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.

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.

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.
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.

Genotype by environment interaction for harvest weight, growth rate and shape between monosex and mixed sex Nile tilapia (Oreochromis niloticus)
Omasaki, S.K. ; Charo-Karisa, H. ; Kahi, A.K. ; Komen, H. - \ 2016
Aquaculture 458 (2016). - ISSN 0044-8486 - p. 75 - 81.
Genotype by environment interaction - Growth rate - Harvest weight - Kenya - Monosex - Nile Tilapia

In Kenya, Nile tilapia (Oreochromis niloticus) is mostly grown in ponds. To avoid excessive reproduction and stunted growth, fingerlings are treated with methyl-testosterone to make all-male populations (monosex). For a national breeding programme that aims to provide genetically improved broodstock to hatcheries that supply monosex fry to smallholder pond farmers, it is important to assess the genetic correlation (rg) for traits between the mixed sex breeding candidates from the breeding nucleus and monosex production fish. The purpose of the study was to estimate genetic parameters for harvest weight (HW), daily growth coefficient (DGC) and body shape and investigate genotype by environment interaction (G × E) for these traits between mixed sex and monosex populations. Forty-eight sires and 76 dams from the F2 generation of a local O. niloticus strain, kept at Sagana Aquaculture Research Station, Kenya were used to produce 76 full-sib families. Mixed sex fry (3 days old) from each full sib family were divided into two groups of 50 individuals each. One group (monosex) was fed a diet treated with methyl-testosterone to induce sex reversal while the other group (mixed sex) was reared on a control diet. After hapa rearing, tagging and weighing, fish were randomly divided and stocked in six earthen ponds, three for mixed sex and three for monosex fish. After 5 months, fish were harvested, photographed and weighed. Genetic parameter estimates for HW, DGC, and shape were obtained on 2105 fish. Heritability estimates for HW, DGC and shape were 0.21 ± 0.03, 0.26 ± 0.04 and 0.12 ± 0.03 for mixed sex respectively. Genetic correlations for HW between monosex and mixed sex was 0.74 ± 0.14, suggesting low G × E. The corresponding rg for DGC and shape were lower; 0.59 ± 0.10, and -0.19 ± 0.11, respectively, denoting the presence of G × E. It is concluded that G × E between the mixed sex nucleus and monosex production fish is important, and that a breeding programme for Nile tilapia needs to include production performance from monosex siblings. Statement of relevance: First study that reports estimates for Genotype by treatment interaction between hormone treated monosex Nile tilapia and mixed sex Nile tilapia, and discusses the consequences for nucleus breeding programmes.

Genetic Variation and Signatures of Selection in the Genomes of Kenyan Indigenous Chicken and Commercial Layers
Ngeno, K. ; Herrero-Medrano, J. ; Waaij, E.H. van der; Kahi, A.K. ; Megens, H.J.W.C. ; Arendonk, J.A.M. van; Crooijmans, R.P.M.A. - \ 2015
In: Improving Indigenous Chicken Productivity for Health and Wealth. - - p. 40 - 40.
Breeding of indigenous chicken in developing countries is mainly done by the resource-poor rural households that raise birds in a scavenging system characterized by low inputs, adverse climatic conditions and high disease pressure. As a result, indigenous chicken may have developed specific genetic adaptations for such challenging environments. In this study, genomic variation of indigenous chicken kept under low input production systems was assessed using autosomal microsatellite markers and whole genome re-sequence data. Indigenous chickens were further compared to high input commercial layers to identify selection signatures and candidate mutations that may explain the phenotypic divergence between these populations. Commercial layers had much lower nucleotide diversity (0.31 - 0.36) than indigenous chicken (0.58 - 0.62). We also identified up to 59 genomic regions with high Fst values (0.44 - 0.85) between indigenous and commercial chickens, overlapping 16 genes. Five genes (SLC26A8, BRPF3, MAPK13, PDIA4 and MRPL32) out of the 16 are associated with the missense variants that could explain partially the phenotypic divergence between these populations. Differently to commercial chickens, indigenous chickens preserved a high genomic variability that may be important, for addressing present and future challenges associated with adaptability to the environment and to cope with farmers breeding goals.
Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers
Ngeno, K. ; Waaij, E.H. van der; Megens, H.J.W.C. ; Kahi, A.K. ; Arendonk, J.A.M. van; Crooijmans, R.P.M.A. - \ 2015
In: Improving Indigenous Chicken Productivity for Health and Wealth. - - p. 33 - 33.
The study investigated the genetic make-up of different ecotypes of indigenous chickens (ICs) in Kenya based on major histocompatibility complex (MHC)-linked and non-MHC microsatellite markers. Blood samples were collected from eight regions (48 birds per region) of Kenya: Kakamega (KK), Siaya (BN), West Pokot (WP), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) and Taita-Taveta (TT) and genotyped using two MHC-linked and ten non-MHC markers. All MHC-linked and non-MHC markers were polymorphic with a total of 140 alleles, of which 56 were identified in MHC-linked markers. Mean number of alleles (Na and Ne), private alleles, heterozygosity and genetic distances were higher for MHC-linked markers compared with non-MHC markers. The ad hoc statistic ¿K detected the true numbers of clusters to be three for MHC-linked markers and two in non-MHC markers. In conclusion, Kenyan ICs belong into two to three genetically distinct groups. Different markers systems have different clustering system. MHC-linked markers divided ICs into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. These IC ecotypes host many and highly diverse MHC-linked alleles. Higher allelic diversity indicated a huge amount of genetic variation in the MHC region of ICs and supported their reputation of being hardy and resistant to diseases.
Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers
Ngeno, K. ; Waaij, E.H. van der; Megens, H.J.W.C. ; Kahi, A.K. ; Arendonk, J.A.M. van; Crooijmans, R.P.M.A. - \ 2015
Animal Genetic Resources 56 (2015). - ISSN 2078-6336 - p. 1 - 7.
The study investigated the genetic make-up of different ecotypes of indigenous chickens (ICs) in Kenya based on major histocompatibility complex (MHC)-linked and non-MHC microsatellite markers. Blood samples were collected from eight regions (48 birds per region) of Kenya: Kakamega (KK), Siaya (BN), West Pokot (WP), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) and Taita-Taveta (TT) and genotyped using two MHC-linked and ten non-MHC markers. All MHC-linked and non-MHC markers were polymorphic with a total of 140 alleles, of which 56 were identified in MHC-linked markers. Mean number of alleles (Na and Ne), private alleles, heterozygosity and genetic distances were higher for MHC-linked markers compared with non-MHC markers. The ad hoc statistic ¿K detected the true numbers of clusters to be three for MHC-linked markers and two in non-MHC markers. In conclusion, Kenyan ICs belong into two to three genetically distinct groups. Different markers systems have different clustering system. MHC-linked markers divided ICs into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. These IC ecotypes host many and highly diverse MHC-linked alleles. Higher allelic diversity indicated a huge amount of genetic variation in the MHC region of ICs and supported their reputation of being hardy and resistant to diseases.
Breeding program for indigenous chicken in Kenya
Ngeno, K. - \ 2015
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789462572775 - 154
kippen - pluimvee - inheems vee - dierveredeling - veredelingsprogramma's - genetische diversiteit - ecotypen - genomen - genetische verbetering - kenya - fowls - poultry - native livestock - animal breeding - breeding programmes - genetic diversity - ecotypes - genomes - genetic improvement - kenya

Abstract

Ngeno, K. (2015). Breeding program for indigenous chicken in Kenya. Analysis of diversity in indigenous chicken populations. PhD thesis, Wageningen University, the Netherlands

The objective of this research was to generate knowledge required for the development of an indigenous chicken (IC) breeding program for enhanced productivity and improved human livelihood in Kenya. The initial step was to review five questions; what, why and how should we conserve IC in an effective and sustainable way, who are the stakeholders and what are their roles in the IC breeding program. The next step of the research focused on detecting distinctive IC ecotypes through morphological and genomic characterization. Indigenous chicken ecotypes were found to be populations with huge variability in the morphological features. Molecular characterization was carried out using microsatellite markers and whole genome re-sequenced data. The studied IC ecotypes are genetically distinct groups. The MHC-linked microsatellite markers divided the eight IC ecotypes studied into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. Analysis revealed high genetic variation within the ecotype with highly diverse MHC-linked alleles which are known to be involved in disease resistance. Whole genome re-sequencing revealed genomic variability, regions affected by selection, candidate genes and mutations that can explain partially the phenotypic divergence between IC and commercial layers. Unlike commercial chickens, IC preserved a high genomic variability that may be important in addressing present and future challenges associated with environmental adaptation and farmers’ breeding goals. Lastly, this study showed that there is an opportunity to improve IC through selection within the population. Genetic improvement utilizing within IC selection requires setting up a breeding program. The study described the systematic and logical steps in designing a breeding program by focusing on farmers’ need, how to improve IC to fit the farming conditions, and management regimes.

Morphological features of indigenous chicken ecotype populations of Kenya
Ngeno, K. ; Waaij, E.H. van der; Kahi, A.K. ; Arendonk, J.A.M. van - \ 2014
Animal Genetic Resources 55 (2014). - ISSN 2078-6336 - p. 115 - 124.
This study characterized indigenous chicken (IC) ecotypes morphologically. Five IC ecotypes studied were Kakamega (KK), Siaya (BN), West Pokot (WP), Narok (NR) and Bomet (BM). Data on morphological features were collected from 1 580 chickens and 151 for zoometric measurements. Descriptive statistics, non-parametric and F tests were used in analysis. A non-parametric Kruskal–Wallis, Binomial test and Mann–Whitney U test was used to evaluate whether the ecotype have effects on the qualitative morphological variables. Zoometric measurements was analysed with the PROC GLM of SAS. Results revealed that, black, black-white striped, brown and red body plumage colours were significantly different (P <0.05) between the ecotypes. Feather morphology (%) were not significantly different (P > 0.05). Distribution of body feathers (%), comb types (%) and zoometric measurements were significantly different (P <0.05). Eye colours varied significantly (P <0.001) within the ecotypes unlike between the populations. In conclusion, IC ecotypes studied are heterogeneous population with huge variability in morphological features.
Indigenous chicken genetic resources in Kenya: their unique attributes and conservation options for improved use
Ngeno, K. ; Waaij, E.H. van der; Kahi, A.K. - \ 2014
Worlds Poultry Science Journal 70 (2014)1. - ISSN 0043-9339 - p. 173 - 184.
native fowl - temperature - association - disease
The indigenous chicken (Gallus gallus domesticus) genetic resources (IC) comprise more than 80% of the overall poultry population in rural villages despite their low productivity. However, a holistic approach that increases productivity without increasing production costs or leading to loss of biodiversity is presently limited. Conversely, in most developing countries, there is almost no organizational structure for breeding programmes for improving and conserving IC. These locally adapted IC can only be conserved in the most rational and sustainable way by ensuring that they are functional part of different production systems. Their conservation should be through utilisation if they are to be of any benefit to the poor rural households. This discussion focuses on five very relevant questions that need to be answered if the conservation of IC is to be effective and sustainable: What, why and how should we conserve, who are the stakeholders and what are their roles in conservation efforts?
Optimizing the design of small-sized nucleus breeding programs for dairy cattle with minimal performance recording
Kariuki, C.M. ; Komen, J. ; Kahi, A.K. ; Arendonk, J.A.M. van - \ 2014
Journal of Dairy Science 97 (2014)12. - ISSN 0022-0302 - p. 7963 - 7974.
genome-wide selection - overlapping generations - predefined rate - prediction - schemes - kenya - improvement - efficiency
Dairy cattle breeding programs in developing countries are constrained by minimal and erratic pedigree and performance recording on cows on commercial farms. Small-sized nucleus breeding programs offer a viable alternative. Deterministic simulations using selection index theory were performed to determine the optimum design for small-sized nucleus schemes for dairy cattle. The nucleus was made up of 197 bulls and 243 cows distributed in 8 non-overlapping age classes. Each year 10 sires and 100 dams were selected to produce the next generation of male and female selection candidates. Conception rates and sex ratio were fixed at 0.90 and 0.50, respectively, translating to 45 male and 45 female candidates joining the nucleus per year. Commercial recorded dams provided information for genetic evaluation of selection candidates (bulls) in the nucleus. Five strategies were defined: nucleus records only [within-nucleus dam performance (DP)], progeny records in addition to nucleus records [progeny testing (PT)], genomic information only [genomic selection (GS)], dam performance records in addition to genomic information (GS+DP), and progeny records in addition to genomic information (GS+PT). Alternative PT, GS, GS+DP, and GS+PT schemes differed in the number of progeny per sire and size of reference population. The maximum number of progeny records per sire was 30, and the maximum size of the reference population was 5,000. Results show that GS schemes had higher responses and lower accuracies compared with other strategies, with the higher response being due to shorter generation intervals. Compared with similar sized progeny-testing schemes, genomic-selection schemes would have lower accuracies but these are offset by higher responses per year, which might provide additional incentive for farmers to participate in recording.
Genetic analyses of N’Dama cattle breed selection schemes
Bosso, N.A. ; Waaij, E.H. van der; Kahi, A.K. ; Arendonk, J.A.M. van - \ 2009
Livestock Research for Rural Development 21 (2009)8. - ISSN 0121-3784 - p. np - np.
Data from the nucleus herd at the International Trypanotolerance Centre (ITC) in The Gambia were used to evaluate the current N'Dama cattle breeding scheme implemented in a low input production system. Opportunities were investigated to further improve the breeding scheme through a comparison of alternatives to the current selection strategy. A deterministic simulation model was used to demonstrate the genetic and economic benefits of the different schemes. The breeding goal consisted of daily weight gain (from 15 to 36 months of age under high tsetse challenge conditions, DWG, g/day) and milk yield (milk off-take in the first 100 days of lactation, MY, kg). Substantial genetic response per year of 3.40 kg in MY and 0.25 g/day in DWG could be achieved. Simulation results showed that early selection of nucleus sires resulted in relatively higher genetic and economic responses compared to all other schemes investigated. For a practical breeding scheme (low input system), the scheme based on early selection of nucleus sires should be recommended since this leads to the best improvements in the overall breeding goal
A new Mathematical Method of Predict Protein and Fat Retention in Domesticated Mammals
Hirooka, H. ; Kahi, A.K. ; Lende, T. van der - \ 2006
Evaluation of Closed Adult Nucleus Multiple Ovulation and Embryo Transfer and Conventional Progeny Testing Breeding Schemes for Milk Production from Crossbred Cattle in the Tropics
Kosgey, I.S. ; Kahi, A.K. ; Arendonk, J.A.M. van - \ 2005
Journal of Dairy Science 88 (2005). - ISSN 0022-0302 - p. 1582 - 1594.
dairy production systems - genetic-improvement - overlapping generations - kenya - selection - populations - performance - strategies - prediction
The potential benefits of closed adult nucleus multiple ovulation and embryo transfer (MOET) and conventional progeny testing (CNS) schemes, and the logistics of their integration into large-scale continuous production of crossbred cattle were studied by deterministic simulation. The latter was based on F1 (Bos taurus x Bos indicus) production using AI or natural mating and MOET, and continuous F2 production by mating of F1 animals. The gene flow and the cumulative discounted expressions (CDES) were also calculated. Both schemes had 8, 16, 32, or 64 dams with 2, 4, 8, 16, or 32 sires selected. In the MOET nucleus scheme (MNS), the test capacity was 1, 2, 8, or 16 offspring, and the number of matings per dam per year was 1, 2, or 4. A scheme of 8 sires with 64 dams and a test capacity of 4 female offspring per dam per year resulted in an annual genetic gain (in phenotypic standard deviation) of 0.324 and 0.081 for MNS and CNS, respectively. In the MNS, there was substantial genetic gain with a relatively small number of animals compared with a CNS. The F1 had the highest, and the F2 scheme the lowest CDES. However, a very large number of B. indicus females would be required in the F1 scheme. This scheme may not be practical under conditions in developing countries. The F2 scheme was logistically attractive because it produces its own replacements, and the number of B. taurus females required would be easy to attain. Accompanying technical and financial constraints of nucleus schemes should be addressed before applying them
Economic evaluation of crossbreeding for dairy production in a pasture based production system in Kenya
Kahi, A.K. ; Thorpe, W. ; Nitter, G. ; Arendonk, J.A.M. van; Gall, C.F. - \ 2000
Livestock Production Science 65 (2000). - ISSN 0301-6226 - p. 167 - 184.
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