Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty
Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Walsh, Siobhan W. ; Evans, Ross D. ; Purfield, Deirdre C. - \ 2020
Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
cattle - genome-wide association study - linear type traits - sequence - single nucleotide polymorphism - skeletal
Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.
Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds
Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Evans, Ross D. ; Walsh, Siobhán W. ; Purfield, Deirdre C. - \ 2020
Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X - 1 p.
BACKGROUND: Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. RESULTS: We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. CONCLUSIONS: The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.
Whole genome sequence GWAS reveals muscularity in beef cattle differs across five cattle breeds
Doyle, J.L. ; Berry, D.P. ; Veerkamp, R.F. ; Carthy, Tara R. ; Walsh, S.W. ; Purfield, Deirdre C. - \ 2019
In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of Abstracts ) - ISBN 9789086863396 - p. 210 - 210.
ISSN ISBN 1382-6077
Genetic co-variance components within and among muscular, skeletal and functional traits differ among contrasting beef breeds
Doyle, Jennifer ; Berry, Donagh P. ; Walsh, Siobhan W. ; Veerkamp, R.F. ; Evans, Ross D. ; Carthy, Tara R. - \ 2018
In: World Congress on Genetics Applied to Livestock Production. - IAVS / Massey University - 8 p.
The potential of unmanned aerial systems for sea turtle research and conservation : A review and future directions
Rees, Alan F. ; Avens, Larisa ; Ballorain, Katia ; Bevan, Elizabeth ; Broderick, Annette C. ; Carthy, Raymond R. ; Christianen, Marjolijn J.A. ; Duclos, Gwénaël ; Heithaus, Michael R. ; Johnston, David W. ; Mangel, Jeffrey C. ; Paladino, Frank ; Pendoley, Kellie ; Reina, Richard D. ; Robinson, Nathan J. ; Ryan, Robert ; Sykora-Bodie, Seth T. ; Tilley, Dominic ; Varela, Miguel R. ; Whitman, Elizabeth R. ; Whittock, Paul A. ; Wibbels, Thane ; Godley, Brendan J. - \ 2018
Endangered Species Research 35 (2018). - ISSN 1863-5407 - p. 81 - 100.
Aerial survey - Behaviour - Conservation - Drone - Ecology - Population biology - Sea turtle - UAV
The use of satellite systems and manned aircraft surveys for remote data collection has been shown to be transformative for sea turtle conservation and research by enabling the collection of data on turtles and their habitats over larger areas than can be achieved by surveys on foot or by boat. Unmanned aerial vehicles (UAVs) or drones are increasingly being adopted to gather data, at previously unprecedented spatial and temporal resolutions in diverse geographic locations. This easily accessible, low-cost tool is improving existing research methods and enabling novel approaches in marine turtle ecology and conservation. Here we review the diverse ways in which incorporating inexpensive UAVs may reduce costs and field time while improving safety and data quality and quantity over existing methods for studies on turtle nesting, at-sea distribution and behaviour surveys, as well as expanding into new avenues such as surveillance against illegal take. Furthermore, we highlight the impact that high-quality aerial imagery captured by UAVs can have for public outreach and engagement. This technology does not come without challenges. We discuss the potential constraints of these systems within the ethical and legal frameworks which researchers must operate and the difficulties that can result with regard to storage and analysis of large amounts of imagery. We then suggest areas where technological development could further expand the utility of UAVs as data-gathering tools; for example, functioning as downloading nodes for data collected by sensors placed on turtles. Development of methods for the use of UAVs in sea turtle research will serve as case studies for use with other marine and terrestrial taxa.
Genetic covariance components within and among linear type traits differ among contrasting beef cattle breeds
Doyle, Jennifer L. ; Berry, Donagh P. ; Walsh, Siobhan W. ; Veerkamp, Roel F. ; Evans, Ross D. ; Carthy, Tara R. - \ 2018
Journal of Animal Science 96 (2018)5. - ISSN 0021-8812 - p. 1628 - 1639.
Beef - Breeds - Cattle - Type traits
Linear type traits describing the skeletal, muscular, and functional characteristics of an animal are routinely scored on live animals in both the dairy and beef cattle industries. Previous studies have demonstrated that genetic parameters for certain performance traits may differ between breeds; no study, however, has attempted to determine if differences exist in genetic parameters of linear type traits among breeds or sexes. Therefore, the objective of the present study was to determine if genetic covariance components for linear type traits differed among five contrasting cattle breeds, and to also investigate if these components differed by sex. A total of 18 linear type traits scored on 3,356 Angus (AA), 31,049 Charolais (CH), 3,004 Hereford (HE), 35,159 Limousin (LM), and 8,632 Simmental (SI) were used in the analysis. Data were analyzed using animal linear mixed models which included the fixed effects of sex of the animal (except in the investigation into the presence of sexual dimorphism), age at scoring, parity of the dam, and contemporary group of herd-date of scoring. Differences (P < 0.05) in heritability estimates, between at least two breeds, existed for 13 out of 18 linear type traits. Differences (P < 0.05) also existed between the pairwise within-breed genetic correlations among the linear type traits. Overall, the linear type traits in the continental breeds (i.e., CH, LM, SI) tended to have similar heritability estimates to each other as well as similar genetic correlations among the same pairwise traits, as did the traits in the British breeds (i.e., AA, HE). The correlation between a linear function of breeding values computed conditional on covariance parameters estimated from the CH breed with a linear function of breeding values computed conditional on covariance parameters estimated from the other breeds was estimated. Replacing the genetic covariance components estimated in the CH breed with those of the LM had least effect but the impact was considerable when the genetic covariance components of the AA were used. Genetic correlations between the same linear type traits in the two sexes were all close to unity (≥0.90) suggesting little advantage in considering these as separate traits for males and females. Results for the present study indicate the potential increase in accuracy of estimated breeding value prediction from considering, at least, the British breed traits separate to continental breed traits.
|Land use efficiency of beef systems in the Northeastern USA from a food supply perspective
Tichenor, Nicole ; Zanten, H.H.E. van; Boer, I.J.M. de; Peters, C.J. ; Carthy, A.C. ; Griffin, T.S. - \ 2016
In: Book of Abstracts of the 10th international conference on Life Cycle Assessment of Food. -
Land use ratio - food security - beef production
One widely recognized strategy to meet future food needs is reducing the amount of arable land used for livestock feed production. Of all livestock products, beef is the largest land user per unit output. Whether beef production results in feedfood competition or a net positive contribution to the food supply, however, may depend largely on whether marginal land is used for forage. Van Zanten et al. (2015) developed the land use ratio (LUR) to identify livestock systems that provide more food than could be produced by converting their suitable feed land to food crops. While Van Zanten et al. (2015) used country and farm-level suitability data, the former may not be high enough resolution for large countries, and the latter may not be available in many countries. We developed a method that integrates geospatial data to estimate crop suitability and yield at multiple scales into the LUR, broadening its applicability. We illustrated this approach with grass-fed beef (GF) and dairy beef (DB) case study systems in the Northeastern USA, including multiple scenarios limiting land conversion. All systems had LURs greater than one, indicating they produce less protein than conversion of their suitable land bases to food cropping would. Because a large fraction of the forage land used in the GF system was suitable for crop production and moderately productive, its LUR was 3-6 times larger (less efficient) than the DB system. Future research should explore mechanisms to improve LUR and life cycle environmental burdens of these regional production systems.
|The social, the transformational and the responsible? The extent to which social enterprises take responsibility into account in innovation
Lubberink, R.J.B. ; Blok, V. ; Ophem, J.A.C. van; Omta, S.W.F. - \ 2014
Social entrepreneurs can be seen as the ‘transformational leaders’ who combine entrepreneurship with a societal vision while building bridges between business, governments and citizens (Purdue, 2001). But how do they take up this role and act as change agents for societal transitions? It is their innovation which is essential for realizing these transitions. The emerging concept of ‘Responsible Research & Innovation’ (RRI), as a transformative and constructive approach (Owen et al., 2013), can help to understand how social entrepreneurs actually stimulate and shape these transitions, since it combines social and economic goals. RRI is a transparent, interactive process where involved actors become mutually responsive to each other, aiming for the innovation process and its marketable products being adopted by society (von Schomberg, 2011). Although, RRI has the potential to understand the transformational leadership of social entrepreneurship. The problem is that the field of corporate innovation is underexposed in current RRI research (cf. Blok, 2013). This raises the question: how in fact is RRI embedded in the innovation practices of social enterprises? In the literature, various reasons are identified why SMEs can have a predisposition for engaging in responsible innovation (Rodgers, 2010 in Halme & Korpela, 2013; Scholten et al., 2013). It is for instance assumed that they are to be more adaptive and responsive to society than (larger) firms or incumbents (Scholten et al., 2013). However, it is still the question how exactly SMEs engage in RRI in practice and how they contribute to societal transitions. Social enterprises are an interesting subgroup of SMEs, and the units of analysis in this paper, because the goal to create social value through social innovations show resemblance with the goals of RRI (viz. a social, environmental and economic positive impact). Furthermore, in order to take care for the future, RRI should be for society and with society through responsive stewardship in the present (Stilgoe et al., 2013). Therefore, the aim of this paper is to answer the question: to what extent do social enterprises take responsibility into account in their innovation processes? To answer this question, we will do a content analyses on approximately 150 cases of social enterprises linked with climate change adaptation and mitigation in urban areas. The data will be obtained from the open database of Ashoka (largest network of social entrepreneurs worldwide). Their platform shares elaborate case descriptions of social enterprises with regard to: the problem that the social enterprises address, the ideas that they have, the strategies to solve to problem and personal information about the social entrepreneurs. These social entrepreneurs provide information via a five step process with regard to: newness, creativity, entrepreneurial quality, social impact and ethical fibre. In order to do such a content analysis, we will first develop a theoretical framework with all the relevant elements of industrial RRI processes, based on a review of the RRI literature (e.g. goals, ethics, stakeholder involvement, technology assessment). Subsequently, we will code the case descriptions based on the operationalized indicators, which implies a deductive content analysis. Finally, we will assess to what extent the individual indicators of responsible innovation are addressed by social enterprises. Because most current work on (industrial) RRI is still conceptual or based on single case studies, this research aims to fill the knowledge gap in RRI literature with more empirical results. References: Blok, V., Hoffmans, L. (2013). Stakeholder Engagement in Companies’ responsible research and innovation processes. Working paper. Choi, N., & Majumdar, S. (2013). Social entrepreneurship as an essentially contested concept: Opening a new avenue for systematic future research. Journal of Business Venturing. Halme, M., & Korpela, M. (2013). Responsible Innovation Toward Sustainable Development in Small and Medium-Sized Enterprises: a Resource Perspective. Business Strategy and the Environment. Owen, R., Stilgoe, J., Macnaghten, P., Gorman, M., Fisher, E., & Guston, D. (2013). A framework for responsible innovation. Responsible Innovation: Managing the Responsible Emergence of Science and Innovation in Society, 27-50. Purdue, D. (2001). Neighbourhood governance: Leadership, trust and social capital. Urban Studies, 38(12), 2211-2224. Rodgers, C. (2010). Sustainable entrepreneurship in SMEs: a case study analysis. Corporate Social Responsibility and Environmental Management, 17(3), 125-132. Scholten, V., Pavie, J., Carthy, D. (2013). Responsible Innovation- A Challenge and Opportunity Nexus for SMEs. 19th ICE & IEEE-ITMC international conference on Responsible Innovation & Entrepreneurship, 24-26 June, The Hague. Stilgoe, J., Owen, R., & Macnaghten, P. (2013). Developing a framework for responsible innovation. Research Policy, 42(9), 1568-1580. von Schomberg, R. (2013). A Vision of Responsible Research and Innovation. Responsible Innovation: Managing the Responsible Emergence of Science and Innovation in Society, Wiley, London, 51-74.
Estimation of genetic parameters for testday milk yield in a seasonal calving system
Mc Carthy, J. ; Veerkamp, R.F. - \ 2011
In: Book of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science, 29 August - 2 September, 2011 Stavanger, Norway. - Wageningen Academic Publishers - ISBN 9789086861774 - p. 113 - 113.