Article
Plant Sciences
Matias F. Schrauf, Gustavo de los Campos, Sebastian Munilla
Summary: In the process of genomic selection, making decisions through cross validation is important, including comparing candidate models in pairs, defining the relevance of performance differences, and introducing new statistical tests. Most hyper-parameters can be learned from data by minimizing REML or using weakly-informative priors to achieve good predictive results. Paired k-fold cross-validation is a generally applicable and statistically powerful methodology to assess differences in model accuracies.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Piter Bijma, Jack C. M. Dekkers
Summary: This study clarifies the apparent contradiction in the accuracy of genomic estimated breeding values (GEBV) when combining information sources based on selection index theory (SIT) and Fisher information (FI). The results show that the discrepancy originates from two factors and that the SIT and FI approaches are equivalent when these factors are accounted for.
GENETICS SELECTION EVOLUTION
(2022)
Article
Plant Sciences
Ping-Yuan Chung, Chen-Tuo Liao
Summary: This study aimed to develop a genomic prediction approach for identifying superior parental lines and provide a software package for its execution. The results showed that incorporating genomic-estimated breeding values and genomic diversity into a selection index could improve the efficiency of selecting desired breeding goals.
FRONTIERS IN PLANT 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
Agriculture, Dairy & Animal Science
Shaileen P. McGovern, Daniel J. Weigel, Brenda C. Fessenden, Dianelys Gonzalez-Pena, Natascha Vukasinovic, Anthony K. McNeel, Fernando A. Di Croce
Summary: Twinning in dairy cattle is a detrimental trait associated with increased costs and culling rates. A genomic prediction tool developed by Zoetis can help producers reduce the likelihood of twin pregnancies, and when combined with management practices, offers a proactive approach to managing twinning in dairy cattle.
Article
Agriculture, Dairy & Animal Science
Richard Osei-Amponsah, Frank R. Dunshea, Brian J. Leury, Archana Abhijith, Surinder S. Chauhan
Summary: Heat waves in Australia are becoming more severe and frequent, causing stress on dairy cattle. A study investigated the relationship between heat-tolerant phenotypes and genomic breeding values for various selection indices. The findings showed positive associations between heat-tolerant phenotypes and breeding values for heat tolerance, fertility, and fat percentage.
Article
Genetics & Heredity
Fatemeh Amini, Guiping Hu, Lizhi Wang, Ruoyu Wu
Summary: Selecting for multiple traits in genomic selection has become increasingly important. This paper proposes a new method called L-shaped selection, which addresses the limitations of index selection and has been proven to find any Pareto optimal solution with appropriate weights. Computational experiments demonstrate the improved performance of L-shaped selection over index selection.
Article
Agriculture, Dairy & Animal Science
Enrico Mancin, Bolivar Samuel Sosa-Madrid, Agustin Blasco, Noelia Ibanez-Escriche
Summary: The study found that genomic selection with genotype imputation is feasible in the rabbit meat industry, considering only genotyping strategies with suitable IA, accuracy of gEBVs, genotyping costs, and response to selection.
Article
Agronomy
Collin M. Lamkey, Aaron J. Lorenz
Summary: The inbred-hybrid system of maize breeding is similar to a reciprocal full-sib selection program. Studying the impact of reciprocal full-sib selection can help answer questions about the roles of selection and genetic drift and understand the nature of adaptation in selection programs.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Yutaka Masuda, Shogo Tsuruta, Matias Bermann, Heather L. Bradford, Ignacy Misztal
Summary: In this study, genetic trends were compared among models with UPG and MF H-inverses, showing that EUPG and MF H-inverses are preferred for their lack of genetic trend biases.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Ecology
Luke A. Yates, Zach Aandahl, Shane A. Richards, Barry W. Brook
Summary: Specifying, assessing, and selecting statistical models are crucial for ecological research. We provide a comprehensive and accessible review on the technical aspects of cross validation for model selection, including bias correction, estimation uncertainty, score choice, and overfitting mitigation. Our recommendations include using leave-one-out cross validation or k-fold with bias correction for minimizing bias and using calibrated selection to mitigate overfitting.
ECOLOGICAL MONOGRAPHS
(2023)
Article
Agronomy
Hans-Juergen Auinger, Christina Lehermeier, Daniel Gianola, Manfred Mayer, Albrecht E. Melchinger, Sofia da Silva, Carsten Knaak, Milena Ouzunova, Chris-Carolin Schoen
Summary: The study analyzed experimental data from a commercial maize breeding program to investigate the role of genomic measures in determining optimal calibration sets for model training. Including data from all selection cycles in model training yielded the best results, with expected reliability of genomic breeding values being the best predictor of accuracies obtained with different calibration sets.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Genetics & Heredity
Ivan Pocrnic, Jana Obsteter, R. Chris Gaynor, Anna Wolc, Gregor Gorjanc
Summary: Nucleus-based breeding programs with intense selection lead to high genetic gain but reduction of genetic variation. Systematic management of genetic variation is necessary. Genomic truncation selection showed immediate benefits compared to conventional truncation selection. Optimal contribution selection can ensure long-term success with a balance between loss of genetic variance and genetic gain.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Jon Bancic, Christian R. Werner, R. Chris Gaynor, Gregor Gorjanc, Damaris A. Odeny, Henry F. Ojulong, Ian K. Dawson, Stephen P. Hoad, John M. Hickey
Summary: Intercrop breeding programs using genomic selection can generate faster genetic gain compared to those using phenotypic selection, regardless of the genetic correlation between monocrop and intercrop yield.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Xu Zheng, Tianliu Zhang, Tianzhen Wang, Qunhao Niu, Jiayuan Wu, Zezhao Wang, Huijiang Gao, Junya Li, Lingyang Xu
Summary: In this study, simulation analysis was conducted to explore the long-term effects of different selection strategies on genetic gain and average kinship coefficients in beef cattle. The results showed that genomic selection can improve genetic gain across generations, with GBLUP outperforming BayesA. Higher trait heritability leads to higher genetic gain. However, the use of GBLUP and BayesA strategies resulted in higher average kinship coefficients.
Article
Agriculture, Dairy & Animal Science
N. Siachos, G. Oikonomou, N. Panousis, V. Tsiamadis, G. Banos, G. Arsenos, G. E. Valergakis
Summary: During the periparturient period, nutrient deficit leads to mobilisation of body energy and protein reserves in cows. Research on fat reserves and mobilisation is extensive, but investigation of muscle mobilisation during this period is limited. This cohort study used ultrasonography to simultaneously investigate the variation and mobilisation of skeletal muscle and subcutaneous fat reserves in Holstein cows from different herds, and assessed potential factors affecting this process.
Article
Agriculture, Dairy & Animal Science
N. Siachos, G. Oikonomou, N. Panousis, V. Tsiamadis, G. Banos, G. Arsenos, G. E. Valergakis
Summary: This study aimed to investigate the association between skeletal muscle and subcutaneous fat reserves, measured by ultrasonography, and postparturient health, reproduction, and milk production traits. The results showed that increased muscle depth was negatively associated with metritis and clinical postparturient diseases, while increased subcutaneous fat reserves were positively associated with these diseases.
Article
Agriculture, Dairy & Animal Science
V. Tsartsianidou, A. Pavlidis, E. Tosiou, G. Arsenos, G. Banos, A. Triantafyllidis
Summary: In this study, pedigree-based analyses and genome-wide association studies were conducted to explore the genetic mechanisms underlying sheep reproduction. Representative reproductive traits such as first lambing age, total prolificacy, and maternal lamb survival were found to be significantly heritable. Novel genome-wide and suggestive significant single-nucleotide polymorphisms (SNPs) associated with age at first lambing were identified. Functional annotation analysis revealed candidate genes involved in osteogenesis, myogenesis, and skeletal and muscle mass development, which are related to the ovulation rate and prolificacy.
Article
Agriculture, Dairy & Animal Science
Matthew Barden, Alkiviadis Anagnostopoulos, Bethany E. Griffiths, Bingjie Li, Cherry Bedford, Chris Watson, Androniki Psifidi, Georgios Banos, Georgios Oikonomou
Summary: This study aimed to estimate the genetic parameters of recovery from sole lesions in dairy cows and evaluate its genetic correlation with overall susceptibility. The findings showed that recovery from sole lesions is heritable and negatively correlated with susceptibility. If confirmed in further research, selective breeding could be used to reduce the frequency of chronically lame cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Microbiology
V Bay, A. Gillespie, E. Ganda, N. J. Evans, S. D. Carter, L. Lenzi, A. Lucaci, S. Haldenby, M. Barden, B. E. Griffiths, E. Sanchez-Molano, R. Bicalho, G. Banos, A. Darby, G. Oikonomou
Summary: This study investigates the bovine foot skin microbiota and its association with Bovine Digital Dermatitis (BDD) in dairy cows. The results show dysbiosis and differences in taxonomy and functional profiles in the foot skin microbiome of healthy animals that develop BDD lesions. The study also provides evidence of host genetic control of certain members of the foot skin microbiota. Overall, this work contributes to understanding the relationship between the foot skin microbiota and BDD, and provides insights for prevention and selective breeding programs.
Article
Agriculture, Dairy & Animal Science
Aikaterini Soufleri, Georgios Banos, Nikolaos Panousis, Alexandros Kougioumtzis, Vangelis Tsiamadis, Georgios Arsenos, Georgios E. E. Valergakis
Summary: The adequate passive transfer of immunity in newborn calves, as well as the health and metabolic status of cows, can be indirectly estimated by measuring serum total proteins. This study investigated the genetic parameters of Holstein dairy cow and calf total proteins concentration. The heritability estimates suggest that genetic selection for these traits is feasible and could contribute to calf and cow health and herd sustainability. The strong positive genetic correlation between calf serum total proteins and colostrum total solids provides the opportunity for simultaneous genetic selection.
Article
Agriculture, Dairy & Animal Science
Karolina Kaseja, Sebastian Mucha, Edward M. Smith, John Yates, Georgios Banos, Joanne Conington
Summary: This article investigates the impact of including genome-wide genotypes into breeding value predictions for UK Texel sheep. The study examines the change in accuracy values for conventional breeding values (EBVs) when animal genotypes are incorporated into genetic evaluations. The results show that using genotypes in breeding value estimation can increase accuracy, especially for un-phenotyped animals with good links to the reference population.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Matthew Barden, Marie M. Phelan, Robert Hyde, Alkiviadis Anagnostopoulos, Bethany E. Griffiths, Cherry Bedford, Martin Green, Androniki Psifidi, Georgios Banos, Georgios Oikonomou
Summary: The strongest evidence of being associated with sole lesions corresponded to phenylalanine and 4 unlabeled metabolites. The serum metabolome, as characterized by proton nuclear magnetic resonance spectroscopy, cannot predict the presence or future development of sole lesions. A small number of metabolites may be associated with sole lesions, but they can only explain a small proportion of the differences between affected and unaffected animals due to poor prediction accuracies. Future metabolomic studies should effectively control for interanimal and extraneous sources of spectral variation to reveal underlying metabolic mechanisms of sole lesion etiopathogenesis in dairy cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
K. Kaseja, S. Mucha, J. Yates, E. Smith, G. Banos, J. Conington
Summary: This study investigated the genetic background of health and production traits in the UK Texel sheep population using phenotypic and SNP data. Results identified significant SNPs associated with birth weight, weaning weight, and scan weight. The study also found other SNPs related to animal health and production traits. The results suggest that these traits have a complex genetic architecture.
Article
Biology
V. Tsiamadis, G. E. Valergakis, A. Soufleri, G. Arsenos, G. Banos, X. Karamanlis
Summary: A retrospective study was conducted to evaluate the temporal patterns of heat stress during the in-uterus period and the post-natal period of dairy heifers, and its association with the age at first calving. The study found that heat stress during the in-uterus period significantly affected the age at first calving.
JOURNAL OF THERMAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Madison MacLeay, Georgios Banos, Francesc Xavier Donadeu
Summary: This study aimed to identify circulating miRNAs associated with early life performance traits and aging in dairy cattle. Six miRNAs were found to be significantly different in calves with poor growth/fertility relative to controls. Furthermore, several miRNAs were associated with specific performance traits such as average daily gain until weaning, live bodyweight at one year of age, age at first service, and number of infections before first calving.
Article
Veterinary Sciences
Georgios Banos
Summary: Bovine tuberculosis (bTB) is still a significant problem in many countries, affecting both public health and the livestock industry. Efforts towards achieving Officially Tuberculosis Free (OTF) status have been intensified in regions with a high incidence and prevalence of new cases. Genetic selection to remove susceptible animals from breeding has been proposed as an additional measure to control the disease, as there is evidence of genetic variation in individual animals' response to Mycobacterium bovis exposure.
IRISH VETERINARY JOURNAL
(2023)
Article
Agriculture, Dairy & Animal Science
Victoria Lindsay-McGee, Enrique Sanchez-Molano, Georgios Banos, Emily L. Clark, Richard J. Piercy, Androniki Psifidi
Summary: Genome analysis of Connemara ponies and Warmblood horses revealed differences in genetic diversity and population structure. Connemara ponies showed slower decay of linkage disequilibrium and a lower degree of recent inbreeding compared to Warmblood horses. The genetic groups in Connemara ponies were associated with non-registered Connemara ponies and Connemara ponies from the US, while the genetic groups in Warmblood horses were associated with Holsteiners, Anglo European, and British Warmblood horses. Both breeds had a similar ratio of effective number of breeders to effective population size.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Bingjie Li, Matthew Barden, Vanessa Kapsona, Enrique Sanchez-Molano, Alkiviadis Anagnostopoulos, Bethany Eloise Griffiths, Cherril Bedford, Xiaoxia Dai, Mike Coffey, Androniki Psifidi, Georgios Oikonomou, Georgios Banos
Summary: This study examined the genetic architecture of foot lesions in dairy cattle and found that they are under genetic control. The traits showed genetic variation and can be improved through breeding.
GENETICS SELECTION EVOLUTION
(2023)
Article
Genetics & Heredity
Angeliki Argyriadou, Sofia Michailidou, Sotiria Vouraki, Valentina Tsartsianidou, Alexandros Triantafyllidis, Athanasios Gelasakis, Georgios Banos, Georgios Arsenos
Summary: Genetic selection has increased the susceptibility of dairy sheep to diseases and environmental stressors. This study identified SNPs and candidate genes associated with resilience traits in Chios and Frizarta dairy ewes, contributing to the understanding of the genomic background of these traits.
FRONTIERS IN GENETICS
(2023)