Value of the Dutch Holstein Friesian germplasm collection to increase genetic variability and improve genetic merit
Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. ; Windig, J. - \ 2018
Journal of Dairy Science 101 (2018)11. - ISSN 0022-0302 - p. 10022 - 10033.
conservation - dairy cow - gene bank collection - genetic diversity - genetic improvement
National gene bank collections for Holstein Friesian (HF) dairy cattle were set up in the 1990s. In this study, we assessed the value of bulls from the Dutch HF germplasm collection, also known as cryobank bulls, to increase genetic variability and improve genetic merit in the current bull population (bulls born in 2010–2015). Genetic variability was defined as 1 minus the mean genomic similarity (SIMSNP) or as 1 minus the mean pedigree-based kinship (fPED). Genetic merit was defined as the mean estimated breeding value for the total merit index or for 1 of 3 subindices (yield, fertility, and udder health). Using optimal contribution selection, we minimized relatedness (maximized variability) or maximized genetic merit at restricted levels of relatedness. We compared breeding schemes with only bulls from 2010 to 2015 with schemes in which cryobank bulls were also included. When we minimized relatedness, inclusion of genotyped cryobank bulls decreased mean SIMSNP by 0.7% and inclusion of both genotyped and nongenotyped cryobank bulls decreased mean fPED by 2.6% (in absolute terms). When we maximized merit at restricted levels of relatedness, inclusion of cryobank bulls provided additional merit at any level of mean SIMSNP or mean fPED except for the total merit index at high levels of mean SIMSNP. Additional merit from cryobank bulls depended on (1) the relative emphasis on genetic variability and (2) the selection criterion. Additional merit was higher when more emphasis was put on genetic variability. For fertility, for example, it was 1.74 SD at a mean SIMSNP restriction of 64.5% and 0.37 SD at a mean SIMSNP restriction of 67.5%. Additional merit was low to nonexistent for the total merit index and higher for the subindices, especially for fertility. At a mean SIMSNP of 64.5%, for example, it was 0.60 SD for the total merit index and 1.74 SD for fertility. In conclusion, Dutch HF cryobank bulls can be used to increase genetic variability and improve genetic merit in the current population, although their value is very limited when selecting for the current total merit index. Anticipating changes in the breeding goal in the future, the germplasm collection is a valuable resource for commercial breeding populations.
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.
Milk progesterone measures to improve genomic selection for fertility in dairy cows
Tenghe, Amabel Manyu Mefru - \ 2017
Wageningen University. Promotor(en): R.F. Veerkamp; B. Berglund, co-promotor(en): D. J. de Koning; A.C. Bouwman. - Wageningen : Wageningen University - ISBN 9789463431330 - 179
dairy cows - fertility - progesterone - milk - genomics - genetic improvement - heritability - genetic parameters - dairy performance - reproductive traits - animal genetics - animal breeding - dairy farming - melkkoeien - vruchtbaarheid - progesteron - melk - genomica - genetische verbetering - heritability - genetische parameters - melkresultaten - voortplantingskenmerken - diergenetica - dierveredeling - melkveehouderij
Improved reproductive performance has a substantial benefit for the overall profitability of dairy cattle farming by decreasing insemination and veterinary treatment costs, shortening calving intervals, and lowering the rate of involuntary culling. Unfortunately, the low heritability of classical fertility traits derived from calving and insemination data makes genetic improvement by traditional animal breeding slow. Therefore, there is an interest in finding novel measures of fertility that have a higher heritability or using genomic information to aid genetic selection for fertility. The overall objective of this thesis was to explore the use of milk progesterone (P4) records and genomic information to improve selection for fertility in dairy cows. In a first step, the use of in-line milk progesterone records to define endocrine fertility traits was investigated, and genetic parameters estimated. Several defined endocrine fertility traits were heritable, and showed a reasonable repeatability. Also, the genetic correlation of milk production traits with endocrine fertility traits were considerably lower than the correlations of milk production with classical fertility traits. In the next step 17 quantitative trait loci (QTL) associated with endocrine fertility traits, were identified on Bos taurus autosomes (BTA) 2, 3, 8, 12, 15, 17, 23, and 25 in a genome-wide association study with single nucleotide polymorphisms. Further, fine-mapping of target regions on BTA 2 and 3, identified several associated variants and potential candidate genes underlying endocrine fertility traits. Subsequently, the optimal use of endocrine fertility traits in genomic evaluations was investigated; using empirical and theoretical predictions for single-trait models, I showed that endocrine fertility traits have more predictive ability than classical fertility traits. The accuracy of genomic prediction was also substantially improved when endocrine and classical fertility traits were combined in multi-trait genomic prediction. Finally, using deterministic predictions, the potential accuracy of multi-trait genomic selection when combining a cow training population measured for the endocrine trait commencement of luteal activity (C-LA), with a training population of bulls with daughter observations for a classical fertility trait was investigated. Results showed that for prediction of fertility, there is no benefit of investing in a cow training population when the breeding goal is based on classical fertility traits. However, when considering a more biological breeding goal for fertility like C-LA, accuracy is substantially improved when endocrine traits are available from a limited number of farms.
Genetic improvement of feed intake and methane emissions of cattle
Manzanilla Pech, Coralia I.V. - \ 2017
Wageningen University. Promotor(en): Roel Veerkamp, co-promotor(en): Yvette de Haas. - Wageningen : Wageningen University - ISBN 9789463430692 - 199
cattle - feed intake - methane production - genetic improvement - genetic parameters - conformation - breeding value - animal genetics - rundvee - voeropname - methaanproductie - genetische verbetering - genetische parameters - bouw (dier) - fokwaarde - diergenetica
Feed costs represent half of the total costs of dairy production. One way to increase profitability of dairy production is to reduce feed costs by improving feed efficiency. As DMI is a trait that varies significantly during and across lactations, it is imperative to understand the underlying genetic architecture of DMI across lactation. Moreover, phenotypes of DMI are scarce, due to the difficulty of recording them (expensive and labor-intensive). Some predictor traits have been suggested to predict DMI. Examples of these predictor traits are those related to production (milk yield (MY) or milk content) or to the maintenance of the cow (body weight (BW) or conformation traits). The ability to determine when predictor traits ideally should be measured in order to achieve an accurate prediction of DMI throughout the whole lactation period is thus important. Recently, with the use of information of single nucleotide polymorphism (SNP) markers, together with phenotypic data and pedigree, genomically estimated breeding values (GEBV) of scarcely recorded traits, such as DMI, have become easier to accurately predict. This approach, combined with predictor traits, could contribute to an increased accuracy of predictions of GEBV of DMI. Methane (CH4) is the second important greenhouse gas, and enteric CH4 is the largest source of anthropogenic CH4, representing 17% of global CH4 emissions. Furthermore, methane emissions represent 2-12% of feed energy losses. Selecting for lower CH4 emitting animals and more feed-efficient animals would aid in mitigating global CH4 emissions. To identify the impact on CH4 emissions of selecting for lower DMI animals, it is important to determine the correlations between DMI and CH4 and to identify whether the same genes that control DMI affect CH4. Therefore, the general objectives of this thesis were to (1) explore the genetic architecture of DMI during lactation, (2) study the relationship of DMI to conformation, production and other related traits, (3) investigate the correlations between DMI and methane traits, and determine the SNP in common between DMI and CH4 through a genome-wide association study (GWAS), and (4) investigate the accuracy of predictions of DMI using predictor traits combined with genomic data.
Genetic improvement of longevity in dairy cows
Pelt, Mathijs van - \ 2017
Wageningen University. Promotor(en): Roel Veerkamp, co-promotor(en): T.H.E. Meuwissen. - Wageningen : Wageningen University - ISBN 9789463430821 - 188
dairy cows - longevity - genetic improvement - breeding value - genetic analysis - survival - animal models - animal genetics - melkkoeien - gebruiksduur - genetische verbetering - fokwaarde - genetische analyse - overleving - diermodellen - diergenetica
Improving longevity helps to increase the profit of the farmer, and it is seen as an important measure of improved animal welfare and sustainability of the sector. Breeding values for longevity have been published since in 1999 in the Netherlands. For AI-companies and farmers it is necessary that breeding values are accurately estimated and will remain stable for the rest of life. However, current breeding values for longevity of bulls seem to fluctuate more than expected. The main aim of this thesis was to revisit the genetics of longevity and develop a genetic evaluation model for longevity, where breeding values reflect the true breeding value quicker during early life and therefore breeding values become more stable. Genetic parameters were estimated for survival up to 72 months after first calving with a random regression model (RRM). Survival rates were higher in early life than later in life (99 vs. 95%). Survival was genetically not the same trait across the entire lifespan, because genetic correlations differ from unity between different time intervals, especially when intervals were further apart. Survival in the first year after first calving was investigated more in depth. Survival of heifers has improved considerably in the past 25 years, initially due to the focus on a high milk production. More recently, the importance of a high milk production for survival has been reduced. Therefore functional survival was defined as survival adjusted for within-herd production level. For survival the optimum age at first calving was around 24 months, whereas for functional survival calving before 24 months resulted in a higher survival. Over years, genetic correlations between survival in different 5-yr intervals were below unity, whereas for functional survival genetic correlations did not indicate that survival changed over years. This suggested that a genetic evaluation using historical data should analyze functional survival rather than survival. A new genetic evaluation system for longevity was developed based on a RRM analyzing functional survival. Based on the correlation between the first breeding value of a bull and his later breeding values, the ranking of bulls was shown to be more stable for RRM than the current genetic evaluation. Bias in breeding value was observed, mainly for bulls with a large proportion of living daughters. Adjusting for within-herd production level reduced this bias in the breeding values greatly. Before implementing this new model for genetic evaluation, the cause of this bias needs to be further investigated.
It is time to bridge the gap between exploring and exploiting : prospects for utilizing intraspecific genetic variation to optimize arthropods for augmentative pest control – a review
Lommen, Suzanne T.E. ; Jong, Peter W. de; Pannebakker, Bart A. - \ 2017
Entomologia Experimentalis et Applicata 162 (2017)2. - ISSN 0013-8703 - p. 108 - 123.
augmentative biological control - genetic improvement - genetics - genomics - native natural enemies - offspring sex ratio - selective breeding - two-spot ladybird beetle
Intraspecific genetic variation in arthropods is often studied in the context of evolution and ecology. Such knowledge, however, can also be very usefully applied to biological pest control. Selection of genotypes with optimal trait values may be a powerful tool to develop more effective biocontrol agents. Although it has repeatedly been proposed, this approach is still hardly applied in the current commercial development of arthropod agents for pest control. In this perspective study, we call to take advantage of the increasing knowledge on the genetics underlying intraspecific variation to improve biological control agents. We argue that it is timely now because at present both the need and the technical possibilities for implementation exist, as there is (1) increased economic importance of biocontrol, (2) reduced availability of exotic biocontrol agents due to stricter legislation, and (3) increased availability of genetic information on non-model species. We present a step-by-step approach towards the exploitation of intraspecific genetic variation for biocontrol, outline that knowledge of the underlying genetic mechanisms is essential for success, and indicate how new molecular techniques can facilitate this. Finally, we exemplify this procedure by two case studies, one focussing on a target trait – offspring sex ratio – across species of hymenopteran parasitoids, and the other on a target species – the two-spot ladybird beetle – where wing length and body colouration can be optimized for aphid control. With this overview, we aim to inspire scientific researchers and biocontrol agent producers to start collaborating on the use of genetic variation for the improvement of natural enemies.
Antibodies and longevity of dairy cattle : genetic analysis
Klerk, B. de - \ 2016
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Jan van der Poel; Bart Ducro. - Wageningen : Wageningen University - ISBN 9789462577589 - 134
dairy cattle - dairy cows - antibodies - longevity - genetic analysis - breeding value - genomes - genetic improvement - animal genetics - melkvee - melkkoeien - antilichamen - gebruiksduur - genetische analyse - fokwaarde - genomen - genetische verbetering - diergenetica
The dairy sector has a big impact on food production for the growing world population and contributes substantially to the world economy. In order to produce food in a sustainable way, dairy cows need to be able to produce milk without problems and as long as possible. Therefore, breeding programs focuses on improvement of important traits for dairy cows. In order to improve desirable traits and obtain genetic gain there is a constant need for optimization of breeding programs and search for useful parameters to include within breeding programs. Over the last several decades, breeding in dairy cattle mainly focused on production and fertility traits, with less emphasis on health traits. Health problems, however, can cause substantial economic losses to the dairy industry. The economic losses, together with the rising awareness of animal welfare, increased herd size, and less attention for individual animals, have led to an increased need to focus more on health traits. Longevity is strongly related to disease resistance, since a more healthy cow will live a longer productive life (longevity). The identification of biomarkers and the detection of genes controlling health and longevity, would not only greatly enhance the understanding of such traits but also offer the opportunity to improve breeding schemes. The objectives of this thesis therefore were 1) to find an easy measurable disease resistance related biomarker in dairy cows, 2) identify the relation between antibodies and longevity, 3) identify genomic regions that are involved with antibody production/expression. In this thesis antibodies are investigated as parameter for longevity. Antibodies might be a novel parameter that enables selection of cows with an improved ability to stay healthy and to remain productive over a longer period of time. In this thesis antibodies bindiging the naive antigen keyhole limpet hemocyanin (KLH) were assumed to be natural antibodies. Antibodies binding bacteria-derived antigens lipoteichoic acid (LTA), lipopolysaccharide (LPS) and peptidoglycan (PGN) were assumed to be specific antibodies. In chapter 2 it was shown that levels of antibodies are heritable (up to h2 = 0.23). Additionally, antibody levels measured in milk and blood are genetically highly correlated (± 0.80) for the two studied isotypes (IgG and IgM). On the other hand, phenotypically, natural antibodies (from both IgG and IgM isotype) measured in milk cannot be interpreted as the same trait (phenotypic correlation = ± 0.40). In chapter 3 and 4 it was shown that levels of antibodies (both natural-and specific antibodies) showed a negative relation with longevity: first lactation cows with low IgM or IgG levels were found to have a longer productive life. When using estimated breeding values for longevity, only a significant relation was found between natural antibody level (IgM binding KLH) and longevity. Lastly chapter 5 reports on a genome-wide-association study (GWAS), to detect genes contributing to genetic variation in natural antibody level. For natural antibody isotype IgG, genomic regions with a significant association were found on chromosome 21 (BTA). These regions included genes have impact on in isotype class switching (from IgM to IgG). The gained knowledge on relations between antibodies and longevity and the gained insight on genes responsible for natural antibodies level make antibodies potential interesting biomarkers for longevity.
Multi-population genomic prediction
Wientjes, Y.C.J. - \ 2016
Wageningen University. Promotor(en): Roel Veerkamp; Mario Calus. - Wageningen : Wageningen University - ISBN 9789462576193 - 267
cum laude - dairy cattle - genomics - prediction - quantitative trait loci - genetic improvement - breeding value - selective breeding - animal breeding - animal genetics - melkvee - genomica - voorspelling - loci voor kwantitatief kenmerk - genetische verbetering - fokwaarde - selectief fokken - dierveredeling - diergenetica
Cum laude graduation
Genomic selection for improved crossbred performance
Lopes, Marcos Soares - \ 2016
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis; John Bastiaansen; E.F. Knol. - Wageningen : Wageningen University - ISBN 9789462576315 - 202
pigs - crossbreds - genomics - selective breeding - performance - genetic improvement - pig breeding - varkens - kruising - genomica - selectief fokken - prestatieniveau - genetische verbetering - varkensfokkerij
Lopes, M.S. (2016). Genomic selection for improved crossbred performance. PhD thesis, Wageningen University, the Netherlands
With the implementation of genomic selection in pig breeding, the genetic progress in purebred populations is expected to increase up to 55% compared to traditional selection based on pedigree information. However, as most of the animals in the pork production system are crossbreds, the increase in genetic progress in purebreds will only be observed on production farms if this progress is expressed in the performance of crossbreds. The main aim of this thesis was to evaluate different models based on genomic information which can be applied to improve performance of crossbred animals. Another aim was to gain insight into genetic architecture of (complex) traits and to investigate how selection history has influenced haplotype patterns of current commercial pigs. This thesis shows that by going beyond traditional genomic selection models, phenotypes can be predicted more accurately. Therefore, these improved models should be considered to improve crossbred performance. Further, this thesis provides important insights into the genetic architecture of the evaluated (complex) traits and also shows evidence that human-driven introgression and selection have shaped the genome of current commercial pig breeds. The research presented in this thesis was performed using data from pigs and the discussion on the practical application of results was focused on pig breeding. The results are relevant for all livestock species where crossbreeding is applied.
Exploiting genomic information on purebred and crossbred pigs
Hidalgo, A.M. - \ 2015
Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): D.J. de Koning; John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789462576018 - 202
varkens - genomica - kruising - inteeltlijnen - genetische verbetering - fokwaarde - drachtigheidsperiode - androstenon - prestatieniveau - varkensfokkerij - diergenetica - pigs - genomics - crossbreds - inbred lines - genetic improvement - breeding value - gestation period - androstenone - performance - pig breeding - animal genetics
Genetic improvement in indigenous chicken of Ethiopia
Woldegiorgiss, W.E. - \ 2015
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; T. Dessie. - Wageningen : Wageningen University - ISBN 9789462573161 - 130
kippen - pluimvee - inheems vee - genetische verbetering - houding van boeren - perceptie - kippenrassen - prestatieniveau - dierveredeling - ethiopië - fowls - poultry - native livestock - genetic improvement - farmers' attitudes - perception - fowl breeds - performance - animal breeding - ethiopia
Wondmeneh Esatu Woldegiorgiss (2015). Genetic improvement in indigenous chicken of Ethiopia. PhD thesis, Wageningen University, the Netherlands
This thesis considered various approaches to study the potential for improvement of village poultry production system using improved indigenous chicken. The approaches were structured survey questionnaire, village poultry simulation model (VIPOSIM), Heckman two-step model (econometric model), and experiments involving laboratory and field. First factors that determine the probability and intensity of adoption of exotic chickens were assessed. The probability of adopting exotic chickens was found to be positively affected by access to an off-farm income and negatively by livestock income. The intensity of adoption was negatively affected by being male household head, having a larger farm size, and having livestock income. Then, perceptions of farmers towards village poultry and impacts of interventions on flock and economic performance were assessed. Farmers’ perceptions affected their decisions about implementation of interventions, and interventions increased productivity but only in a few cases the increased revenues outweighed the additional costs. Subsequently, the evaluation of the breeds was conducted by comparing the natural antibody and productivity of improved indigenous chicken with crossbred, commercial and unimproved indigenous chickens. The results revealed that not only the NAb levels but also the effect of NAbs on survival differ between indigenous and improved breeds. NAb levels are associated with survival in commercial layer breed, but reduced survival in indigenous chickens placed in confinement. Improved indigenous chickens showed higher performance than unimproved one for all traits measured on-station, but remains lighter and developed more into a laying type than meat through the short-term selective breeding program. Overall, the present studies indicate that interventions need to be tailored towards the local situation to ensure that they lead not only to improved productivity but also to improved income.
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
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.
Cooperative and uniform fish? : social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia
Khaw, H.L. - \ 2015
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma; R.W. Ponzoni. - Wageningen : Wageningen University - ISBN 9789462572157 - 161
oreochromis niloticus - sociaal gedrag - lichaamsgewicht - variatie - genetische effecten - inteelt - kenmerken - heritability - genotype-milieu interactie - genotypische variatie - genetische verbetering - veredelingsprogramma's - visteelt - maleisië - oreochromis niloticus - social behaviour - body weight - variation - genetic effects - inbreeding - traits - heritability - genotype environment interaction - genetic variance - genetic improvement - breeding programmes - fish culture - malaysia
Khaw, HL. (2014). Cooperative and uniform fish? Social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia. PhD thesis, Wageningen University, the Netherlands.
Social interactions are present everywhere in the living world. Such social interactions may lead to indirect genetic effects (IGE), which are heritable effects of an individual on trait values of the other individuals its interacts with. IGEs may affect the direction and magnitude of response to selection in breeding programs. Moreover, social interactions may affect variability of traits. In aquaculture, competition for resources inflates size variation within populations. In this thesis, we used the Genetically Improved Farmed Tilapia (GIFT; Oreochromis niloticus) strain to investigate the genetic basis for social interactions and variability in harvest weight for tropical finfish. Social interaction experiments were established for quantifying the genetic and non-genetic indirect effects on harvest weight in the GIFT strain. We found evidence for IGEs on harvest weight, and a negative direct-indirect genetic correlation, which suggesting heritable competitive interactions for harvest weight in GIFT. Hence, breeding schemes may need to be adapted to avoid an increase in competition. A stochastic simulation study was conducted to examine the effect of BLUP selection on the rate of inbreeding for socially affected traits. The rates of inbreeding for scenarios with IGEs were greater than for scenarios without IGE. Therefore, with IGEs there is a greater need for a selection algorithm that restricts the increase of mean kinship. In aquaculture industry, there is a wide range of commercial production environments, which may leads to genotype by environment (GxE) interaction, for example due to differential social interactions. The GIFT fish were tested in ponds and cages to study the GxE interaction. The genetic correlations between environments (0.73 to 0.85, for harvest weight and body measurements) indicate little GxE-interaction. The data collected from the social interaction experiments were also used to investigate the presence of genetic variation in uniformity for harvest weight. The genetic coefficient of variation for standard deviation of harvest weight (0.17) shows that uniformity of harvest weight is heritable and can be increased by selective breeding. In the General Discussion of this thesis, the uniformity study was extended to incorporate IGE. The result indicates that more cooperative fish are not necessary more uniform for harvest weight. Overall, our results suggest that genetic improvement in fish breeding programs can be increased by accounting for social interactions.
JATROPT (Jatropha curcas: Applied and Technological Research on Plant Traits) : Final report EU FP7 Grant 245236 (2010-2013)
Loo, E.N. van; Jongschaap, R.E.E. - \ 2014
Plant Research International - 31
jatropha curcas - fuel crops - plant breeding - new crops - genetic improvement - yield increases - biofuels - biobased economy - jatropha curcas - brandstofgewassen - plantenveredeling - nieuwe cultuurgewassen - genetische verbetering - oogsttoename - biobrandstoffen - biobased economy
JATROPT aimed to improve jatropha production systems through developing advanced genetics tools for breeding and for development of jatropha agro-systems.
Genetic progress in Dutch crop yields
Rijk, H.C.A. ; Ittersum, M.K. van; Withagen, J.C.M. - \ 2013
plant breeding and genetics - winter wheat - spring barley - potato - sugar beet - crop yield - genetic improvement
This dataset contains the underlying data for the study: Rijk, B., Ittersum, M. van, Withagen, J. "Genetic progress in Dutch crop yields". Field Crops Research 149 (2013) 262–268, http://dx.doi.org/10.1016/j.fcr.2013.05.008
Optimizing genomic selection for scarcely recorded traits
Pszczola, M.J. - \ 2013
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Mario Calus; T. Strabel. - Wageningen : Wageningen UR - ISBN 9789461737663 - 158
melkvee - genomen - selectief fokken - genetische verbetering - fokwaarde - fenotypen - genotypen - kenmerken - voeropname - dierveredeling - dairy cattle - genomes - selective breeding - genetic improvement - breeding value - phenotypes - genotypes - traits - feed intake - animal breeding
Animal breeding aims to genetically improve animal populations by selecting the best individuals as parents of the next generation. New traits are being introduced to breeding goals to satisfy new demands faced by livestock production. Selecting for novel traits is especially challenging when recording is laborious and expensive and large scale recording is not possible. Genetic improvement of novel traits may be thus limited due to the small number of observations. New breeding tools, such as genomic selection, are therefore needed to enable the genetic improvement of novel traits. Using the limited available data optimally may, however, require alternative approaches and methodologies than currently used for conventional breeding goal traits. The overall objective of this thesis was to investigate different options for optimizing genomic selection for scarcely recorded novel traits. The investigated options were: (1) genotype imputation for ungenotyped but phenotyped animals to be used to enlarge the reference population; (2) optimization of the design of the reference population with respect to the relationships among the animals included in it; (3) prioritizing genotyping of the reference population or the selection candidates; and (4) using easily recordable predictor traits to improve the accuracy of breeding values for scarcely recorded traits. Results showed that: (1) including ungenotyped animals to the reference population can lead to a limited increase in the breeding values accuracy; (2) the reference population is designed optimally when the relationship within the reference are minimized and between reference population and potential selection candidates maximized; (3) the main gain in accuracy when moving from traditional to genomic selection is due to genotyping the selection candidates, but preferably both reference population and selection candidates should be genotyped; and (4) including the predictor traits in the analysis when it is recorded on both reference population and selection candidates can lead to a significant increase in the selection accuracy. The key factors for successful implementation of selection for a novel trait in a breeding scheme are: (1) maximizing accuracy of genotype prediction for ungenotyped animals to be used for updating the reference population; (2) optimizing the design of the reference population; (3) determining easy to record indicator traits that are also available on the selection candidates (4) developing large scale phenotyping techniques; and (5) establishing strategies and policies for increasing the engagement of farmers in the recording of novel traits.
Animal genetic resources: conservation-breeding-regulatory framework
Hiemstra, Sipke Joost - \ 2012
livestock farming - agro-biodiversity - genetic diversity - animal genetic resources - genetic improvement - animal breeding - sustainable animal husbandry - gene banks - breeds - distribution
The role of new on-farm technologies in sustainable farm management and dairy herd improvement (DHI)
Koning, Kees de - \ 2011
dairy farming - dairy equipment - sensors - milking parlours - precision agriculture - dairy technology - dairy farming systems - genetic improvement
The role of reproductive technologies in breeding schemes for livestock populations in developing countries
Arendonk, J.A.M. van - \ 2011
Livestock Science 136 (2011)1. - ISSN 1871-1413 - p. 29 - 37.
fokkerijmethoden - dierveredeling - ontwikkelingslanden - vee - genetische bronnen van diersoorten - genetische diversiteit - veredelingsprogramma's - kunstmatige inseminatie - inteelt - genetische verbetering - animal breeding methods - animal breeding - developing countries - livestock - animal genetic resources - genetic diversity - breeding programmes - artificial insemination - inbreeding - genetic improvement - dairy-cattle - genetic-variation - embryo transfer - predefined rate - selection - programs - impact - rates - prediction - sheep
The world is faced with the challenge to meet the increasing demand for livestock products while conserving animal genetic resource diversity and maintaining environmental integrity. Genetic improvement of local breeds can help to improve the livelihood of the livestock keepers, to increase the production of animal products and to conserve genetic diversity. Implementing breeding schemes in developing countries has proven to be very difficult. The objective of this paper is to discuss the role of reproductive technologies for the creation and dissemination of genetic improvement in livestock populations in developing countries. In the paper opportunities are discussed for implementing breeding schemes which minimize the need for extensive pedigree and performance recording. It is shown that genetic progress can be generated in a small population. Community-based breeding schemes offer a good starting point for involving farmers in improving local breeds. Artificial insemination to exchange genetic material between communities offers an opportunity to increase the rate of genetic improvement while restricting the rate of inbreeding. Furthermore, artificial insemination is a promising technique for dissemination of genetic gain to producers at a relatively low cost. Opportunities to use semen sexing in a crossbreeding scheme are presented. It is concluded that tailor-made solutions and long-term commitment are needed in order to meet the needs of farmers to increase their livelihoods and to meet the needs of the growing population of consumers.