Article
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Matti Taskinen, Esa A. Mantysaari, Timo Pitkanen, Gert Pedersen Aamand, Ismo Stranden
Summary: Approximate multistep methods were developed to calculate reliabilities for estimated breeding values in large genetic evaluations. This study utilized a traditional animal model and genomic data to approximate the reliabilities for genotyped animals in a single-step genomic BLUP model. Reliabilities for nongenotyped animals were also calculated using a traditional animal model with pseudo-record counts. The developed approach was found to be efficient and suitable for large datasets.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
H. Alkhoder, Z. Liu, D. Segelke, R. Reents
Summary: The single-step genomic evaluation model in German Holsteins shows higher prediction correlation and greater genomic breeding values variance compared to the current multistep genomic model. There was no overprediction of young animals for conformation traits by the single-step SNP BLUP model in German Holsteins.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
A. Cesarani, D. Lourenco, S. Tsuruta, A. Legarra, E. L. Nicolazzi, P. M. VanRaden, I Misztal
Summary: Official multibreed genomic evaluations for dairy cattle in the United States are based on multibreed BLUP evaluation. This study developed ssGBLUP multibreed genomic predictions for US dairy cattle and found that single-step large-scale multibreed evaluations are computationally feasible, but fine tuning is needed.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Artem Kabanov, Ekaterina Melnikova, Sergey Nikitin, Maria Somova, Oleg Fomenko, Valeria Volkova, Olga Kostyunina, Tatiana Karpushkina, Elena Martynova, Elena Trebunskikh
Summary: This study compared three methods for assessing the breeding value of pigs and evaluated the changes in accuracy of genomic estimates using different reference groups. The results showed that the wssGBLUP method has higher reliability compared to ssGBLUP, and a reference group size of more than 1000 individuals leads to more stable results.
Article
Agriculture, Dairy & Animal Science
Rostam Abdollahi-Arpanahi, Daniela Lourenco, Ignacy Misztal
Summary: Genomic selection has been widely adopted in various livestock and plant species nationally and internationally. The start date of genomic selection for economically important traits in pigs, cattle, and broiler chickens can be determined by analyzing the differences between genetic and Realized Mendelian sampling (RMS) trends obtained using BLUP and single-step genomic BLUP (ssGBLUP). The results showed that the effective onset of genomic selection varied across species, with notable divergences in trends between BLUP and ssGBLUP for certain traits.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Jeremie Vandenplas, Herwin Eding, Mario P. L. Calus
Summary: Genetic groups, known as unknown or phantom parent groups, are often used in dairy cattle genetic evaluations to account for selection that cannot be explained by known genetic relationships. The Quaas and Pollak transformation can be applied to include genetic groups in the pedigree, reducing memory burden and computational costs compared to fitting genetic groups as covariates.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Genetics & Heredity
Masoumeh Naserkheil, Hossein Mehrban, Deukmin Lee, Mi Na Park
Summary: This study compared the prediction accuracy of conventional pedigree-based BLUP and single-step genomic BLUP methods for 10 primal cut traits in Hanwoo cattle, with ssGBLUP showing better performance overall. The ssGBLUP method demonstrated more accurate and less biased predictions across the studied traits, making it more suitable for improving accuracy in predicting primal cut yields.
Article
Agriculture, Dairy & Animal Science
S. Buaban, S. Prempree, P. Sumreddee, M. Duangjinda, Y. Masuda
Summary: Cow genotypes have a positive effect on the accuracy of genomic estimated breeding values for young dairy bulls in Thailand, with an increase in individual and validation accuracies when including cow genotypes in the analysis. Genomic evaluation using a single-step random regression test-day model is feasible for selection of young bulls in Thai dairy cattle, and should consider genotypes of both sires and cows for improved accuracy.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Matias Bermann, Daniela Lourenco, Ignacy Misztal
Summary: The study aimed to develop an efficient algorithm, using the Algorithm for Proven and Young (APY), for calculating prediction error variances (PEVs) in genomic best linear unbiased prediction (GBLUP) models, and extend it to single-step GBLUP (ssGBLUP). The algorithm was used to approximate the theoretical reliabilities for both single- and multiple-trait models in ssGBLUP.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Takefumi Osawa, Yutaka Masuda, Junichi Saburi, Keita Hirumachi
Summary: This study investigated the computational performance and predictive ability of a single-step SNP BLUP model (ssSNPBLUP) in genotyped young animals with unknown parent groups (UPG) for type traits using genetic evaluation data from the Japanese Holstein population. Different combinations of genotyped animals were compared, and it was found that the group including all genotyped animals had the highest predictive ability. Minimal differences were observed in predictive abilities with different parameters of residual polygenic variance. Overall, the results demonstrated that the ssSNPBLUP model, including UPG, is feasible for the national evaluation of type traits in Japanese Holsteins.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Sirlene F. Lazaro, Humberto Tonhati, Hinayah R. Oliveira, Alessandra A. Silva, Andre Nascimento, Daniel J. A. Santos, Gabriela Stefani, Luiz F. Brito
Summary: This study focused on implementing genomic selection in Murrah buffalo to estimate variance components and evaluate the performance of genomic prediction for milk-related traits. It also explored longitudinal SNP effects and candidate genes associated with variation in milk production traits across multiple lactation stages. The results revealed significant genetic correlations between traits at different lactation stages and highlighted the importance of incorporating genomic information in the genetic evaluation of longitudinal traits in dairy buffalo.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
F. B. Lopes, F. Baldi, T. L. Passafaro, L. C. Brunes, M. F. O. Costa, E. C. Eifert, M. G. Narciso, G. J. M. Rosa, R. B. Lobo, C. U. Magnabosco
Summary: This study assessed the accuracy of genomic prediction for carcass and meat quality traits in Nelore cattle using single- and multiple-trait approaches. The study showed that genomic information had an impact on genetic evaluations in beef cattle using the multiple-trait model, which was advantageous compared to the single-trait model.
Article
Agriculture, Dairy & Animal Science
Trine M. Villumsen, Guosheng Su, Bernt Guldbrandtsen, Torben Asp, Mogens S. Lund
Summary: Genomic selection in mink using genotyping by sequencing (GBS) showed that the SSGBLUP model outperformed traditional BLUP model in accurately selecting superior animals, leading to increased genetic gain in breeding programs. Additionally, GBS data proved to be effective in genomic prediction for mink, demonstrating the potential of GBS for genomic selection in livestock species.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
S-L Klein, T. Yin, H. H. Swalve, S. Koenig
Summary: Milk fatty acids have been proposed as biomarkers for metabolic diseases and fertility status. This study aimed to investigate genetic and genomic associations between fatty acids, ketosis, and the interval from calving to first insemination. Genetic correlations were found between ketosis and certain fatty acids, while fatty acid concentrations in milk were identified as valuable predictors for ketosis and the interval from calving to first insemination.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
G. R. Gowane, Rani Alex, Anupama Mukherjee, Vikas Vohra
Summary: This study aimed to propose a genomic prediction strategy for predicting sex-limited traits GEBV in shallow pedigree scenarios, and the results showed that ssGBLUPF can achieve more accurate and unbiased GEBV estimates. For populations with shallow pedigree, using ssGBLUPF can lead to desirable outcomes when resources are limited.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2022)
Article
Forestry
Marianella Quezada, Ignacio Aguilar, Gustavo Balmelli
Summary: This study compared the accuracy of estimating genetic parameters and predicting breeding values using the conventional pedigree-based model (ABLUP) and the pedigree-genomic single-step model (ssGBLUP) in forest tree breeding programs. The inclusion of selfing rate improved the estimation of genetic parameters and reduced the bias in heritability estimates. The ssGBLUP model consistently outperformed the ABLUP model in terms of predictive abilities. This study also proposed a straightforward approach for estimating the actual selfing rate in a breeding population, which can improve the reliability of genetic parameter estimation.
TREE GENETICS & GENOMES
(2022)
Article
Agriculture, Dairy & Animal Science
A. Cesarani, D. Lourenco, S. Tsuruta, A. Legarra, E. L. Nicolazzi, P. M. VanRaden, I Misztal
Summary: Official multibreed genomic evaluations for dairy cattle in the United States are based on multibreed BLUP evaluation. This study developed ssGBLUP multibreed genomic predictions for US dairy cattle and found that single-step large-scale multibreed evaluations are computationally feasible, but fine tuning is needed.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Taylor M. McWhorter, Matias Bermann, Andre L. S. Garcia, Andres Legarra, Ignacio Aguilar, Ignacy Misztal, Daniela Lourenco
Summary: This study compares the effects of tuning before blending and blending before tuning on genomic predictions and SNP effects in single-step genomic BLUP. The results suggest that tuning before blending has negligible impact on genomic predictions and SNP effects.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Ludmilla Costa Brunes, Carina Ubirajara de Faria, Claudio Ulhoa Magnabosco, Raysildo Barbosa Lobo, Elisa Peripolli, Ignacio Aguilar, Fernando Baldi
Summary: This study aimed to estimate the prediction ability and genetic parameters of RFI in Nellore beef cattle using regression equations for each test and the entire population. The study also evaluated the correlations between RFI and various traits. The results showed that the RFI population had higher additive genetic variance and genetic correlations with growth, reproductive, and carcass traits compared to the RFI from individual tests.
JOURNAL OF APPLIED GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Juan Diego Rodriguez, Elisa Peripolli, Marisol Londono-Gil, Rafael Espigolan, Raysildo Barbosa Lobo, Rodrigo Lopez-Correa, Ignacio Aguilar, Fernando Baldi
Summary: This study evaluated the impact of SNP marker density and MAF on genomic predictions and imputation performance for beef cattle using ssGBLUP methodology. The results showed that at least 5% of SNP markers from a high-density array are necessary to obtain reliable genomic predictions and imputed genotypes. The findings suggest that developing low-density customised arrays based on MAF and even distribution of SNPs could be a cost-effective approach for implementing genomic selection in beef cattle.
ANIMAL PRODUCTION SCIENCE
(2023)
Article
Agronomy
Ines Rebollo, Ignacio Aguilar, Fernando Perez de Vida, Federico Molina, Lucia Gutierrez, Juan Eduardo Rosas
Summary: Genotype by environment interaction is a major challenge in plant breeding. Random regression models offer a promising approach to deal with this interaction.
Article
Agronomy
Ines Rebollo, Sheila Scheffel, Pedro Blanco, Federico Molina, Sebastian Martinez, Gonzalo Carracelas, Ignacio Aguilar, Fernando Perez de Vida, Juan Eduardo Rosas
Summary: This research work describes the process of consolidating 23 years of phenotypic, pedigree, and genomic records from the Uruguayan national rice breeding program into a relational database. The database includes data from 996 trials, 12 locations, and a span of 23 years, with information on 14 phenotypic variables, pedigree for 19,447 genotypes, and genomic information regarding 61,260 SNP markers for 965 genotypes. This comprehensive and structured database will serve as a valuable resource for rice breeding.
Article
Agriculture, Dairy & Animal Science
Maria Isabel Pravia, Elly Ana Navajas, Ignacio Aguilar, Olga Ravagnolo
Summary: Feed efficiency is the goal for genetic breeding programs in beef cattle. Residual feed intake has been used to reduce feed intake without compromising performance traits. However, measuring feed intake is expensive and only a small percentage of candidates are tested. Genomic selection has become an important tool for genetic progress in these traits.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Y. Steyn, T. Lawlor, Y. Masuda, S. Tsuruta, A. Legarra, D. Lourenco, I. Misztal
Summary: Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. Stratifying selected candidates into sub-populations using K-means clustering successfully separated genetically different groups.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
M. Wicki, J. Raoul, A. Legarra
Summary: This study investigates the impact of genomic selection on prediction accuracy in Lacaune dairy breed. Despite the divergence between the two subpopulations split in 1972, there is still a close genetic relationship. The joint genomic prediction shows slight gains in accuracy, indicating the advantage of combined evaluation.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
S. Id-Lahoucine, A. Canovas, A. Legarra, J. Casellas
Summary: Transmission ratio distortion (TRD) is associated with reproductive traits, but has limited impact on genomic prediction accuracy. However, TRD regions have significant effects on stillbirth and nonpregnancy, especially regions with allelic TRD pattern.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Marisol Londono-Gil, Daniel Cardona-Cifuentes, Rafael Espigolan, Elisa Peripolli, Raysildo B. Lobo, Angelica S. C. Pereira, Ignacio Aguilar, Fernando Baldi
Summary: The aim of this study was to assess the impact of using genomic information in situations of pedigree uncertainty on genetic evaluations for growth and cow productivity traits in Nelore commercial herds. Different approaches were used to estimate genetic values, including with or without genomic information and varying pedigree structures. The results showed that the accuracy of genetic value estimation decreased as the proportion of unknown sires and maternal grandsires increased. The use of genomic information improved the accuracy of prediction for young animals without known pedigrees.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Genetics & Heredity
Andres Legarra, David Omar Gonzalez-Dieguez, Alain Charcosset, Zulma G. Vitezica
Summary: The improvement of crosses between close populations in crops and livestock depends on the amount of dominance deviations and heterosis. The distance between populations is related quadratically to the amount of dominance deviations and linearly to the expected heterosis. Dominance deviations decrease with genetic distance until allele frequencies are uncorrelated, then increase for negatively correlated frequencies. Heterosis always increases with genetic distance.
Article
Agriculture, Dairy & Animal Science
S. Antonios, A. Legarra, R. Pong-Wong, J. M. Astruc, S. T. Rodriguez-Ramilo, Z. G. Vitezica
Summary: The genetic trend of milk yield for four French dairy sheep breeds was analyzed based on categories of animals defined by sex and selection pathways. Females, especially dams of males and AI males, were the most important sources of genetic progress. Natural mating males and discarded males did not significantly contribute to the trend. In addition, Mendelian sampling was found to be more important than parent average in determining selection decisions and long-term contributions.
JOURNAL OF DAIRY SCIENCE
(2023)