Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Addiction systems antagonize bacterial adaptive immunity
Sluijs, Lisa van; Houte, Stineke van; Oost, John van der; Brouns, Stan J.J. ; Buckling, Angus ; Westra, Edze R. - \ 2019
FEMS Microbiology Letters 366 (2019)5. - ISSN 0378-1097
adaptive immunity - bacteria - CRISPR - plasmid - TA - toxin

CRISPR-Cas systems provide adaptive immunity against mobile genetic elements, but employment of this resistance mechanism is often reported with a fitness cost for the host. Whether or not CRISPR-Cas systems are important barriers for the horizontal spread of conjugative plasmids, which play a crucial role in the spread of antibiotic resistance, will depend on the fitness costs of employing CRISPR-based defences and the benefits of resisting conjugative plasmids. To estimate these costs and benefits we measured bacterial fitness associated with plasmid immunity using Escherichia coli and the conjugative plasmid pOX38-Cm. We find that CRISPR-mediated immunity fails to confer a fitness benefit in the absence of antibiotics, despite the large fitness cost associated with carrying the plasmid in this context. Similar to many other conjugative plasmids, pOX38-Cm carries a CcdAB toxin-anti-toxin (TA) addiction system. These addiction systems encode long-lived toxins and short-lived anti-toxins, resulting in toxic effects following the loss of the TA genes from the bacterial host. Our data suggest that the lack of a fitness benefit associated with CRISPR-mediated defence is due to expression of the TA system before plasmid detection and degradation. As most antibiotic resistance plasmids encode TA systems this could have important consequences for the role of CRISPR-Cas systems in limiting the spread of antibiotic resistance.

Benthic effects of offshore renewables: identification of knowledge gaps and urgently needed research
Dannheim, Jennifer ; Bergström, Lena ; Birchenough, Silvana N.R. ; Brzana, Radosław ; Boon, Arjen R. ; Coolen, Joop W.P. ; Dauvin, Jean-Claude ; Mesel, Ilse De; Derweduwen, Jozefien ; Gill, Andrew B. ; Hutchison, Zoë L. ; Jackson, Angus C. ; Janas, Urszula ; Martin, Georg ; Raoux, Aurore ; Reubens, Jan ; Rostin, Liis ; Vanaverbeke, Jan ; Wilding, Thomas A. ; Wilhelmsson, Dan ; Degraer, Steven ; Norkko, Joanna - \ 2019
ICES Journal of Marine Science (2019). - ISSN 1054-3139 - 17 p.
benthos - environmental impact - knowlegde gaps - marine ecology - offshore wind farms - renewable energy
As the EU's commitment to renewable energy is projected to grow to 20% of energy generation by 2020, the use of marine renewable energy from wind, wave and tidal resources is increasing. This literature review (233 studies) (i) summarizes knowledge on how marine renewable energy devices affect benthic environments, (ii) explains how these effects could alter ecosystem processes that support major ecosystem services and (iii) provides an approach to determine urgent research needs. Conceptual diagrams were set up to structure hypothesized cause-effect relationships (i.e. paths). Paths were scored for (i) temporal and spatial scale of the effect, (ii) benthic sensitivity to these effects, (iii) the effect consistency and iv) scoring confidence, and consecutively ranked. This approach identified prominent knowledge gaps and research needs about (a) hydrodynamic changes possibly resulting in altered primary production with potential consequences for filter feeders, (b) the introduction and range expansion of non-native species (through stepping stone effects) and, (c) noise and vibration effects on benthic organisms. Our results further provide evidence that benthic sensitivity to offshore renewable effects is higher than previously indicated. Knowledge on changes of ecological functioning through cascading effects is limited and requires distinct hypothesis-driven research combined with integrative ecological modelling.
Book review: Domingues da Silva, Daniel B. The Atlantic Slave Trade from West Central Africa, 1780–1867
Dalrymple-Smith, Angus - \ 2018
International Review of Social History 63 (2018)3. - ISSN 0020-8590 - p. 523 - 526.
Report of the Working Group on Marine Benthal and Renewable Energy Developments (WGMBRED) : 6-9 March 2018, Galway, Ireland
Dannheim, Jennifer ; Gill, Andrew B. ; Boon, Arjen ; Brzana, Radoslaw ; Coolen, J.W.P. ; Dauvin, Jean-Claude ; Degraer, Steven ; Jackson, Angus ; Janas, Urszula ; Mesel, I.G. de; O'Beirn, Francis ; Pezy, Jean-Philippe ; Raoux, Aurore ; Sheehan, Emma ; Vanaverbeke, Jan - \ 2018
International Council for the Exploration of the Sea (ICES WGMBRED Report 2018/HAPISG:02) - 68 p.
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.

Major threats of pollution and climate change to global coastal ecosystems and enhanced management for sustainability
Lu, Y. ; Yuan, J. ; Lu, X. ; Su, Chao ; Zhang, Y. ; Wang, C. ; Cao, X. ; Li, Q. ; Su, Jilan ; Ittekkot, Venugopalan ; Garbutt, Richard Angus ; Bush, S.R. ; Fletcher, Stephen ; Wagey, Tonny ; Kachur, Anatolii ; Sweijd, Neville - \ 2018
Environmental Pollution 239 (2018). - ISSN 0269-7491 - p. 670 - 680.
coastal ecosystem - marine pollution - climate change - ecological impacts - coastal sustainability
Coastal zone is of great importance in the provision of various valuable ecosystem services. However, it is also sensitive and vulnerable to environmental changes due to high human populations and interactions between the land and ocean. Major threats of pollution from over enrichment of nutrients, increasing metals and persistent organic pollutants (POPs), and climate change have led to severe ecological degradation in the coastal zone, while few studies have focused on the combined impacts of pollution and climate change on the coastal ecosystems at the global level. A global overview of nutrients, metals, POPs, and major environmental changes due to climate change and their impacts on coastal ecosystems was carried out in this study. Coasts of the Eastern Atlantic and Western Pacific were hotspots of concentrations of several pollutants, and mostly affected by warming climate. These hotspots shared the same features of large populations, heavy industry and (semi-) closed sea. Estimation of coastal ocean capital, integrated management of land-ocean interaction in the coastal zone, enhancement of integrated global observation system, and coastal ecosystem-based management can play effective roles in promoting sustainable management of coastal marine ecosystems. Enhanced management from the perspective of mitigating pollution and climate change was proposed.
Editorial: Public health ethics-10 years on
Verweij, Marcel ; Dawson, Angus - \ 2018
Public Health Ethics 11 (2018)1. - ISSN 1754-9973 - p. 1 - 5.
Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
A comparative history of commercial transition in three West African slave trading economies, 1630 to 1860
Dalrymple-Smith, Angus - \ 2017
Wageningen University. Promotor(en): Ewout Frankema; Elise van Nederveen Meerkerk, co-promotor(en): M. van Rossum. - Wageningen : Wageningen University - ISBN 9789463436199 - 283
slavery - history - colonialism - trade - commodities - gold - law - social change - economic change - west africa - slavernij - geschiedenis - kolonialisme - handel - basisproducten - goud - recht - sociale verandering - economische verandering - west-afrika

The nineteenth century ‘commercial transition’ from export economies based on slaves to ones dominated by commodities like palm oil has been a central theme in West African history. However, most studies have tended to focus on the impact of the change and assumed that its causes were largely a result of the British decision to abolish their transatlantic slave trade in 1807 and subsequently persuading or forcing other nations to do the same. This thesis makes two principal contributions to this debate. Firstly, it reviews new evidence which shows that the commercial transition in West Africa’s most important slave exporting regions, the Gold Coast, the Bight of Biafra and the Bight of Benin, can be predicted by the patterns of trade established in previous centuries. It then presents a model of analysis which sets out which interrelated factors shaped their export economies and ultimately determined how they responded to the changing political and economic environment of the Atlantic world from the seventeenth to the nineteenth centuries. This study offers an important comparative, long term quantitative perspective on the transition from slave exports to so-called ‘legitimate commerce’.

Chapter 1 shows that the speed and timing of the nineteenth century commercial transition differed considerably across the case study regions. Along the Gold Coast there was a sudden, and effectively total end to transatlantic slave trading after 1807. In the Bight of Biafra slave exports gradually declined until largely ceasing in the 1830s. Lastly in the Bight of Benin export slavery continued until the 1850s. The chapter argues that earlier studies have tended to ignore long term trends and also lack a comparative approach, as many are focused on individual regions. It then suggests a new model of analysis and dismisses two factors as irrelevant; the British slave trade patrol and changing demands for, or changing supply of, African slaves. The chapter argues that regional variations can be explained by five key factors: 1) the nature and duration of long-term trade relations; 2) the identity of the principal European trade partner; 3) certain aspects of the ecology of the different regions; 4) the regional political contexts; and 5) the development of institutions that either encouraged or discouraged elite participation in non-slave exports.

Chapter 2 provides a broad overview of each case study region’s patterns of trade from the fifteenth to the eighteenth Centuries based on secondary and primary qualitative sources. It then reviews quantitative evidence of commodity trading patterns from the earlier eighteenth century from British and Dutch commodity traders and slaving vessels that bought commodities. It argues that the expansion of slavery in the Bight of Biafra did not crowd out other forms of commerce. On the Gold Coast the early eighteenth century saw continued engagement in commodity exports while the slave trade expanded. However, by the 1780s, both slave and commodity exports seem to have begun to decline. In the Dahomean-controlled area of the Bight of Benin, there is no evidence of slavery crowding out other forms of commerce, as captives were always the only item of trade with the Atlantic world.

Chapter 3 investigates the extent to which the 18th century intensification of the trans-Atlantic slave trade boosted commercial agriculture in the coastal areas of West Africa and in particular in the case study regions. It explores the provisioning strategies of 187 British, French, Dutch and Danish slave voyages conducted between 1681 and 1807, and calls for a major downward adjustment of available estimates of the slave trade induced demand impulse. It shows that during the 18th century, an increasing share of the foodstuffs required to feed African slaves were taken on board in Europe instead of West Africa. However, there was considerable variation in provisioning strategies among slave trading nations and across main regions of slave embarkation. The Bight of Benin never significantly engaged in provisioning trade. Traders along the Gold Coast provided relatively large quantities of food to slaving vessels, but in the Bight of Biafra, British demand stimulated a considerable trade in foodstuffs. The chapter explains these trends and variation in terms of the relative (seasonal) security of European versus African food supplies, the falling relative costs of European provisions and the increasing risks in the late 18th century trade, putting a premium on faster embarkation times.

Chapter 4 uses a newly constructed dataset on the quantities and prices of African commodities on the coast and in British markets over the long eighteenth century and provides new insights into the changing nature of Britain’s non-slave trade. It improves on previous work by Johnson et al. (1990) and finds that earlier estimates of the volume and value of commodity trade have been underestimates and fail to account for regional changes in output. The data suggests that from the 1770s the focus of Britain’s commodity trade shifted from Senegambia to the Bight of Biafra and that in the later eighteenth century non-slave goods were primarily purchased by slave ships, not specialist bi-lateral traders. The chapter argues that these changes were motivated by a number of factors; conflicts between Atlantic powers, the prices of British trade goods and African imports, increasing levels of risk faced by British slave merchants and the fact that traders in the Bight of Biafra were both willing and able to supply desirable commodities.

Part 1 establishes that the Gold Coast had a far long history of commodity trading and seemed to have been moving away from the slave trade at the end of the eighteenth century. The region of the Bight of Benin controlled by Dahomey always focused exclusively on slaves. The Bight of Biafra had a considerable non-slave export economy that was growing at the end of the eighteenth century. Part 2 of the thesis applies the model of analysis to the case study regions.

Chapter 5 argues that that for the Gold Coast and more particularly the Asante empire British abolition policies and the slave forts can explain the timing of the end of transatlantic slavery but not why it ended. Following the model of analysis, the chapter shows that the presence of gold determined both long term political development and the nature of the region’s trade relationship with the Atlantic. In addition, gold became essential as a means of marking status and wealth at all levels of society and for domestic exchange. This meant that slaves were always essential for the production of gold, meaning that there was an important competing domestic market for coerced labour. Over the eighteenth-century gold became scarcer leading to slaves being pulled out of the Atlantic market to focus on production. In addition, well-developed trade relations with the interior and a rise in demand from the Islamic states in the Sokoto caliphate led to an expansion of kola exports which demanded yet more labour. Most importantly, the chapter argues that both households and elite groups could profit more from commodity than slave exports which explains the rapid move away from the transatlantic slavery and towards the production of commodities.

In Chapter 6 it is argued that in the Bight of Biafra, the slave and commodity trades were not only compatible but complementary. The region’s riverine transport networks, long established coastal-interior trade relations and suitability for the growing of yams, palm oil and tropical hardwoods meant that the provisioning and commodity trades could function alongside slave exports. The relatively late opening of central Igboland to the Atlantic slave markets meant that the region did not see the influx of wealth in the seventeenth century that spurred the development of states in the other case study areas. Instead the region followed a different institutional path which saw the development small political entities linked together through the Aro trade network. Elites in the interior and at the coast were reliant on trade for both power and status, but not specifically the slave trade. As a result, abolition was not a serious economic shock as commodities and slaves had always been traded side by side. As in Gold Coast both commoners and elites benefited from commodity trading. Atlantic goods allowed many more people to purchase goods to improve their standards of living, while elites benefitted from the less volatile commodity trade. Furthermore, the British state also perhaps unintentionally supported the development of the palm oil trade through its customs policies. Eventually, this led to palm oil crowding out slave exports through greater demands for domestic labour.

Chapter 7 investigates why the region of the Bight of Benin controlled by Dahomey only ever exported slaves. It shows that this region possessed no gold and had less favourable geography for commodity exports than the Bight of Biafra. The early expansion of export slavery in the seventeenth century spurred the development of states and elites who were entirely dependent on slave exports to maintain their wealth and power. It led to the development of a militaristic culture and institutions based on large scale slave raiding that were highly effective as a means of controlling and harnessing elite violence, generating wealth and defending the state from powerful external threats and economic competition. The demands of the army and elites took much of the kingdom’s potential labour away from households. In addition, constant warfare led to a serious demographic decline across the region further reducing the amount of available labour. The chapter argues that it was never in the interests of elites to switch to an alternative economic system and there was, until the 1850s, always sufficient external demand. In the end abolition efforts were a necessary condition to ending the slave trade.

Chapter 8 concludes with a summary of the main contributions of thesis; the importance of long term patterns of trade in determining nineteenth century commercial transition and a modified model of analysis to explain the diverging trajectories of the different case study regions. It also argues that the impact of Britain’s abolition campaign should be reassessed. In the Gold Coast and the Bight of Biafra it was not an important factor in ending transatlantic slavery, while in the Bight of Benin it was. The chapter ends with suggestions for future research.

Accounting for carbon stocks in soils and measuring GHGs emission fluxes from soils : Do we have the necessary standards?
Bispo, Antonio ; Andersen, Lizzi ; Angers, Denis A. ; Bernoux, Martial ; Brossard, Michel ; Cécillon, Lauric ; Comans, Rob N.J. ; Harmsen, Joop ; Jonassen, Knut ; Lamé, Frank ; Lhuillery, Caroline ; Maly, Stanislav ; Martin, Edith ; Mcelnea, Angus E. ; Sakai, Hiro ; Watabe, Yoichi ; Eglin, Thomas K. - \ 2017
Frontiers in Environmental Science 5 (2017)JUL. - ISSN 2296-665X
Carbon sequestration - Methane - Nitrous oxide - Soil - Standards
Soil is a key compartment for climate regulation as a source of greenhouse gases (GHGs) emissions and as a sink of carbon. Thus, soil carbon sequestration strategies should be considered alongside reduction strategies for other greenhouse gas emissions. Taking this into account, several international and European policies on climate change are now acknowledging the importance of soils, which means that proper, comparable and reliable information is needed to report on carbon stocks and GHGs emissions from soil. It also implies a need for consensus on the adoption and verification of mitigation options that soil can provide. Where consensus is a key aspect, formal standards and guidelines come into play. This paper describes the existing ISO soil quality standards that can be used in this context, and calls for new ones to be developed through (international) collaboration. Available standards cover the relevant basic soil parameters including carbon and nitrogen content but do not yet consider the dynamics of those elements. Such methods have to be developed together with guidelines consistent with the scale to be investigated and the specific use of the collected data. We argue that this standardization strategy will improve the reliability of the reporting procedures and results of the different climate models that rely on soil quality data.
Slave ship provisioning in the long 18th century. A boost to West African commercial agriculture?
Dalrymple-Smith, Angus ; Frankema, Ewout - \ 2017
European Review of Economic History 21 (2017)2. - ISSN 1361-4916 - p. 185 - 235.

To what extent did the 18th century intensification of the transatlantic slave trade boost commercial agriculture in the coastal areas of West Africa? Exploring the provisioning strategies of 187 British, French, Dutch, and Danish slave voyages conducted between 1681 and 1807, we call for a major downward adjustment of available estimates of the slave trade- induced demand impulse. We show that during the 18th century, an increasing share of the foodstuffs required to feed African slaves were taken on board in Europe instead of West Africa. We also document considerable variation in provisioning strategies among slave trading nations and across main regions of slave embarkation. We explain these trends and variation in terms of the relative (seasonal) security of European versus African food supplies, the falling relative costs of European provisions and the increasing risks in the late 18th century trade, putting a premium on faster embarkation times.

European salt marshes : ecology and conservation in a changing world
Garbutt, Angus ; Groot, Alma de; Smit, Chris ; Pétillon, Julien - \ 2017
Journal of Coastal Conservation 21 (2017)3. - ISSN 1400-0350 - p. 405 - 408.
Biogeomorphology - Conference proceedings - Ecosystem functioning - Tidal marsh
Case 2: Exceptions to National MRSA Prevention Policy for a Medical Resident with Untreatable MRSA Colonization
Rump, B. ; Kessler, C. ; Fanoy, Ewout ; Wassenberg, Marjan ; Krom, André ; Verweij, M.F. ; Steenbergen, Jim van - \ 2016
In: Public Health Ethics / Barrett, Drue H., Ortmann, Leonard W., Dawson, Angus, Saenz, Carla, Reis, Andreas, Bolan, Gail, Springer (Public Health Ethics Analysis ) - ISBN 9783319238463 - p. 191 - 194.
A Dutch medical student has the potentially more virulent Panton-Valentine leukocidin (PVL) form of MRSA colonization yet shows no signs or symptoms of infection. More than a year ago, a routine MRSA screening of health care personnel providing care for MRSA-positive patients detected the colonization. Since then, the student has been treated intensively but unsuccessfully in an attempt to decolonize her. During this decolonization period, the medical student was barred from performing patient-related interventions, temporarily interrupting her medical residency. After initial treatment with mupirocin nasal ointment and antibiotics proved ineffective, a more stringent hygiene regime was added that included hand, nose, hair, and body scrubbing with disinfecting soap. Additional precautions included simultaneous treatment of household members and disinfection of the family home. Despite these efforts, her MRSA status has remained positive. WIP guideline s bar any health care worker diagnosed with MRSA from performing patient-related interventions. Unable to complete the residency requirement of at least 1 year of patient care, the medical student was advised to pursue a career in another profession.
Ottawa Statement from the Sparking Solutions Summit on Population Health Intervention Research : Déclaration d’Ottawa issue du sommet Provoquer des solutions sur la recherche interventionnelle en santé des populations
Ruggiero, Erica Di; Potvin, Louise ; Allegrante, John P. ; Dawson, Angus ; Verweij, Marcel ; Leeuw, Evelyn De; Dunn, James R. ; Franco, Eduardo ; Frohlich, Katherine L. ; Geneau, Robert ; Jackson, Suzanne ; Kaufman, Jay S. ; Morabia, Alfredo ; Mcleroy, Kenneth R. ; Ridde, Valéry - \ 2016
Canadian Journal of Public Health 107 (2016)6. - ISSN 1920-7476 - p. e492 - e496.
Slave Ship Provisioning in the Long 18th Century. A Boost to West African Commercial Agriculture?
Dalrymple-Smith, Angus - \ 2016
CEPR-CAGE-NYUAB Economic History Conference
Dalrymple-Smith, Angus - \ 2016
Slave Ship Provisioning in the Long 18th Century. A Boost to West African Commercial Agriculture?
Symposium on African Soils, Climate and Historical Agriculture
Dalrymple-Smith, Angus - \ 2016
Slave Ship Provisioning in the Long 18th Century. A Boost to West African Commercial Agriculture?
Slave Ship Provisioning in the Long 18th Century. A Boost to West African Commercial Agriculture?
Dalrymple-Smith, Angus - \ 2016
Genome wide association study (GWAS) of methane emissions in Australian Angus
Manzanilla Pech, C.I.V. ; Haas, Y. de; Veerkamp, R.F. ; Donoghue, K.A. ; Arthur, P.F. ; Pryce, J.E. - \ 2016
In: Book of Abstracts of the 67st Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (Book of abstracts 22) - ISBN 9789086862849 - p. 451 - 451.
Genomewide association study of methane emissions in angus beef cattle with validation in dairy cattle
Manzanilla-Pech, C.I.V. ; Haas, Y. de; Hayes, B.J. ; Veerkamp, R.F. ; Khansefid, M. ; Donoghue, K.A. ; Arthur, P.F. ; Pryce, J.E. - \ 2016
Journal of Animal Science 94 (2016)10. - ISSN 0021-8812 - p. 4151 - 4166.
Feed intake - Methane production - Residual methane

Methane (CH4) is a product of enteric fermentation in ruminants, and it represents around 17% of global CH4 emissions. There has been substantial effort from the livestock scientific community toward tools that can help reduce this percentage. One approach is to select for lower emitting animals. To achieve this, accurate genetic parameters and identification of the genomic basis of CH4 traits are required. Therefore, the objectives of this study were 1) to perform a genomewide association study to identify SNP associated with several CH4 traits in Angus beef cattle (1,020 animals) and validate them in a lactating Holstein population (population 1 [POP1]; 205 animals); 2) to validate significant SNP for DMI and weight at test (WT) from a second Holstein population, from a previous study (population 2 [POP2]; 903 animals), in an Angus population; and 3) to evaluate 2 different residual CH4 traits and determine if the genes associated with CH4 also control residual CH4 traits. Phenotypes calculated for the genotyped Angus population included CH4 production (MeP), CH4 yield (MeY), CH4 intensity (MI), DMI, and WT. The Holstein population (POP1) was multiparous, with phenotypes on CH4 traits (MeP, MeY, and MI) plus genotypes. Additionally, 2 CH4 traits, residual genetic CH4 (RGM) and residual phenotypic CH4 (RPM), were calculated by adjusting MeP for DMI and WT. Estimated heritabilities in the Angus population were 0.30, 0.19, and 0.15 for MeP, RGM, and RPM, respectively, and genetic correlations of MeP with DMI and WT were 0.83 and 0.80, respectively. Estimated heritabilities in Holstein POP1 were 0.23, 0.30, and 0.42 for MeP, MeY, and MI, respectively. Strong associations with MeP were found on chromosomes 4, 12, 14, 20, and 30 at P <0.001, and those chromosomes also had significant SNP for DMI in Holstein POP1. In the Angus population, the number of significant SNP for MeP at P <0.005 was 3,304, and approximately 630 of those SNP also were important for DMI and WT. When a set (approximately 3,300) of significant SNP for DMI and WT in the Angus population was used to estimate genetic parameters for MeP and MeY in Holstein POP1, the genetic variance and, consequently, the heritability slightly increased, meaning that most of the genetic variation is largely captured by these SNP. Residual traits could be a good option to include in the breeding goal, as this would facilitate selection for lower emitting animals without compromising DMI and WT.

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