Heterogeneity of variance for milk, fat and protein yield in small cattle populations: The Rendena breed as a case study
TL;DR: The need for a correction method for the heterogeneous variance in the small cattle breed used as a case study is suggested, particularly in the selection of best cows that are more susceptible to biases in EBVs.
About: This article is published in Livestock Science.The article was published on 2018-07-01. It has received 7 citations till now. The article focuses on the topics: Population.
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TL;DR: This study elucidates the requirements for variance component estimation in honeybees and provides the theoretical groundwork for simplified honeybee models and yielded plausible parameter estimates for almost all settings.
Abstract: Abstract Estimating genetic parameters of quantitative traits is a prerequisite for animal breeding. In honeybees, the genetic variance separates into queen and worker effects. However, under data paucity, parameter estimations that account for this peculiarity often yield implausible results. Consequently, simplified models that attribute all genetic contributions to either the queen (queen model) or the workers (worker model) are often used to estimate variance components in honeybees. However, the causes for estimations with the complete model (colony model) to fail and the consequences of simplified models for variance estimates are little understood. We newly developed the necessary theory to compare parameter estimates that were achieved by the colony model with those of the queen and worker models. Furthermore, we performed computer simulations to quantify the influence of model choice, estimation algorithm, true genetic parameters, rates of controlled mating, apiary sizes, and phenotype data completeness on the success of genetic parameter estimations. We found that successful estimations with the colony model were only possible if at least some of the queens mated controlled on mating stations. In that case, estimates were largely unbiased if more than 20% of the colonies had phenotype records. The simplified queen and worker models proved more stable and yielded plausible parameter estimates for almost all settings. Results obtained from these models were unbiased when mating was uncontrolled, but with controlled mating, the simplified models consistently overestimated heritabilities. This study elucidates the requirements for variance component estimation in honeybees and provides the theoretical groundwork for simplified honeybee models.
7 citations
TL;DR: It is argued that the results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide, which could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.
Abstract: Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals’ life, a potentially important aspect in the study of the traits’ genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50–60 Mb), while the hotspot associated with CF and DP was on BTA18 (55–62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.
2 citations
TL;DR: In this paper , the impact of genotype by environmental interaction (GxE) in local dual-purpose cattle was investigated in Rendena cattle under diverse environmental conditions, including altitude, housing, feeding system, and use of summer pasture.
Abstract: Simple Summary This study aimed at investigating the impact of genotype by environmental interaction (GxE) in local dual-purpose cattle. Environmental conditions were based on altitude, housing, feeding system, and use of summer pasture. Genetic variability for production traits was larger in farms in plain areas, without the use of summer pasture, with loose housing and feeding of total mixed rations. On the other hand, a greater response for most conformation traits was found for mountain farms, using loose housing, hay-based feeding, and no summer pasture. This study confirms the relevance of considering GxE in local breeds reared in various environments. Abstract Local breeds are often reared in various environmental conditions (EC), suggesting that genotype by environment interaction (GxE) could influence genetic progress. This study aimed at investigating GxE and response to selection (R) in Rendena cattle under diverse EC. Traits included milk, fat, and protein yields, fat and protein percentage, and somatic cell score, three-factor scores and 24 linear type traits. The traits belonged to 11,085 cows (615 sires). Variance components were estimated in a two-step reaction norm model (RNM). A single trait animal model was run to obtain the solutions of herd-EC effect, then included in a random regression sire model. A multivariate response to selection (R) in different EC was computed for traits under selection including beef traits from a performance test. GxE accounted on average for 10% of phenotypic variance, and an average rank correlation of over 0.97 was found between bull estimated breeding values (EBVs) by either including or not including GxE, with changing top ranks. For various traits, significantly greater genetic components and R were observed in plain farms, loose housing rearing system, feeding total mixed ration, and without summer pasture. Conversely, for beef traits, a greater R was found for mountain farms, loose housing, hay-based feeding and summer pasture.
1 citations
TL;DR: The study confirmed the benefit of OCS as effective tool for long-term preservation of small local breeds under selection, which is important for biodiversity and sustainable use of the genetic resources.
Abstract: Submitted 2020-07-24 | Accepted 2020-09-09 | Available 2020-12-01 https://doi.org/10.15414/afz.2020.23.mi-fpap.287-295 The present study aimed to evaluate the effects of optimum contribution selection (OCS) in a small native cattle breed. In practical animal breeding, the genetic improvement is often accompanied by an increase of inbreeding level due to the preferential use of closely related animals, particularly in small populations. This may lead to a reduction of genetic variability and to detrimental effects on some traits. The OCS maximizes the genetic merit of newborns while putting a restriction on the average relationship of the current generation. Despite the benefits, OCS has not been widely applied in practical breeding plans yet. This study considered the effects of OCS in the dual-purpose Rendena cattle, by applying different penalties to the average relationship of current generation (from 0 to -100,000). The OCS was applied on the candidate bull-dams and bull-sires for the years 2014 to 2019, and compared with simulations of random mating, traditional selection and mating system used by the breeders association. Considering the mating of 2014 and 2015, OCS allowed to obtain a predicted offspring with lower genetic merit than in traditional selection, but also with a lower inbreeding. When OCS was routinely introduced in the breed, in 2016, a reduction in genetic merit but also a consistent reduction in the average relatedness and inbreeding rate were observed. Subsequent years showed the actual effects of the OCS program: after the introduction of the optimization, the inbreeding rate did not increase over years. Moreover, the traditional mating system results were suboptimal in respect to OCS simulations. The study confirmed the benefit of OCS as effective tool for long-term preservation of small local breeds under selection, which is important for biodiversity and sustainable use of the genetic resources. Keywords: optimal contribution selection, native cattle, small population, inbreeding, Rendena References Berg, P., Nielsen, J. and Sorensen, M. K. (2006). EVA: Realized and predicted optimal genetic contributions. In Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006 (pp. 27-09). http://www.wcgalp8.org.br Biscarini, F. et al. (2015). Challenges and opportunities in genetic improvement of local livestock breeds. Frontiers in Genetics, 6, 33. https://doi.org/10.3389/fgene.2015.00033 Clark, S. A. et al. (2013). The effect of genomic information on optimal contribution selection in livestock breeding programs. Genetics Selection Evolution, 45(1), 44. https://doi.org/10.1186/1297-9686-45-44 Gandini, G. et al. (2014). Selection with inbreeding control in simulated young bull schemes for local dairy cattle breeds. Journal of Dairy Science, 97(3), 1790-1798. https://doi.org/10.3168/jds.2013-7184 Gorjanc, G. and Hickey, J. M. (2018). AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs. Bioinformatics, 34(19), 3408-3411. https://doi.org/10.1093/bioinformatics/bty375 Gourdine, J. L., Sorensen A. C. and Rydhmer, L. (2012). There is room for selection in a small local pig breed when using optimum contribution selection: a simulation study. Journal of Animal Science, 90(1), 76-84. https://doi.org/10.2527/jas.2011-3898 Guzzo, N., Sartori, C. and Mantovani, R. (2018). Heterogeneity of variance for milk, fat and protein yield in small cattle populations: The Rendena breed as a case study. Livestock Science, 213, 54-60. https://doi.org/10.1016/j.livsci.2018.05.002 Hasler, H. et al. (2011). Genetic diversity in an indigenous horse breed–implications for mating strategies and the control of future inbreeding. Journal of Animal Breeding and Genetics, 128(5), 394-406. https://doi.org/10.1111/j.1439-0388.2011.00932.x Henryon, M. et al. (2015). Most of the long-term genetic gain from optimum-contribution selection can be realised with restrictions imposed during optimisation. Genetics Selection Evolution, 47(1), 21. https://doi.org/10.1186/s12711-015-0107-7 Kjetsa, M. H. (2016). Optimal Contribution Selection Applied to the Norwegian Cheviot Sheep Population. Master's thesis, Norwegian University of Life Sciences, As, 2016. http://hdl.handle.net/11250/2399694 Kettunen, A. and Berg, P. (2017). Faroese Horse: Population status & conservation possibilities. urn:nbn:se:norden:org:diva-5822 Kohl, S., Wellmann, R. and Herold, P. (2020). Advanced optimum contribution selection as a tool to improve regional cattle breeds: a feasibility study for Vorderwald cattle. Animal, 14(1), 1-12. https://doi.org/10.1017/S1751731119001484 Leroy, G. (2014). Inbreeding depression in livestock species: review and meta‐analysis. Animal Genetics, 45(5), 618-628. https://doi.org/10.1111/age.12178 Meuwissen, T. H. E. (1997). Maximizing the response of selection with a predefined rate of inbreeding. Journal of Animal Science, 75(4), 934-940. https://doi.org/10.2527/1997.754934x Meuwissen, T. H. E. and Luo, Z. (1992). Computing inbreeding coefficients in large populations. Genetics Selection Evolution, 24(4), 1-9. https://doi.org/10.1186/1297-9686-24-4-305 Mwangi, S. I. et al. (2020). Effect of controlling future rate of inbreeding on expected genetic gain and genetic variability in small livestock populations. Animal Production Science. https://doi.org/10.1071/AN19123 Olsen, H. F., Meuwissen, T. and Klemetsdal, G. (2013). Optimal contribution selection applied to the Norwegian and the North‐Swedish cold‐blooded trotter–a feasibility study. Journal of Animal Breeding and Genetics, 130(3), 170-177. https://doi.org/10.1111/j.1439-0388.2012.01005.x Sartori, C. et al. (2018). Genetic correlations among milk yield, morphology, performance test traits and somatic cells in dual-purpose Rendena breed. Animal, 12(5), 906-914. https://doi.org/10.1017/S1751731117002543 Sole, M. et al. (2013). Implementation of Optimum Contributions Selection in endangered local breeds: the case of the Menorca Horse population. Journal of Animal Breeding and Genetics, 130(3), 218-226. https://doi.org/10.1111/jbg.12023 Sonesson, A. K. and Meuwissen, T. H. (2000). Mating schemes for optimum contribution selection with constrained rates of inbreeding. Genetics Selection Evolution, 32(3), 231-248. https://doi.org/10.1051/gse:2000116 Sorensen, M. K. et al. (2008). Optimal genetic contribution selection in Danish Holstein depends on pedigree quality. Livestock Science, 118(3), 212-222. https://doi.org/10.1016/j.livsci.2008.01.027 Wang, Y., Bennewitz, J. and Wellmann, R. (2017). Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration. Genetics Selection Evolution, 49(1), 45. https://doi.org/10.1186/s12711-017-0320-7 Wellmann, R., Hartwig, S. and Bennewitz, J. (2012). Optimum contribution selection for conserved populations with historic migration. Genetics Selection Evolution, 44(1), 34. https://doi.org/10.1186/1297-9686-44-34 Wray, N. R. and Goddard, M. E. (1994). Increasing long-term response to selection. Genetics Selection Evolution, 26(5), 1-21. https://doi.org/10.1186/1297-9686-26-5-431
1 citations
Cites background from "Heterogeneity of variance for milk,..."
...Rendena cattle is a rustic breed native from Rendena Valley (Trento Province, Italy) and currently reared both in plains and in alpine mountain farms (Guzzo et al., 2018)....
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DOI•
TL;DR: In this paper , the main Italian dual-purpose breeds in terms of feed efficiency and behaviour, the dry matter intakes (DMI) of 890 young bulls were collected using automatic feeding systems in two Italian genetic centres.
Abstract: Abstract To characterise the main Italian dual-purpose breeds in terms of feed efficiency and behaviour, the dry matter intakes (DMI) of 890 young bulls were collected using automatic feeding systems in two Italian genetic centres. In Experiment 1, Italian Simmental (IS), Rendena (RE) and Alpine Grey (AG) young bulls were fed total mixed ration for 46 days. In Experiment 2, Valdostana Red Pied (VR) and Black Pied and Chestnut (VB) young bulls were fed hay and concentrate for 60 days. The IS and RE bulls grew faster than AG (1.6 vs. 1.3 kg/d, p < .01). The DMI was highest for IS and lowest for AG while all breeds had similar values for DMI expressed as relative to body weight. Overall, RE and AG bulls were more efficient than IS. Regarding feeding behaviour, the number of feeding events for IS and AG was higher than for RE, while the feeding time was not different between breeds. The IS bulls showed a higher value of feeding rate (FR) than RE and AG (98.2 vs. 83.1–86.5 g DM/min, p < .01). Overall AG breed, despite its high feeding activity, was particularly efficient. In addition, efficient animals showed a low FR compared to inefficient ones. In Experiment 2, VR and VB strains were quite similar in terms of growth capacity but VR was more efficient despite its higher daily activity. In conclusion, dual-purpose breeds can reach notable growths and feed efficiencies and FR is well related to feed efficiency. Highlights Rendena and Alpine Grey bulls are slightly more efficient than Italian Simmental bulls Valdostana strains differ for feed efficiency but not for growth capacity Feeding rate is a useful behaviour trait to consider in the study of feed efficiency
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1,051 citations
TL;DR: Formulation of the genotype-environment interaction in terms of a genetic correlation leads easily to a solution of problems connected with selection and a precise answer can be given to the question whether it is better to carry out selection in the environment in which the improved breed is required eventually to live, or in some other environment more favorable to the expression of the desired character.
Abstract: Situations involving an interaction between genotype and environment may be treated by the methods of genetic correlation, if only two different environments are considered. Formulation of the genotype-environment interaction in terms of a genetic correlation leads easily to a solution of problems connected with selection. In this way a precise answer can be given to the question whether it is better to carry out selection in the environment in which the improved breed is required eventually to live, or in some other environment more favorable to the expression of the desired character. Performance in the two environments is regarded as two different characters which are genetically correlated. Selection for one character will then bring about a correlated response of the other character. The magnitude of this correlated response may then be compared with that of the direct response to selection for the desired character itself. The ratio of the correlated to the direct response may be expressed in a simp...
910 citations
TL;DR: The best known application of RRM has been to genetic evaluation of dairy cattle using test day production records, and the basic structure of a RRM is given.
468 citations
TL;DR: It is concluded that a negative correlation between artificial and natural selection should be avoided and a large increase in the critical effective population size is needed to prevent a decline in fitness.
Abstract: In livestock populations, fitness may decrease due to inbreeding depression or as a negatively correlated response to artificial selection. On the other hand, fitness may increase due to natural selection. In the absence of a correlated response due to artificial selection, the critical population size at which the increase due to natural selection and the decrease due to inbreeding depression balance each other is approximately D/2σwa
2, where D=the inbreeding depression of fitness with complete inbreeding, and σwa
2=the additive genetic variance of fitness. This simple expression agrees well with results from transmission probability matrix methods. If fitness declines as a correlated negative response to artificial selection, then a large increase in the critical effective population size is needed. However, if the negative response is larger than the response to natural selection, a reduction in fitness cannot be prevented. From these results it is concluded that a negative correlation between artificial and natural selection should be avoided. Effective sizes to prevent a decline in fitness are usually larger than those which maximize genetic gain of overall efficiency, i.e., the former is a more stringent restriction on effective size. In the examples presented, effective sizes ranged from 31 to 250 animals per generation.
210 citations
TL;DR: The analysis shows that consistent differences can be observed in the cultural values of local breeds, both as historical witness and as custodian, today, of local traditions.
Abstract: Summary
The article analyses the potential cultural value of local livestock breeds with the aim of identifying useful elements to both conserve and attribute value to them. Local breeds can be considered cultural properties in relation to their role as historical witnesses as they often play a central part in the agriculture tenures and in the social life of rural populations. Local breeds can also be likened to cultural properties because they contribute to the preservation of ancient local traditions. To analyse the historical value of a local breed, a methodology is proposed which is based on a set of parameters including antiquity, role in the agricultural system, farming techniques, role in landscape, gastronomy, folklore and handicrafts and presence in forms of higher artistic expression. To assess the role of the breed as a custodian of local traditions, additional parameters are proposed to evaluate its contribution in maintaining traditional landscape, gastronomy, folklore and handicrafts. The proposed methodology is applied to a set of nine local cattle breeds, covering a wide spectrum of farming settings. The analysis shows that consistent differences can be observed in the cultural values of local breeds, both as historical witness and as custodian, today, of local traditions.
Zusammenfassung
Untersuchung des kulturellen Wertes lokaler Haustierrassen: eine Methode
Es werden lokale Haustierrassen auf Eigenschaften untersucht, die nutzlich fur die Erhaltung ihres kulturellen Wertes sind oder diesen einen solchen zuordnen lassen. Lokalen Rassen kann ein Wert als kulturhistorisches Zeugnis zugeordnet werden, da sie haufig eine zentrale Rolle im landwirtschaftlichen Besitz und im sozialen Leben der landlichen Bevolkerung spielten. Sie konnen auch als aktuell kulturelles Eigentum angesehen werden, weil sie zur Erhaltung lokaler historisch gewachsener Traditionen beitragen. Zur Analyse des historischen Wertes lokaler Rassen wird eine Methode vorgeschlagen, die auf mehreren Parametern aufbaut: Alter, Funktion im landwirtschaftlichen System und innerhalb landbaulicher Methoden, Bedeutung fur die Landschaftspflege, Gastronomie, Folklore und Handwerk, sowie deren Darstellung in der Kunst. Zur Beurteilung der Rassen als Huter lokaler Traditionen werden zusatzliche Parameter vorgeschlagen, um ihren Beitrag zur Erhaltung der traditionellen Kulturlandschaft, Gastronomie, Folklore und Handwerk zu erhalten. Die vorgeschlagene Methode wird auf neun lokale Rassen angewandt, die ein weites landwirtschaftliches Spektrum umfassen. Die Untersuchung zeigt, dass konsistente Unterschiede im kulturellen Wert lokaler Rassen beobachtet werden konnen, und zwar sowohl als kulturhistorisches Zeugnis als auch als Huter historisch gewachsener lokaler Traditionen.
188 citations