Article
Genetics & Heredity
Enrico Mancin, Lucio Flavio Macedo Mota, Beniamino Tuliozi, Rina Verdiglione, Roberto Mantovani, Cristina Sartori
Summary: Genomic selection has become a routine method in many livestock breeding contexts, but its use is still limited in small-population local breeds. In this study, alternative methods were tested to improve the accuracy of genomic selection in small populations, and it was found that using variable selection methods improved accuracy without impacting bias and dispersion of breeding values.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
M. P. Sanchez, T. Tribout, S. Fritz, V Wolf, C. Laithier, M. Brochard, D. Boichard
Summary: As part of the From'MIR project, this study assessed the reliability of ssEBVs for CMP, estimated genetic trends, and simulated different breeding objectives for the Montbeliarde breed. Reliability of ssEBVs ranged from 61% to 64%, with the TD3 model being the most accurate. The inclusion of additional candidate SNPs improved the reliabilities of ssEBVs and led to positive genetic trends for all CMP traits. The TMI-Cheese scenario yielded the best responses for CMP traits.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
E. Manzocchi, A. Ferlay, Y. Farizon, F. Enjalbert, M. Bouchon, K. Giller, M. Kreuzer, J. Berard, B. Martin, M. Coppa
Summary: Compared with maize silage-and concentrate-based diets, herbage-based diets have a positive impact on the milk fatty acid profile. However, the effect of herbage feeding mode and conservation method on the milk fatty acid profile remains unclear.
Article
Agriculture, Dairy & Animal Science
Valentino Palombo, Sara Pegolo, Giuseppe Conte, Alberto Cesarani, Nicolo Pietro Paolo Macciotta, Bruno Stefanon, Paolo Ajmone Marsan, Marcello Mele, Alessio Cecchinato, Mariasilvia D'Andrea
Summary: Genomic selection reports on milk fatty acid profiles are still few, but using dimension reduction methods can help address the complexity of this trait. By analyzing milk fat from different cattle breeds, it was found that using multivariate factor analysis can provide valuable genetic insights for breeding programs. The addition of genomic information led to more accurate predictions and improved breeding values compared to traditional methods.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Rasoul Farzaneh Dizaj, Mehdi Amin-Afshar, Saeid Esmaeilkhanian, Nasser Emamjomeh-Kashan, Mohammad Hossein Banabazi
Summary: The present study analyzed allelic-specific expression in Purebred Sistani and its crossbreed with Holstein, Simmental, and Montbeliarde breeds. The analysis identified different SNP types and revealed the involvement of expressed genes in different biological classifications. Conducting such studies helps in identifying genes with different expressions.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Genetics & Heredity
Abdessamad Ouhrouch, Simon Boitard, Frederic Boyer, Bertrand Servin, Anne Da Silva, Francois Pompanon, Abdelmajid Haddioui, Badr Benjelloun
Summary: Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. The study revealed that Moroccan local sheep breeds exhibit high genetic diversity and a large set of adaptive variations, making them a valuable genetic resource for the conservation of sheep in the context of climate change.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
G. M. Pereira, L. B. Hansen, B. J. Heins
Summary: This study compared calves of different breeds in terms of gestation length, calf weight at birth, calving difficulty, and stillbirth. The results showed that there were differences among the different breeds in these indicators, but certain breeds could increase gestation length and calf weight without increasing calving difficulty and stillbirth.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Riccardo Moretti, Stefania Chessa, Stefano Sartore, Dominga Soglia, Daniele Giaccone, Francesca Tiziana Cannizzo, Paola Sacchi
Summary: This study examined the application of genomic tools in animal selection on farms and found that well-managed farms rear animals with better genomic indexes. Selecting heifers based on their wellness genomic indexes can improve their economic value and disease resistance. Genomic selection is a fast and cost-effective method for animal evaluation, although it is mainly used for sire line and performance traits.
Article
Mathematics
Yuanying Zhao, Dengke Xu
Summary: In this paper, a Bayesian variable selection method based on spike and slab prior for regression parameters is proposed for spatial autoregressive (SAR) quantile models. The proposed approach combines robust parametric estimation and variable selection in the context of SAR quantile models. Bayesian statistical inferences are implemented using a detailed Markov chain Monte Carlo (MCMC) procedure that combines Gibbs samplers with a probability integral transformation (PIT) algorithm. Empirical numerical examples, including simulation studies and a Boston housing price data analysis, are provided to demonstrate the newly developed methodologies.
Article
Agriculture, Dairy & Animal Science
Maria Kjetsa, Arne B. Gjuvsland, Oyvind Nordbo, Eli Grindflek, Theo Meuwissen
Summary: The aim of this study was to compare the accuracy of three genomic prediction methods for maternal traits in Landrace sows and found that BayesGC generally achieved higher accuracy. The study also revealed that maternal traits in sows are difficult to record and have lower heritabilities.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Robert Wijma, Daniel J. Weigel, Natascha Vukasinovic, Dianelys Gonzalez-Pena, Shaileen P. McGovern, Brenda C. Fessenden, Anthony K. McNeel, Fernando A. Di Croce
Summary: Pregnancy losses in dairy cattle can have negative impacts on both animal health and economic outcomes. This study developed a genomic prediction model to identify high-risk cows and aid in the selection of more profitable and productive animals. The results showed that the model effectively predicted the risk of abortion in lactating Holstein dairy cows, providing valuable information for genetic selection towards healthier cows.
Article
Multidisciplinary Sciences
Matteo Cortellari, Mario Barbato, Andrea Talenti, Arianna Bionda, Antonello Carta, Roberta Ciampolini, Elena Ciani, Alessandra Crisa, Stefano Frattini, Emiliano Lasagna, Donata Marletta, Salvatore Mastrangelo, Alessio Negro, Ettore Randi, Francesca M. Sarti, Stefano Sartore, Dominga Soglia, Luigi Liotta, Alessandra Stella, Paolo Ajmone-Marsan, Fabio Pilla, Licia Colli, Paola Crepaldi
Summary: The study investigated the genetic structure of Italian goat populations and their link with the environment, revealing three distinct groups reflective of the country's geography and historical background. Landscape genomics analysis identified SNPs associated with growth, circadian rhythm, fertility, and inflammatory response, with calculations of future genotypic frequencies to evaluate long-term effects on genetic structure. Overall, the results provide insight into the past and future of Italian goat populations, aiding in the development of conservation strategies in the face of climate change.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Xiaopeng Wang, Guixin Li, Yongchuang Jiang, Jianhong Tang, Yin Fan, Jun Ren
Summary: Conservation and population genetic analyses of two Chinese indigenous goat breeds, Guangfeng and Ganxi, provide insights into their conservation status, genetic structure, selection signatures, and artificial introgression. These analyses are conducted in comparison to 36 global goat breeds. The study also identifies candidate genes associated with fertility, growth, immunity, and meat quality in these two breeds, and highlights the potential benefits of introgression from exotic goats for improving performance and productivity. It offers guidelines for conservation and breeding programs for these breeds and emphasizes the impact of human-mediated introgression on economic traits in Chinese indigenous goats.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Veterinary Sciences
Yangfeng Li, Min Huang, Zhenjie Wang, Xueyuan Liu, Shan He, Tao Wang, Baicheng Ma, Jianyun Liu, Xingnuan Li, Jianjun Xiong, Jinlian Hua, Junhua Ye, Anmin Lei, Qianyong Yang
Summary: The significant morphological differences and abundant germplasm resources of Chinese indigenous dog breeds can be attributed to the diverse geographical environment, natural and artificial selection, and a long history of raising dogs. In this study, run of homozygosity (ROH) and proportion of the autosomal genome covered by ROHs (FROH) were calculated for 10 representative Chinese indigenous dog breeds. The results showed differences in inbreeding levels among breeds and subpopulations, as well as identified genes related to coat color, altitude adaptability, and ear shape.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Heidi Signer-Hasler, Lucas Casanova, Alex Barenco, Blaise Maitre, Alessandro Bagnato, Mario Vevey, Beate Berger, Mojca Simcic, Denis Boichon, Aurelien Capitan, Ivica Medugorac, Joern Bennewitz, Gabor Meszaros, Johann Soelkner, Cord Droegemueller, Christine Flury
Summary: We analyzed genome-wide SNP data from 18 local cattle breeds from the Alpine region to understand their population structure and identify genomic regions involved in positive selection. Different breeds like Evolener, Eringer, Valdostana Pezzata Nera, and Valdostana Castana showed distinct genetic differences compared to other Alpine breeds. We found selection signatures on chromosome 6 near genes related to coat color and body size, and identified 47 genome regions with ROH islands using high-density SNP data. The results provide insights into adaptation to the alpine environment and specific characteristics in local Alpine cattle breeds.
Article
Agriculture, Dairy & Animal Science
S. Antonios, S. T. Rodriguez-Ramilo, I Aguilar, J. M. Astruc, A. Legarra, Z. G. Vitezica
Summary: Inbreeding depression is associated with decreased performance and fitness of animals. This study evaluated pedigree-based and genomic methods to estimate inbreeding and its effects on sperm traits in Basco-Bearnaise sheep, finding significant impact on sperm motility.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Genetics & Heredity
Andres Legarra, Carolina A. Garcia-Baccino, Yvonne C. J. Wientjes, Zulma G. Vitezica
Summary: The article discusses how allele substitution effects vary across populations and generations, and outlines a statistical method for estimating these differences to predict the similarity of genomic effects.
Article
Genetics & Heredity
Ole F. Christensen, Vinzent Borner, Luis Varona, Andres Legarra
Summary: This paper introduces a joint model for phenotypes and omics data, along with methods for estimating breeding values. Three equivalent methods for best linear unbiased prediction of breeding values are presented for complete omics data. Extensions of two of these methods are also presented for incomplete omics data, involving extending an omics-related similarity matrix.
Article
Agriculture, Dairy & Animal Science
F. L. Macedo, J. M. Astruc, T. H. E. Meuwissen, A. Legarra
Summary: This study analyzed 40 years of records from a dairy sheep breeding program to evaluate bias in genetic evaluations. The results showed that most models and scenarios exhibited bias, with an overestimate of genetic trend for milk yield and an underestimate for other traits. The study also found that using multiple-trait models and including genomic information can reduce bias, but only deletion of historical data completely eliminated bias.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Statistics & Probability
Victor Elvira, Luca Martino, Christian P. Robert
Summary: This paper revisits the approximation of effective sample size (ESS) in the context of importance sampling and finds the existing approximations problematic. The authors propose new research directions for multiple importance sampling and alternative metrics.
INTERNATIONAL STATISTICAL REVIEW
(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
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)
Editorial Material
Multidisciplinary Sciences
Christian P. Robert, Judith Rousseau
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(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)
Meeting Abstract
Agriculture, Dairy & Animal Science
A. Cesarani, D. Lourenco, S. Tsuruta, A. Legarra, E. L. Nicolazzi, P. M. VanRaden, I. Misztal
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Andres Legarra, David Gonzalez-Dieguez, Zulma G. Vitezica
Summary: In the context of multi-breed genomic prediction, the traditional equations may become less practical when non-additive effects are considered. Different models have their own advantages and inconveniences, with the GLS + SI method being the least consuming in terms of operations and memory usage, but requiring dedicated programming.
GENETICS SELECTION EVOLUTION
(2022)