Article
Agriculture, Dairy & Animal Science
M. Williams, C. P. Murphy, R. D. Sleator, S. C. Ring, D. P. Berry
Summary: Measuring dry matter intake in grazing dairy cows using current techniques is invasive and costly. This study aimed to find an alternative way to predict dry matter intake by estimating the genetic correlations between body-related linear type traits and dry matter intake. The results showed moderate heritability for all linear type traits and significant genetic correlations between these traits and dry matter intake. However, the predicted dry matter intake based on the genetic evaluation of linear type traits did not strongly correlate with actual dry matter intake in validation animals, especially when body weight data was available.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Amir Aliakbari, Olivier Zemb, Yvon Billon, Celine Barilly, Ingrid Ahn, Juliette Riquet, Helene Gilbert
Summary: This study found genetic variations in the gut microbial community are associated with feed efficiency and production traits in pigs, suggesting potential for selection for feed efficiency using gut microbiome composition.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Review
Genetics & Heredity
Pourya Davoudi, Duy Ngoc Do, Stefanie M. Colombo, Bruce Rathgeber, Younes Miar
Summary: This review comprehensively discusses the topics related to feed efficiency (FE) in pigs, including measurements, genetics, genomics, biological pathways, and advanced technologies for improvement. A deeper understanding of the biology underlying FE is crucial for genetic improvement of FE traits.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Patricia L. Johnson, Sharon Hickey, Kevin Knowler, Janine Wing, Brooke Bryson, Melanie Hall, Arjan Jonker, Peter H. Janssen, Ken G. Dodds, John C. McEwan, Suzanne J. Rowe
Summary: The study on New Zealand maternal sheep revealed a complex relationship between feed efficiency and methane emissions, with different genetic correlations that need to be taken into account in genetic improvement programs.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Cameron A. Olson, Changxi Li, Hushton Block, Lisa McKeown, John A. Basarab
Summary: The study identified phenotypic and genetic correlations between early-life feeding behaviors, dry matter intake, and feed efficiency with cow performance and lifetime productivity traits. These traits were also found to be related to cow weight, genetic factors, and calving interval.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Article
Biochemical Research Methods
Jian Cheng, Christian Maltecca, Paul M. VanRaden, Jeffrey R. O'Connell, Li Ma, Jicai Jiang
Summary: SLEMM is a new software tool for large-scale genomic prediction, which can improve prediction accuracy through SNP weighting. Extensive analyses on multiple datasets showed that SLEMM had the best predictive ability and computational performance compared to other genomic prediction methods. Simulation analyses also demonstrated that SLEMM had comparable accuracy to BayesR.
Article
Fisheries
Wenchao Yu, Junyu Liu, Feng Yu, Yawei Shen, Shihai Gong, Yisha Lu, Wenzhu Peng, Yi Wang, Yang Gan, Qizhen Xiao, Xuan Luo, Weiwei You, Caihuan Ke
Summary: This study measured the growth and feed efficiency traits of Pacific abalone and established an individual-based accurate measurement method. The results showed that residual feed intake (RFI) can be used as a suitable trait for indicating the feed efficiency of abalone, and it is genetically correlated with other traits.
Article
Agriculture, Dairy & Animal Science
Hongding Gao, Guosheng Su, Just Jensen, Per Madsen, Ole F. Christensen, Birgitte Ask, Bjarke G. Poulsen, Tage Ostersen, Bjarne Nielsen
Summary: The study found that group- and individual-level feed intake traits are genetically correlated but different. It is important to consider the differences between these traits in pig breeding programs. Adding information from individual records can improve prediction accuracy for animals with group records.
GENETICS SELECTION EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Richard Border, Georgios Athanasiadis, Alfonso Buil, Andrew J. Schork, Na Cai, Alexander I. Young, Thomas Werge, Jonathan Flint, Kenneth S. Kendler, Sriram Sankararaman, Andy W. Dahl, Noah A. Zaitlen
Summary: The study introduces cross-trait assortative mating (xAM) as an alternative explanation for genetic correlations between different human traits, showing that xAM affects various phenotypes and can plausibly account for a substantial portion of genetic correlation estimates. The results suggest that previous reports may have overestimated the true genetic similarity between many phenotypes.
Article
Agronomy
Ramsey S. S. Lewis
Summary: Inverse genetic correlations between cured leaf yields and alkaloid accumulation in flue-cured tobacco complicate breeding efforts. The introduction of genomic regions from exotic source material could enhance the development of improved cultivars. Germplasm accessions TI 464 and TI 959 are potentially useful for this purpose.
Article
Genetics & Heredity
Andrew D. Grotzinger, Travis T. Mallard, Wonuola A. Akingbuwa, Hill F. Ip, Mark J. Adams, Cathryn M. Lewis, Andrew M. McIntosh, Jakob Grove, Soren Dalsgaard, Klaus-Peter Lesch, Nora Strom, Sandra M. Meier, Manuel Mattheisen, Anders D. Borglum, Ole Mors, Gerome Breen, Phil H. Lee, Kenneth S. Kendler, Jordan W. Smoller, Elliot M. Tucker-Drob, Michel G. Nivard
Summary: A joint analysis of 11 major psychiatric disorders identified four broad factors underlying the genetic correlations among the disorders, along with multiple loci acting on these factors. These findings suggest the presence of genetic overlap among different psychiatric disorders, but also highlight the heterogeneity within each factor. However, a single dimension of genetic risk does not appear to be useful in explaining the biobehavioral correlates or individual variants of psychiatric disorders.
Review
Agriculture, Multidisciplinary
T. Eriksson, C. J. Picard
Summary: This review summarizes the tools and resources available for the insects as food and feed industry, highlighting the importance of optimizing insect strains for economic and biological traits through genetic and genomic selection.
JOURNAL OF INSECTS AS FOOD AND FEED
(2021)
Article
Fisheries
M. Prchal, Ch. Palaiokostas, D. Gela, V. Piackova, S. Reschova, M. Kocour
Summary: We investigated the efficiency of a low-density SNP panel for estimating genetic parameters and breeding values to Koi herpesvirus disease (KHVD) resistance in the Amur mirror carp (AMC). The heritability estimates of KHVD resistance were very high for both populations. Selection for KHVD resistance using the low-density SNP panel could lead to a 7% increase in prediction accuracy compared to pedigree-based selection.
AQUACULTURE REPORTS
(2023)
Article
Agriculture, Dairy & Animal Science
Laura Vargovic, Susanne Hermesch, Rebecca Z. Athorn, Kim L. Bunter
Summary: Electronic sow feeding (ESF) systems are used to monitor feed intake and behavior in group-housed sows, with the study finding moderate to high heritability and repeatability for time-related traits, indicating genetic variation among individuals in their feeding behaviors. Individual phenotypes derived from ESF data could be valuable for genetic evaluations, but differences in the capabilities of ESF systems hindered comparison between farms.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Qianqian Zhou, Fangren Lan, Shuang Gu, Guangqi Li, Guiqin Wu, Yiyuan Yan, Xiaochang Li, Jiaming Jin, Chaoliang Wen, Congjiao Sun, Ning Yang
Summary: In this study, the researchers investigated the effects of host genetics and gut microbiota on feed efficiency in laying hens. They found that genetic factors and gut microbiota both play important roles in determining feed efficiency, with RFI having the highest microbial influence. They also identified three microbial genera that were negatively correlated with RFI and positively contributed to improving feed efficiency.
Article
Agriculture, Dairy & Animal Science
M. Poppe, R. F. Veerkamp, H. A. Mulder, H. Hogeveen
Summary: This study investigates the association between resilience and lifetime gross margin in cows. The resilience indicators, including LnVar and r(auto), were calculated from fluctuations in daily milk yield. The results show that cows with low LnVar, indicating stable milk yield in parity 1, generate higher lifetime gross margin compared to cows with higher fluctuations. However, r(auto) does not have a significant association with lifetime gross margin. The economic advantage of resilience is mainly attributed to the benefits of a longer lifespan.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Harmen P. Doekes, Henk Bovenhuis, Tom V. L. Berghof, Katrijn Peeters, Jeroen Visscher, Han A. Mulder
Summary: Resilience is the capacity of an animal to withstand disturbances and quickly recover. A study was conducted to analyze resilience indicators and natural antibodies in a purebred layer line. The findings indicate that these traits are likely controlled by multiple genes and no significant associations were found.
Article
Genetics & Heredity
Bruno C. Perez, Marco C. A. M. Bink, Karen L. Svenson, Gary A. Churchill, Mario P. L. Calus
Summary: This study evaluated the performance of parametric and nonparametric models in genomic prediction using transcriptomics, and proposed a new model called GTCBLUP. The results showed that gradient boosting machine models were better at capturing phenotypic variation, but their predictive performance did not surpass that of best linear unbiased prediction models for most traits. Models leveraging gene transcripts performed better in capturing phenotypic variance when measured closer to the moment of measuring gene transcripts. The combination of multiple layers was not able to outperform single-omics models in most cases. Using only gene transcripts, the gradient boosting machine model outperformed best linear unbiased prediction for most traits except body weight, but the same pattern was not observed when using both single nucleotide polymorphism genotypes and gene transcripts. The GTCBLUP model showed the highest accuracies for breeding values for 9 out of 13 traits.
G3-GENES GENOMES GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Ibrahim Jibrila, Jan ten Napel, Jeremie Vandenplas, Rob Bergsma, Roel F. Veerkamp, Mario P. L. Calus
Summary: This study examined the impact of genomic preselection on the accuracy and bias of ssGBLUP evaluation for a scarcely recorded trait in pig breeding. It was found that intense genomic preselection had little effect on the accuracy, but could lead to deflation of the genomic breeding values for the target trait.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Genetics & Heredity
Bo Cui, Zhongxu Guo, Hongbo Cao, Mario Calus, Qianqian Zhang
Summary: With advanced genotyping and sequencing technology, researchers in conservation genetics can now obtain genotypes or sequences of individuals from a population sample. The identification of genomic variants and genes that are strongly selected or eliminated during adaptive introgression or long-term hybridization is crucial. We introduce a platform that integrates a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping, which is the first of its kind. Our platform allows compact functions like file input, rIBD calculation, and presentation of rIBD scores. Through analysis of simulated data, we found that the average rIBD score is 0.061 with a standard deviation of 0.124. We determined cut-off values of 0.432 and -0.310 for positive and negative rIBD scores, respectively, to identify significant introgression signals. The platform provides a list of genomic regions with calculated rIBD scores and presents the scores in plots. It is a user-friendly tool for mapping functional genomic variants due to adaptive introgression or long-term hybridization.
FRONTIERS IN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
H. Wilmot, T. Druet, I. Hulsegge, N. Gengler, M. P. L. Calus
Summary: Enhancing collaboration between related breeds is crucial for improving competitiveness and sustainability of local breeds. Developing an across-breed reference population can better manage local breeds, but how different red-pied cattle breeds collaborate in the Benelux region is unclear. This study aims to estimate inbreeding levels, determine genomic relatedness, and detect genomically close animals for building a reference population for two endangered breeds.
Review
Agriculture, Dairy & Animal Science
M. P. L. Calus, Y. C. J. Wientjes, J. Bos, P. Duenk
Summary: This article reviews the research on the purebred-crossbred genetic correlation (rpc) in poultry and finds significant variations in rpc values across different traits. The existing studies might have overestimated rpc values. Future research should aim for more accurate rpc estimations and investigate the impact of genotype by environment interactions on rpc.
Article
Agriculture, Dairy & Animal Science
Helene Wilmot, Tobias Niehoff, Helene Soyeurt, Nicolas Gengler, Mario P. L. Calus
Summary: To develop a breed assignment model, three main steps are generally followed: the selection of breed informative single nucleotide polymorphism (SNP); the training of a model based on a reference population to classify animals to their breed of origin; and the validation of the developed model on external animals. However, there is no consensus on the methodology for SNP selection. This study proposes the use of a genomic relationship matrix (GRM) for breed assignment, which was compared with a model based on selected SNP.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Jeremie Vandenplas, Jan ten Napel, Saeid Naderi Darbaghshahi, Ross Evans, Mario P. L. Calus, Roel Veerkamp, Andrew Cromie, Esa A. Mantysaari, Ismo Stranden
Summary: This study compares two equivalent ssGBLUP models and presents computationally-fast indirect approaches to compute GEBV for genotyped selection candidates. The results show that the indirect approaches can accurately approximate GEBV and are more efficient in terms of storage and computation.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Renzo Bonifazi, Mario P. L. Calus, Jan ten Napel, Roel F. Veerkamp, Stefano Biffani, Martino Cassandro, Simone Savoia, Jeremie Vandenplas
Summary: International evaluations provide more information for breeding value estimation, but differences exist between international and national evaluations. This study aimed to integrate international sires' breeding values and reliabilities into national evaluations, improving the consistency between them.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Michael Aldridge, Jeremie Vandenplas, Pascal Duenk, John Henshall, Rachel Hawken, Mario Calus
Summary: In genomic prediction, it is common to centre the genotypes of single nucleotide polymorphisms based on the allele frequencies in the current population. The fitting of a 'J-factor' as a fixed effect can improve the accuracy and dispersion bias of sire genomic estimated breeding values (GEBV). This study investigated the benefits of fitting multiple J-factors for each breed in a three-way crossbred population.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Charlie A. de Hollander, Vivian P. Breen, John Henshall, Fernando B. Lopes, Mario P. L. Calus
Summary: In broiler breeding, measuring body weights on sibs of selection candidates in a commercial environment and genotyping them could increase genetic progress. This study aimed to evaluate different genotyping strategies and proportions of sibs genotyped to optimize a sib-testing breeding program in broilers using real data. Results showed that genotyping sibs with extreme phenotypes resulted in higher accuracy of genomic estimated breeding values (GEBV), especially at genotyping proportions of 12.5% or 25%.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Pascal Duenk, Yvonne C. J. Wientjes, Piter Bijma, Maja W. Iversen, Marcos S. Lopes, Mario P. L. Calus
Summary: This study proposes and compares three methods for approximating the required variance components, and validates that using REML estimates of variance components provides better predictions for r(pc) than methods based on GEBV.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Aixin Ni, Mario P. L. Calus, Henk Bovenhuis, Jingwei Yuan, Yuanmei Wang, Yanyan Sun, Jilan Chen
Summary: The study focused on analyzing the genetic background and estimating the heterosis of egg-laying traits in reciprocal crosses between an indigenous Beijing-You and an elite commercial White Leghorn layer line. The results showed that the crossbreds performed better in egg production traits, indicating the importance of non-additive genetic effects in hybrid offspring.
GENETICS SELECTION EVOLUTION
(2023)
Meeting Abstract
Agriculture, Dairy & Animal Science
Y. C. J. Wientjes, P. Bijma, J. van den Heuvel, B. J. Zwaan, Z. G. Vitezica, M. P. L. Calus
JOURNAL OF DAIRY SCIENCE
(2022)
