and their correlations with fertility and milk production traits in dairy cattle. Based on records from 58,549 lactating cows calved between 2015 and 2021, a total
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Conditioning on the causal network prevents indirect response to selection J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-09-19 Martin Bonamy, María Elena Fernández, Guillermo Giovambattista, Sebastián Munilla
Multiple trait animal models (MTM) allow to estimate the breeding values (BV) of several traits simultaneously while accounting for genetic and environmental correlations among them. However, relationships among traits may not be reciprocal but rather causal in nature. In these cases, and given a causal network, structural equations models (SEM) arise as a more appropriate methodology. Although MTM
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Genetic parameters for carcass and meat quality traits in Jinhua, Duroc, and their crossbred pigs J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-09-05 Kei Terada, Toshiyuki Ohtani, Shinichiro Ogawa, Hiroyuki Hirooka
Jinhua pigs have excellent meat quality and intramuscular fat content (IMF). Crossbreeding of Jinhua with Duroc pigs with high productivity was conducted to develop a new composite breed that possesses the beneficial characteristics of both breeds. The objective of this study was to estimate the crossbreeding parameters (additive breed, dominance, and epistatic loss effects) using the Kinghorn model
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Assessing the predictability of racing performance of Thoroughbreds using mixed-effects model J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-08-28 Daiki Oda, Akio Onogi
The inheritance of racing performance in Thoroughbreds is of interest to breeders and geneticists. Therefore, the genetic parameters of racing performance have been investigated in various populations of Thoroughbreds. However, the predictability of the racing performance of a racehorse has not been assessed well. In this study, we built mixed-effects models for Japanese Thoroughbreds and assessed
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Bayesian estimates of genetic effects on calf survival in Hardhenu (Bos taurus × Bos indicus) cattle J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-08-23 Devesh Kumar Yadav, Zile S. Malik, Spandan Shashwat Dash, Pushpa, Yogesh C. Bangar, Ankit Magotra
The aim of the present study is to carry out a risk analysis and Bayesian estimates of genetic effects on calf survival in Hardhenu cattle using data records of 2593 calves born to 102 sires and 790 dams over 25 years. The Bayesian analysis using Gibbs sampling was employed towards threshold animal models to estimate direct and maternal effects on animal survival of studied population. The results
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Breeding objectives for Central Highland goats using participatory and bio-economic modelling approaches J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-08-22 Zeleke Tesema, Belay Derbie, Abiy Shenkute, Mulatu Gobeze, Alemu Kefale, Solomon Gizaw
The breeding objectives of Central Highland goats rearing under a low-input production system were defined through a participatory proportional piling method and bio-economic model. Additionally, the economic values and relative economic value of the breeding objective traits were derived. A participatory proportional piling method was used to estimate the relative weights of farmers attached to a
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Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-08-12 Y. Chen, H. Atashi, R. R. Mota, C. Grelet, S. Vanderick, H. Hu, , N. Gengler
Nitrogen (N) use efficiency (NUE) is an economically important trait for dairy cows. Recently, we proposed a new N efficiency index (NEI), that simultaneously considers both NUE and N pollution. This study aimed to validate the genomic prediction for NEI and its composition traits and investigate the relationship between SNP effects estimated directly from NEI and indirectly from its composition traits
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Alternative SNP weighting for multi-step and single-step genomic BLUP in the presence of causative variants J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-08-07 Bruna Folegatti Santana, Molly Riser, El Hamidi A. Hay, Breno de Oliveira Fragomeni
The accuracy of genetic selection in dairy can be increased by the adoption of new technologies, such as the inclusion of sequence data. In simulation studies, assigning different weights to causative single-nucleotide polymorphism (SNP) markers led to better predictions depending on the genomic prediction method used. However, it is still not clear how the weights should be calculated. Our objective
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Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-07-12 Mohamad Ballan, Samuele Bovo, Francesca Bertolini, Giuseppina Schiavo, Michele Schiavitto, Riccardo Negrini, Luca Fontanesi
Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne
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Inbreeding depression and its effect on sperm quality traits in Pietrain pigs J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-07-06 Gyembo Tsheten, Birgit Fuerst-Waltl, Christina Pfeiffer, Johann Sölkner, Henk Bovenhuis, Gábor Mészáros
In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (FPED) and genomic data based on runs of homozygosity (ROH)
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Impact of multi-output and stacking methods on feed efficiency prediction from genotype using machine learning algorithms J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-07-05 Mónica Mora, Pablo González, José Ramón Quevedo, Elena Montañés, Llibertat Tusell, Rob Bergsma, Miriam Piles
Feeding represents the largest economic cost in meat production; therefore, selection to improve traits related to feed efficiency is a goal in most livestock breeding programs. Residual feed intake (RFI), that is, the difference between the actual and the expected feed intake based on animal's requirements, has been used as the selection criteria to improve feed efficiency since it was proposed by
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Genome-wide association studies for epistatic genetic effects on fertility and reproduction traits in Holstein cattle J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-06-22 Kristen Alves, Luiz F. Brito, Mehdi Sargolzaei, Flavio S. Schenkel
Non-additive genetic effects are well known to play an important role in the phenotypic expression of complex traits, such as fertility and reproduction. In this study, a genome scan was performed using 41,640 single nucleotide polymorphism (SNP) markers to identify genomic regions associated with epistatic (additive-by-additive) effects in fertility and reproduction traits in Holstein cattle. Nine
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Genetic parameter estimation for pork production and litter performance traits of Landrace, Large White, and Duroc pigs in Japan J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-06-20 Shinichiro Ogawa, Hiroshi Takahashi, Masahiro Satoh
We estimated genetic parameters for two pork production and six litter performance traits of Landrace, Large White, and Duroc pigs reared in Japan. Pork production traits were average daily gain from birth to end of performance testing and backfat thickness at end of testing (46,042 records for Landrace, 40,467 records for Large White, and 42,920 records for Duroc). Litter performance traits were number
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Quantitative analysis of parent-of-origin effect in reproductive and morphological selection criteria in the Pura Raza Española horse J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-06-07 Davinia I. Perdomo-González, Luis Varona, Antonio Molina, Nora Laseca, Mercedes Valera
It is generally assumed that parents make a genetically equal contribution to their offspring, but this assumption might not always hold. This is because the expression of a gene can be blocked by methylation during gametogenesis, and the degree of methylation can depend on the origin of the parental gene (imprinting) or by preferential management associated with genetic merit. The first consequences
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Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-06-06 Wellington B. Santos, Camila B. Pereira, Amanda M. Maiorano, Cherlynn D. Silva Arce, Welder A. Baldassini, Guilherme L. Pereira, Luis Artur L. Chardulo, Otávio R. M. Neto, Henrique N. Oliveira, Rogério A. Curi
With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding
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Genomic prediction of fertility and calving traits in Holstein cattle based on models including epistatic genetic effects J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-05-30 Kristen Alves, Luiz F. Brito, Flavio S. Schenkel
The goal of this study was to investigate whether the inclusion of genomic information and epistatic (additive by additive) genetic effects would increase the accuracy of predicting phenotypes adjusted for known environmental effects, reduce prediction bias and minimize the confounding between additive and additive by additive epistatic effects on fertility and calving traits in Holstein cattle. Phenotypic
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A genome-wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-05-24 Slim Ben Jemaa, Marco Tolone, Maria Teresa Sardina, Rosalia Di Gerlando, Giorgio Chessari, Andrea Criscione, Christian Persichilli, Baldassare Portolano, Salvatore Mastrangelo
About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide
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Embryo survival and fertility differ in lines divergently selected for birth weight homogeneity in mice J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-05-07 Nora Formoso-Rafferty, Laila El-Ouazizi El-Kahia, María Arias-Álvarez, Juan Pablo Gutiérrez, Isabel Cervantes
The selection of animals for lower environment sensitivity around the optimum trait value can also provide benefits in productivity and welfare. A divergent selection experiment for birth weight environmental variability in mice was successfully conducted over 17 generations. Animals from low variability selected line (L-line) were more robust by having a higher litter size and survival at weaning
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Incorporation of feeding behaviour traits to increase the genetic gain of feed efficiency in Pietrain pigs J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-26 Pedro Núñez, Sofía Gol, Josep Reixach, Cristina Casto-Rebollo, Noelia Ibáñez-Escriche
Improved feed efficiency is an essential goal for the sustainability of pig production in economic and environmental terms. Traits such as feed conversion rate (FCR), residual feed intake (RFI), residual body weight gain (RG) and feeding behaviour, such as duration (TPV) and feeding rate per visit (FR) can now be measured by automatic feeding systems. The aim of this study was to evaluate the benefits
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Assessment of genomic breeding values and their accuracies for carcass traits in Jeju Black cattle using whole-genome SNP chip panels J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-26 Md Azizul Haque, Asif Iqbal, Haechang Bae, Seung Eun Lee, Sepil Park, Yun Mi Lee, Jong Joo Kim
The objective of the present study was to evaluate the breeding value and accuracy of genomic estimated breeding values (GEBVs) of carcass traits in Jeju Black cattle (JBC) using Hanwoo steers and JBC as a reference population using the single-trait animal model. Our research included genotype and phenotype information on 19,154 Hanwoo steers with 1097 JBC acting as the reference population. Likewise
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Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-26 Carolina Guimarães Ramos Matosinho, Pablo Augusto de Souza Fonseca, Maria Gabriela Campolina Diniz Peixoto, Izinara Cruz Rosse, Fernando César Ferraz Lopes, Thalia Zózimo, Aníbal Eugênio Vercesi Filho, Frank Ângelo Tomita Bruneli, Maria Raquel Santos Carvalho, Marco Antonio Sundfeld Gama
Individual variation in milk fatty acid (FA) composition has been partially attributed to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of
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Prediction ability of an alternative multi-trait genomic evaluation for residual feed intake J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-25 Maria Isabel Pravia, Elly Ana Navajas, Ignacio Aguilar, Olga Ravagnolo
Selection for feed efficiency is the goal for many genetic breeding programs in beef cattle. Residual feed intake has been included in genetic evaluations to reduce feed intake without compromising performance traits as liveweight, body gain or carcass traits. However, measuring feed intake is expensive, and only a small percentage of selection candidates are phenotyped. Genomic selection has become
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Single-step SNPBLUP evaluation in six German beef cattle breeds J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-16 Damilola Adekale, Hatem Alkhoder, Zengting Liu, Dierck Segelke, Jens Tetens
The implementation of genomic selection for six German beef cattle populations was evaluated. Although the multiple-step implementation of genomic selection is the status quo in most national dairy cattle evaluations, the breeding structure of German beef cattle, coupled with the shortcoming and complexity of the multiple-step method, makes single step a more attractive option to implement genomic
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Multi-trait genomic prediction in pigs using single and multistep methods based on the absorption of ungenotyped animals J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-04 Tu Luan, Øyvind Nordbø, Ina Andersen-Ranberg, Theo H. E. Meuwissen
Many quantitative traits measured in breeding programs are genetically correlated. The genetic correlations between the traits indicate that the measurement of one trait carries information on others. To benefit from this information, multi-trait genomic prediction (MTGP) is preferable to use. However, MTGP is more difficult to implement compared to single-trait genomic prediction (STGP), and even
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Including genotypic information in genetic evaluations increases the accuracy of sheep breeding values J. Anim. Breed. Genet. (IF 2.6) Pub Date : 2023-04-01 Karolina Kaseja, Sebastian Mucha, Ed Smith, John Yates, Georgios Banos, Joanne Conington
The impact of inclusion of genome-wide genotypes into breeding value predictions for UK Texel sheep is addressed in this article. The main aim was to investigate the level of change in the accuracy values for EBVs when information from animal genotypes is incorporated into the genetic evaluations. New genetic parameters for a range of lamb growth, carcass composition and health traits are described