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.

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Deterministic simulations to determine the impacts of economic and non-economic breeding objectives on sustainable intensification of developing smallholder dairy farms
Kariuki, C.M. ; Arendonk, J.A.M. van; Kahi, A.K. ; Komen, H. - \ 2019
Livestock Science 226 (2019). - ISSN 1871-1413 - p. 7 - 12.
Breeding objectives - Developing dairy cattle systems - Non-market weights - Sustainability

Dairy cattle farming in developing countries is mainly by resource poor smallholder farmers. Intensification of production within smallholder production systems is being driven by increasing demand for animal products. Current intensification is driven by importation of high-input high-output genotypes. This puts in question the sustainability of these resource constrained systems under harsh environmental conditions. Sustainability of production systems can be defined as long-term resilience and productivity. We use deterministic simulations to compare the impacts of three criteria to define breeding objectives i.e., economic, desired gains and non-market value, on annual genetic and monetary gains in production (market) and functional (non-market) traits for a small-sized nucleus genomic selection breeding program under developing country conditions. Market traits considered were milk yield (MY) and mature body weight (MBW). Non-market traits were calving interval (CI) and production lifetime (PLT). Fat yield (FY) was also considered a non-market trait as it had no market value. With the economic objective, traits were weighted on economic values. Weights for desired gains and non-market (NM) values were derived iteratively. Economic objectives placed highest emphasis on MY with very little gains in non-market traits but had the highest returns on investment. For desired gains objective, maximal achievable gains in PLT, CI and FY were lower than the indicated desired gains. The non-market value objective achieved the best compromise between gains in MY and other traits. We conclude that non-market value objectives can be applied to direct selection towards more robust genotypes but with loss in monetary gain. Breeding robust genotypes can contribute to sustainable intensification in developing small-holder dairy systems. However, for such objectives to be satisfactory, a sound criterion is required to determine declines in genetic gains for market traits that are acceptable by producers.

Production system and participatory identification of breeding objective traits for indigenous goat breeds of Uganda
Onzima, R.B. ; Gizaw, S. ; Kugonza, D.R. ; Arendonk, J.A.M. van; Kanis, E. - \ 2018
Small Ruminant Research 163 (2018). - ISSN 0921-4488 - p. 51 - 59.
Breed preference - Breeding objectives - Breeding programs - Indigenous goats - Production/adaptation traits - Smallholder farmers

The success of breeding programs in improving indigenous livestock breeds in Uganda has hitherto been limited due to lack of involvement of the key stakeholders. Thus, participatory approaches are being promoted for designing community based improvement programs. The aim of this study was to characterize the indigenous goat production systems and assess in a participatory manner farmer preferred traits for establishing breeding objectives for indigenous goat breeds in Uganda. 217 farm households representing three goat production systems (combinations of breed and region) were individually interviewed to assess the socio-economic characteristics of the regions and the preferences of the farmers for indigenous goat breeds. The three breed/region combinations were 78 households with the Small East African breed in Arua, 81 with the Mubende breed in Mubende and 58 with the Kigezi breed in Kabale. An index based approach was used to rank farmers' choices of traits considered important for their production systems. Descriptive statistics show that overall the production systems were not significantly different in terms of the nature of the farms and the trait preferences of the farmers. The sale of live animals was considered a primary objective for keeping goats by farmers across all the production systems studied. Adaptation traits (disease resistance, heat tolerance and survival) were considered critical in the farmers' preferred breed. Production traits (better prolificacy and faster growth rate) and marketing ease were other characteristics considered by the farmers. The results from the study are useful for designing farmer-participatory breeding programs for goats in the different production systems in Uganda.

Fine-mapping of BTA17 using imputed sequences for associations with de novo synthesized fatty acids in bovine milk
Duchemin, S.I. ; Bovenhuis, H. ; Megens, H.J. ; Arendonk, J.A.M. Van; Visker, M.H.P.W. - \ 2017
Journal of Dairy Science 100 (2017)11. - ISSN 0022-0302 - p. 9125 - 9135.
Genome-wide association studies - Imputation - Milk fat composition - Quantitative trait loci
The aim of this study was to fine-map a genomic region associated with milk fatty acids (FA) on Bos taurus autosome (BTA) 17. This genomic region has been discovered with 50,000 (50k) single nucleotide polymorphisms (SNP) imputed to 777,000 (777k) SNP. In this study, high-density genotypes were imputed to whole-genome sequences level to identify candidate gene(s) associated with milk FA composition on BTA17. Phenotypes and genotypes were available for 1,640 cows sampled in winter, and for 1,581 cows sampled in summer. Phenotypes consisted of gas chromatography measurements in winter and in summer milk samples of 6 individual FA and the indicator of de novo synthesis, C6:0-C14:0. Genotypes consisted of imputed 777k SNP, and 89 sequenced ancestors of the population of genotyped cows. In addition, 450 whole-genome sequences from the 1,000 Bull Genome Consortium were available. Using 495 Holstein-Friesian sequences as a reference population, the 777k SNP genotypes of the cows were imputed to sequence level. We then applied single-variant analyses with an animal model, and identified thousands of significant associations with C6:0, C8:0, C10:0, C12:0, C14:0, and C6:0-C14:0. For C8:0 in summer milk samples, the genomic region located between 29 and 34 Mbp on BTA17 revealed a total of 646 significant associations. The most significant associations [-log10(P-value) = 7.82] were 8 SNP in perfect linkage disequilibrium. After fitting one of these 8 SNP as a fixed effect in the model, and re-running the single-variant analyses, no further significant associations were found for any of the 6 FA or C6:0-C14:0. These findings suggest that one polymorphism underlying this QTL on BTA17 influences multiple de novo synthesized milk FA. Thirteen genes in the QTL region were identified and analyzed carefully. Six out of the 8 SNP that showed the strongest associations were located in the La ribonucleoprotein domain family, member 1B (LARP1B) gene, and we suggest LARP1B as a primary candidate gene. Another gene of interest for this QTL region might be PKL4. None of these suggested candidate genes have previously been associated with milk fat synthesis or milk FA composition.
Genomic selection for crossbred performance accounting for breed-specific effects
Soares Lopes, Marcos ; Bovenhuis, Henk ; Marubayashi Hidalgo, Andre ; Arendonk, Johan A.M. Van; Knol, Egbert F. ; Bastiaansen, John W.M. - \ 2017
Genetics, Selection, Evolution 49 (2017)1. - ISSN 0999-193X

Background: Breed-specific effects are observed when the same allele of a given genetic marker has a different effect depending on its breed origin, which results in different allele substitution effects across breeds. In such a case, single-breed breeding values may not be the most accurate predictors of crossbred performance. Our aim was to estimate the contribution of alleles from each parental breed to the genetic variance of traits that are measured in crossbred offspring, and to compare the prediction accuracies of estimated direct genomic values (DGV) from a traditional genomic selection model (GS) that are trained on purebred or crossbred data, with accuracies of DGV from a model that accounts for breed-specific effects (BS), trained on purebred or crossbred data. The final dataset was composed of 924 Large White, 924 Landrace and 924 two-way cross (F1) genotyped and phenotyped animals. The traits evaluated were litter size (LS) and gestation length (GL) in pigs. Results: The genetic correlation between purebred and crossbred performance was higher than 0.88 for both LS and GL. For both traits, the additive genetic variance was larger for alleles inherited from the Large White breed compared to alleles inherited from the Landrace breed (0.74 and 0.56 for LS, and 0.42 and 0.40 for GL, respectively). The highest prediction accuracies of crossbred performance were obtained when training was done on crossbred data. For LS, prediction accuracies were the same for GS and BS DGV (0.23), while for GL, prediction accuracy for BS DGV was similar to the accuracy of GS DGV (0.53 and 0.52, respectively). Conclusions: In this study, training on crossbred data resulted in higher prediction accuracy than training on purebred data and evidence of breed-specific effects for LS and GL was demonstrated. However, when training was done on crossbred data, both GS and BS models resulted in similar prediction accuracies. In future studies, traits with a lower genetic correlation between purebred and crossbred performance should be included to further assess the value of the BS model in genomic predictions.

Multiple criteria decision-making process to derive consensus desired genetic gains for a dairy cattle breeding objective for diverse production systems
Kariuki, C.M. ; Arendonk, J.A.M. van; Kahi, A.K. ; Komen, H. - \ 2017
Journal of Dairy Science 100 (2017)6. - ISSN 0022-0302 - p. 4671 - 4682.
Consensus desired gains - Developing dairy cattle industries - Multi-criteria decision making process - Trait preferences aggregation

Dairy cattle industries contribute to food and nutrition security and are a source of income for numerous households in many developing countries. Selective breeding can enhance efficiency in these industries. Developing dairy industries are characterized by diverse production and marketing systems. In this paper, we use weighted goal aggregating procedure to derive consensus trait preferences for different producer categories and processors. We based the study on the dairy industry in Kenya. The analytic hierarchy process was used to derive individual preferences for milk yield (MY), calving interval (CIN), production lifetime (PLT), mature body weight (MBW), and fat yield (FY). Results show that classical classification of production systems into large-scale and smallholder systems does not capture all differences in trait preferences. These differences became apparent when classification was based on productivity at the individual animal level, with high and low intensity producers and processors as the most important groups. High intensity producers had highest preferences for PLT and MY, whereas low intensity producers had highest preference for CIN and PLT; processors preferred MY and FY the most. The highest disagreements between the groups were observed for FY, PLT, and MY. Individual and group preferences were aggregated into consensus preferences using weighted goal programming. Desired gains were obtained as a product of consensus preferences and percentage genetic gains (G%). These were 2.42, 0.22, 2.51, 0.15, and 0.87 for MY, CIN, PLT, MBW, and FY, respectively. Consensus preferences can be used to derive a single compromise breeding objective for situations where the same genetic resources are used in diverse production and marketing circumstances.

Breeding strategies for sustainable intensification of developing smallholder dairy cattle production systems
Kariuki, Charles Mbogo - \ 2017
Wageningen University. Promotor(en): J. Komen, co-promotor(en): J.A.M. Arendonk; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789463430951 - 134
dairy cattle - small businesses - sustainable animal husbandry - intensification - breeding programmes - progeny testing - genetic improvement - dairy performance - developing countries - melkvee - kleine bedrijven - duurzame veehouderij - intensivering - veredelingsprogramma's - nakomelingenonderzoek - genetische verbetering - melkresultaten - ontwikkelingslanden

Smallholder dairy cattle production systems in Africa are intensifying production through importation of germplasm from breeding programs conducted in temperate regions to improve commercial cow populations. Presence of genotype by environment interaction results in unfavorable correlated responses. The aim this thesis was to develop strategies for breeding programs in developing countries that can support sustainable intensification of these systems. Specific objectives were (a) to determine desired gains for breeding objective traits, (b) compare progeny testing (PT) and genomic selection (GS) selection strategies, (c) evaluate the economic performance of PT and GS selection strategies and (d) compare genetic gains for economic and non-economic breeding objectives; the Kenya dairy cattle sector was used as a working example. To account for the limited pedigree and performance recording, a five-trait breeding objective and small-sized breeding program were studied. Breeding objective traits, determined based on producer preferences, were milk yield (MY), production lifetime (PLT), calving interval (CI), fat yield (FY) and mature body weight (MBW). Producers were categorized into high intensive group, who placed highest preference on PLT and MY, and low intensity group that placed highest preferences on CI and PLT. MY and FY were the most important traits for processors. Consensus desired gains, based on weighted goal programming, were 2.51, 2.42, 0.22, 0.87 and 0.15% for PLT, MY, CI, FY and MBW, respectively. Comparison of breeding schemes shows that GS schemes had lower accuracies but gave higher responses per year due to shorter generation intervals. Besides genetic gains, economic performance underpins the adoption of selection strategies. GS schemes had between 3.2 and 5.2-fold higher cumulated genetic gain in the commercial cow population and higher gross margins compared to PT schemes. Semen storage made PT schemes more profitable but less so than GS schemes. Functional traits can increase the sustainability of resource poor smallholder systems under harsh environments. Economic breeding objectives yielded undesirable responses in functional traits. Breeding objectives based on desired gains or non-market objectives improved response in functional traits but at a monetary cost. It is concluded that sustainable productivity of smallholder systems can be improved by implementation of local breeding program based on GS, but this requires more emphasis on functional traits, which can be achieved by use of non-economic objectives.

Optimization of breeding schemes for Nile tilapia (Oreochromis niloticus) in smallholder production systems in Kenya
Omasaki, Simion Kipkemboi - \ 2017
Wageningen University. Promotor(en): J. Komen, co-promotor(en): J.A.M. Arendonk; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789463431064 - 167
oreochromis niloticus - tilapia - breeding programmes - selective breeding - genetic improvement - small farms - sustainability - fish culture - aquaculture - kenya - oreochromis niloticus - tilapia - veredelingsprogramma's - selectief fokken - genetische verbetering - kleine landbouwbedrijven - duurzaamheid (sustainability) - visteelt - aquacultuur - kenya

The aim of this thesis was to develop a sustainable low cost breeding program for Nile tilapia that addresses both genetic and economic aspects of smallholder fish farmers in Kenya. First, Analytical Hierarchy Process Technique was used to define a breeding goal based on farmer’s preferences for traits. Farmers’ preferences for traits differed significantly depending on income and market orientation. Low and medium income farmers preferred harvest weight (HW) while high income farmers preferred growth (GR) and survival (S) traits. Grouping farmers according to market objective (fingerling production or fattening) showed that fingerling producers preferred GR and S while fattening farmers preferred HW and S. Consensus preference values were obtained using weighted goal programming and these values were used to derive desired gains for a breeding goal that takes into account farmers’ diverse backgrounds and preferences for traits. Secondly, the existence of genetic variation for traits of interest was investigated. Substantial additive genetic effects for HW, GR and shape traits were present that can be exploited through selection under low input production system. Heritability estimates for HW, GR and shape were 0.21 ± 0.03, 0.26 ± 0.04 and 0.12 ± 0.03 for mixed sex (nucleus) respectively. The calculation of economic values for breeding goal traits revealed that economic values for GR differed depending on the definition of the breeding goal and that selection for feed efficiency is the key factor to economic profitability of Nile tilapia breeding programs. A significant genotype by environment re-ranking was found for GR between the mixed sex nucleus and monosex production environments. Genotype by environment interaction (G x E) led to lower genetic gain for GR in production environment. Incorporating sib information from monosex production environment into the selection index resulted in a more accurate estimation of breeding values which increased genetic gain in growth. Using desired gain approach, weights for desired gains in harvest weight, growth rate and survival were derived that maximized genetic gains for these breeding goal traits. It is concluded that these results can be used to develop a sustainable centralized breeding program. However, a reliable well planned and organized decentralized strategy for dissemination of genetically improved fry of Nile tilapia to farmers is paramount.

Effect of production quotas on economic and environmental values of growth rate and feed efficiency in sea cage fish farming
Besson, M. ; Boer, I.J.M. de; Vandeputte, M. ; Arendonk, J.A.M. van; Quillet, E. ; Komen, H. ; Aubin, J. - \ 2017
PLoS ONE 12 (2017)3. - ISSN 1932-6203

In sea cage fish farming, production quotas aim to constrain the impact of fish farming on the surrounding ecosystem. It is unknown how these quotas affect economic profitability and environmental impact of genetic improvement. We combined bioeconomic modelling with life cycle assessment (LCA) to calculate the economic (EV) and environmental (ENV) values of thermal growth coefficient (TGC) and feed conversion ratio (FCR) of sea bass reared in sea cages, given four types of quota commonly used in Europe: annual production (Qprod), annual feed distributed (Qannual-feed), standing stock (Qstock), and daily feed distributed (Qdaily-feed). ENV were calculated for LCA impact categories climate change, eutrophication and acidification. ENV were expressed per ton of fish produced per year (ENV(fish)) and per farm per year (ENV(farm)). Results show that irrespective of quota used, EV of FCR as well as ENV(fish) and ENV(farm) were always positive, meaning that improving FCR increased profit and decreased environmental impacts. However, the EV and the ENV(fish) of TGC were positive only when quota was Qstock or Qdaily-feed. Moreover, the ENV(farm) of TGC was negative in Qstock and Qdaily-feed quotas, meaning that improving TGC increased the environmental impact of the farm. We conclude that Qstock quota and Qdaily-feed quota are economically favorable to a genetic improvement of TGC, a major trait for farmers. However, improving TGC increases the environmental impact of the farm. Improving FCR represents a good opportunity to balance out this increase but more information on its genetic background is needed to develop breeding programs improving FCR.

Selection for pure- and crossbred performance in Charolais
Vallée-Dassonneville, Amélie - \ 2017
Wageningen University. Promotor(en): Johan van Arendonk; Henk Bovenhuis. - Wageningen : Wageningen University - ISBN 9789463430180 - 151
charolais - cattle - animal breeding - crossbreeding - crossbreds - selection - beef cattle - genomes - genetic parameters - charolais - rundvee - dierveredeling - kruisingsfokkerij - kruising - selectie - vleesvee - genomen - genetische parameters

Two categories of beef production exist; i.e. (i) purebred animals from a beef sire and a beef dam and (ii) crossbred animals from a beef sire and a dairy dam.

For the purebred beef production, there is a growing interest to include behavior and type traits in the breeding goal. Heritabilities for behavior traits, estimated using subjective data scored by farmers, range from 0.02 to 0.19. Heritabilities for type traits range from 0.02 to 0.35. Results show that there are good opportunities to implement selection for behavior traits using a simple on-farm recording system to allow collection of large data set, and for type traits in Charolais. A genome-wide association study detected 16 genomic regions with small effect on behavior and type traits. This suggests that behavior and type traits are influenced by many genes each explaining a small part of the genetic variance.

The two main dairy breeds mated to Charolais sires for crossbred beef production in France are Montbéliard and Holstein. The genetic correlation between the same trait measured on Montbéliard x Charolais and on Holstein x Charolais was 0.99 for muscular development, 0.96 for birth weight; and 0.91 for calving difficulty, 0.80 for height, and 0.70 for bone thinness. Thus, for these last three traits, results show evidence for re-ranking of Charolais sires depending on whether they are mated to Montbéliard or Holstein cows. When using genomic prediction, the Montbéliard x Charolais and Holstein x Charolais populations could be combined into a single reference population to increase size and accuracy of genomic prediction. Results indicate that the higher the genetic correlation is between the two crossbred populations, the higher the gain in accuracy is achieved when combining the two populations into a single reference.

The selection of Charolais sires to produce purebred or crossbred animals is made through distinct breeding programs. An alternative could be to combine selection into one breeding program. Decision for combining or keeping breeding programs separate is determined by the correlation between the breeding objectives, the selection intensity, the difference in level of genetic merit, the accuracy of selection, and the recent implementation of genomic evaluation. Considering all parameters and based on estimations for selection on birth weight, I recommend combining both breeding programs because this will lead to higher genetic gain, and might simplify operating organization and reduce associated costs.

Economic evaluation of progeny-testing and genomic selection schemes for small-sized nucleus dairy cattle breeding programs in developing countries
Kariuki, Charles ; Brascamp, Pim ; Komen, H. ; Kahi, A.K. ; Arendonk, Johan van - \ 2017
Journal of Dairy Science 100 (2017)3. - ISSN 0022-0302 - p. 2258 - 2268.
In developing countries minimal and erratic performance and pedigree recording impede implementation of large-sized breeding programs. Small-sized nucleus programs offer an alternative but rely on their economic performance for their viability. We investigated the economic performance of 2 alternative small-sized dairy nucleus programs [i.e., progeny testing (PT) and genomic selection (GS)] over a 20-yr investment period. The nucleus was made up of 453 male and 360 female animals distributed in 8 non-overlapping age classes. Each year 10 active sires and 100 elite dams were selected. Populations of commercial recorded cows (CRC) of sizes 12,592 and 25,184 were used to produce test daughters in PT or to create a reference population in GS, respectively. Economic performance was defined as gross margins, calculated as discounted revenues minus discounted costs following a single generation of selection. Revenues were calculated as cumulative discounted expressions (CDE, kg) × 0.32 (€/kg of milk) × 100,000 (size commercial population). Genetic superiorities, deterministically simulated using pseudo-BLUP index and CDE, were determined using gene flow. Costs were for one generation of selection. Results show that GS schemes had higher cumulated genetic gain in the commercial cow population and higher gross margins compared with PT schemes. Gross margins were between 3.2- and 5.2-fold higher for GS, depending on size of the CRC population. The increase in gross margin was mostly due to a decreased generation interval and lower running costs in GS schemes. In PT schemes many bulls are culled before selection. We therefore also compared 2 schemes in which semen was stored instead of keeping live bulls. As expected, semen storage resulted in an increase in gross margins in PT schemes, but gross margins remained lower than those of GS schemes. We conclude that implementation of small-sized GS breeding schemes can be economically viable for developing countries.
Genetic correlations between dressage, show jumping and studbook-entry inspection traits in a process of specialization in Dutch Warmblood horses
Rovere, G. ; Ducro, B.J. ; Arendonk, J.A.M. van; Norberg, E. ; Madsen, P. - \ 2017
Journal of Animal Breeding and Genetics 134 (2017)2. - ISSN 0931-2668 - p. 162 - 171.
Genetic parameter - Specialization - Sport horse
Sport performance in dressage and show jumping are two important traits in the breeding goals of many studbooks. To determine the optimum selection scheme for jumping and dressage, knowledge is needed on the genetic correlation between both disciplines and between traits measured early in life and performance in competition in each discipline. This study aimed to estimate genetic parameters to support decision-making on specialization of breeding horses for dressage and show jumping in Dutch warmblood horses. Genetic correlations between performance of horses in dressage and show jumping were estimated as well as the genetic correlation between traits recorded during studbook-entry inspections and performance in dressage and show jumping competitions. The information on competition comprised the performance of 82 694 horses in dressage and 62 072 horses in show jumping, recorded in the period 1993-2012. For 26 056 horses, information was available for both disciplines. The information on traits recorded at studbook-entry inspections comprised 62 628 horses, recorded in the period 1992-2013. Genetic parameters were estimated from the whole dataset and from a subset without horses recorded in both disciplines. Additionally, the genetic parameters were estimated in three different time periods defined by horses' birth year. The genetic correlation between dressage and show jumping in the whole dataset was -0.23, and it was -0.03 when it was estimated from horses recorded in only one discipline. The genetic correlation between dressage and show jumping was more negative in the most recent time period in all the cases. The more negative correlation between disciplines in more recent time periods was not reflected in changes in the correlations between competitions traits and the traits recorded in the studbook-first inspection. These results suggest that a breeding programme under specialization might be most effective defining two separate aggregate breeding goals for each of the disciplines.
Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle
Upadhyay, M.R. ; Chen, W. ; Lenstra, J.A. ; Goderie, C.R.J. ; MacHugh, D.E. ; Park, S.D.E. ; Magee, D.A. ; Matassino, D. ; Ciani, F. ; Megens, H.J. ; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 2017
Heredity 118 (2017). - ISSN 0018-067X - p. 169 - 176.

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.

Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle
Upadhyay, M.R. ; Chen, W. ; Lenstra, J.A. ; Goderie, C.R.J. ; Machugh, D.E. ; Park, S.D.E. ; Magee, D.A. ; Matassino, D. ; Ciani, F. ; Megens, H.J.W.C. ; Arendonk, J.A.M. van; Groenen, M. - \ 2016
aurochs - primitive cattle - SNP - gene flow - runs of homozygosity
This file contains the information for 777,962 markers genotyped in 143 samples using the Illumina BovineHD BeadChip. The vcf file contains the aurochs genotypes, which corresponds to SNP positions in Illumina BovineHD Beadchip.
Between breed variation in resistance to H. contortus in three indigenous goat breeds in Uganda
Onzima, Robert ; Mukiibi, Robert ; Katali, B.K. ; Arendonk, J.A.M. van; Kanis, E. ; Komen, J. - \ 2016
In: Book of Abstracts of the 67th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of abstracts 22) - ISBN 9789086862849 - p. 427 - 427.
Defining a breeding objective for Nile tilapia for Kenyan smallholder production system
Omasaki, Simion ; Arendonk, J.A.M. van; Kahi, Alexander ; Komen, J. - \ 2016
In: Book of Abstracts of the 67th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of abstracts 22) - ISBN 9789086862849 - p. 429 - 429.
Defining consensus desired gains for a Kenyan Holstein-Friesian breeding goal
Kariuki, Charles ; Arendonk, J.A.M. van; Kahi, Alexander ; Komen, J. - \ 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. 310 - 310.
Defining a breeding objective for Nile tilapia that takes into account the diversity of smallholder production systems
Omasaki, S.K. ; Arendonk, J.A.M. van; Kahi, A.K. ; Komen, H. - \ 2016
Journal of Animal Breeding and Genetics 133 (2016)5. - ISSN 0931-2668 - p. 404 - 413.
Breeding goal - desired genetic gain - Nile tilapia - participatory approach - smallholder production

In general, livestock and fish farming systems in developing countries tend to be highly diverse in terms of agro-ecological conditions and market orientation. There are no studies that have investigated if and how this diversity translates to varying preferences for breeding objective traits. This is particularly important for breeding programmes that are organized on a national level (e.g. government-supported nucleus breeding programmes). The aim of this study was to investigate whether Nile tilapia farmers with diverse production systems and economic constraints have different preferences for breeding objective traits. The second objective was to derive a consensus breeding goal, using weighted goal programming that could be used for a national breeding programme for Nile tilapia. A survey was conducted among 100 smallholder Nile tilapia farmers in Kenya to obtain preference values for traits of economic importance, by using multiple pairwise comparisons. Individual and group preference values were estimated using analytical hierarchy process. Low-income farmers preferred harvest weight, while medium- and high-income farmers preferred growth rate and survival. Grouping farmers according to market objective (fingerling production or fattening) showed that fingerling producers preferred growth rate and survival, while fattening farmers preferred harvest weight, height and thickness. Weighted goal programming was used to obtain consensus preference values, and these were used to derive desired gains for a breeding goal of a national breeding programme that takes into account the diversity of smallholder production systems.

Village poultry production system : Perception of farmers and simulation of impacts of interventions
Wondmeneh, E. ; Waaij, E.H. van der; Udo, H.M.J. ; Tadelle, D. ; Arendonk, J.A.M. van - \ 2016
African Journal of Agricultural Research 11 (2016)24. - ISSN 1991-637X - p. 2075 - 2081.
This study identified perception of poultry farmers’ on impact of interventions in village poultry production and quantified the impacts of interventions on flock and economic performance using modelling. A structured questionnaire was used to collect data on perceptions of poultry keeping and performances from 240 randomly selected households in two districts of Ethiopia. Crop was the major source of income, and poultry generated supplementary income. Farmers perceived that demand and price of poultry products increased. Majority of the farmers believed that additional inputs would not lead to higher income. A dynamic simulation showed that the base situation made a positive financial
contribution. Vaccinations had the largest positive impact on flock performances and using improved indigenous chicken had the smallest. Application of interventions had the largest effect on flock performances in the base situation but did not lead to profitability. The sensitivity analysis showed that feed cost had the largest impact on the profitability followed by housing, vaccination and breed. Farmers’ perceptions affected their decisions regarding implementation of interventions. Simulated interventions increased productivity but only in a few cases the increased incomes outweighed the additional costs. Interventions need to be tailored towards the local situation to ensure improved productivity and improved income
Genome-wide association study for behavior, type traits, and muscular development in Charolais beef cattle
Vallée, A. ; Daures, J. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2016
Journal of Animal Science 94 (2016)6. - ISSN 0021-8812 - p. 2307 - 2316.
Association study - Beef cattle - Behavior traits - Charolais - Muscular development - Type traits

Behavior, type traits, and muscular development are of interest for beef cattle breeding. Genome-wide association studies (GWAS) enable the identification of candidate genes, which enables genebased selection and provides insight in the genetic architecture of these traits. The objective of the current study was to perform a GWAS for 3 behavior traits, 12 type traits, and muscular development in Charolais cattle. Behavior traits, including aggressiveness at parturition, aggressiveness during gestation period, and maternal care, were scored by farmers. Type traits, including udder conformation, teat, feet and legs, and locomotion, were scored by trained classifiers. Data used in the GWAS consisted of 3,274 cows with phenotypic records and genotyping information for 44,930 SNP. When SNP had a false discovery rate (FDR) smaller than 0.05, they were referred to as significant. When SNP had a FDR between 0.05 and 0.20, they were referred to as suggestive. Four significant and 12 suggestive regions were detected for aggressiveness during gestation, maternal care, udder balance, teat thinness, teat length, foot angle, foot depth, and locomotion. These 4 significant and 12 suggestive regions were not supported by other significant SNP in close proximity. No SNP with major effects were detected for behavior and type traits, and SNP associations for these traits were spread across the genome, suggesting that behavior and type traits were influenced by many genes, each explaining a small part of genetic variance. The GWAS identified 1 region on chromosome 2 significantly associated with muscular development, which included the myostatin gene (GDF8), which is known to affect muscularity. No other regions associated with muscular development were found. Results showed that the myostatin region associated with muscular development had pleiotropic effects on udder volume, teat thinness, rear leg, and leg angle.

Analysis of competition performance in dressage and show jumping of Dutch Warmblood horses
Rovere, G. ; Ducro, B.J. ; Arendonk, J.A.M. van; Norberg, E. ; Madsen, P. - \ 2016
Journal of Animal Breeding and Genetics 133 (2016)6. - ISSN 0931-2668 - p. 503 - 512.
Censoring - Genetic evaluation - Preselection - Rider effect - Sport horse

Most Warmblood horse studbooks aim to improve the performance in dressage and show jumping. The Dutch Royal Warmblood Studbook (KWPN) includes the highest score achieved in competition by a horse to evaluate its genetic ability of performance. However, the records collected during competition are associated with some aspects that might affect the quality of the genetic evaluation based on these records. These aspects include the influence of rider, censoring and preselection of the data. The aim of this study was to quantify the impact of rider effect, censoring and preselection on the genetic analysis of competition data of dressage and show jumping of KWPN. Different models including rider effect were evaluated. To assess the impact of censoring, genetic parameters were estimated in data sets that differed in the degree of censoring. The effect of preselection on variance components was analysed by defining a binary trait (sport-status) depending on whether the horse has a competition record or not. This trait was included in a bivariate model with the competition trait and used all horses registered by KWPN since 1984. Results showed that performance in competition for dressage and show jumping is a heritable trait (h2 ~ 0.11-0.13) and that it is important to account for the effect of rider in the genetic analysis. Censoring had a small effect on the genetic parameter for highest performance achieved by the horse. A moderate heritability obtained for sport-status indicates that preselection has a genetic basis, but the effect on genetic parameters was relatively small.

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