Staff Publications

Staff Publications

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

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

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

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

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Dossier Nieuwe technieken plantenveredeling
Lotz, L.A.P. ; Wiel, C.C.M. van de - \ 2017
Wageningen : Groen Kennisnet
cultivation - greenhouse horticulture - vegetable growing - breeding methods - breeding programmes - fruit growing - arable farming
In de plantenveredeling vindt op dit moment zeer snelle innovatie plaats. Een deel van deze innovatie is onderdeel van een maatschappelijk debat. Dit dossier bevat lesmateriaal om nieuwe wetenschappelijke kennis en inzichten door te laten stromen naar verschillende niveaus in het Groene onderwijs. Ultiem doel is jongeren zodanig van kennis te voorzien dat zij zelf een goed onderbouwde mening kunnen formuleren over kansen en risico’s van gebruik van nieuwe technieken in de veredeling, en daarmee ook een bijdrage kunnen leveren aan genoemd maatschappelijk debat.
Breeding strategies for sustainable intensification of developing smallholder dairy cattle production systems
Kariuki, Charles Mbogo - \ 2017
University. Promotor(en): Hans Komen, co-promotor(en): Johan van 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
University. Promotor(en): Hans Komen, co-promotor(en): Johan van 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 - veredelingsprogramma's - selectief fokken - genetische verbetering - kleine landbouwbedrijven - duurzaamheid (sustainability) - visteelt - aquacultuur

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.

Resistentieveredeling - Veredeling gericht op resistentie : Kennisclip Bogo-project e-learning
Hop, M.E.C.M. ; Looman, B.H.M. - \ 2016
Groen Kennisnet
resistance breeding - plant breeding - selection - selection methods - breeding programmes - breeding methods - plant protection - genetic resistance - teaching materials - resistentieveredeling - plantenveredeling - selectie - selectiemethoden - veredelingsprogramma - veredelingsmethoden - gewasbescherming - genetisch bepaalde resistentie - lesmaterialen
Deze kennisclip maakt onderdeel uit van de lesmodule Resistentie Veredeling van het CIV T&U.
Sport horses : breeding specialist from a single breeding programme?
Rovere, G.A. - \ 2016
University; Aarhus University. Promotor(en): Johan van Arendonk, co-promotor(en): P. Madsen; Bart Ducro; E. Norberg. - Wageningen : Wageningen University - ISBN 9789462576353 - 151 p.
horses - racehorses - studbooks - show jumping - sport performance - pedigree - genetic correlation - horse breeding - breeding programmes - paarden - renpaarden - paardenstamboeken - jachtspringen - sportprestatie - stamboom - genetische correlatie - paardenfokkerij - veredelingsprogramma's

Summary

The general goal of this thesis was to provide information useful for the breeding programme of the Royal Dutch Warmblood Studbook (KWPN) in relation with the ongoing specialisation of the population. Data provided by KWPN consisted of records from studbook-first inspection, competition performance on dressage and show-jumping, and pedigree information. Firstly, the effect of specialisation was studied on the connectedness between the subpopulations of dressage and show-jumping horses, using the pedigree information. Results indicated that relatedness between horses in the two subpopulations has been reduced to a low level, while relatedness within both subpopulations has been increasing consistently. A reduction in the number of influential ancestors in both subpopulations was observed. Secondly, it was analysed whether the specialisation for either dressage or show jumping has affected genetic parameters of traits recorded in the two subpopulations. Traits recorded at studbook-entry inspection were defined as a dressage trait or a show-jumping trait according to the type of horse that received the inspection. Bivariate analyses were performed to estimate the genetic correlation between the two traits. Results indicated that the specialisation process has resulted in a difference in mean trait values between dressage and show-jumping horses. However, differences in heritabilities for traits defined as dressage or show-jumping did not differ significantly, and the genetic correlations between them were not different from one considering their posterior standard deviation. Thirdly, the model to analyse performance in competition of dressage and show-jumping was studied. 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. Fourthly, it was estimated the genetic correlation between the performance of horses in dressage and show-jumping competition, and the genetic correlations between traits measured early in life and performance in competition in each of the disciplines. Results showed that the genetic correlation between performance of horses in dressage and show-jumping was slightly unfavourable (-0.12). The genetic correlation between dressage and show-jumping tended to become more unfavourable over time, but this trend was not reflected in changes in the correlations between competition traits and traits recorded in the studbook-entry inspection. From this study it can be concluded that no extra benefit is to be expected from definition of a combined breeding goal. However, entirely separated breeding programmes for both disciplines are therefore not advisable. Constructing separate selection indexes would allow for optimal weighting of information sources such as studbook-entry inspection traits in accordance to the breeding goal of each sports discipline.

Veredelaars moeten meer 'ondergronds' gaan : Edith Lammers van Bueren geïnterviewd door twee collega's van het LBI
Lammerts van Bueren, Edith - \ 2015
organic farming - breeding programmes - breeding methods - varieties - university research - plant breeding - organic plant breeding

Edith Lammerts van Bueren is onderzoekster veredeling op het Louis Bolk Instituut en daarnaast al tien jaar buitengewoon hoogleraar Biologische Plantenveredeling aan Wageningen University. Ze vervult een brugfunctie tussen de biologische sector en de Wageningse wetenschappelijke wereld. Ze wordt veel gevraagd in publieke debatten over gentechnologie versus biologische veredeling. Onlangs is haar hoogleraarschap voor een derde termijn goedgekeurd. Tijd om de resultaten van de eerste tien jaar en de plannen voor de toekomst te belichten.

Selectie en genetische variatie in een fokprogramma
Oldenbroek, Kor ; Maurice - Van Eijndhoven, Myrthe - \ 2015
Zeldzaam huisdier 40 (2015)4. - ISSN 0929-905X - p. 14 - 17.
dierveredeling - veredelingsprogramma's - genetische variatie - selectie - zeldzame rassen - heritability - inteelt - verwantschap - groninger paard - animal breeding - breeding programmes - genetic variation - selection - rare breeds - inbreeding - kinship - groningen horse
In drie voorgaande artikelen in deze serie zijn achtereenvolgens het fokdoel, de registratie van gegevens en de basisprincipes van de erfelijkheid besproken. In dit laatste artikel wordt het belang van genetische variatie en de selectie van ouderdieren besproken. Twee belangrijke elementen in het fokprogramma van een zeldzaam ras.
Smaakpanel test ook gevoelswaarde bloemen en planten : liefdesverdrietboeket trekt Wageningse studenten
Arkesteijn, M. ; Verkerke, W. - \ 2015
Onder Glas 12 (2015)9. - p. 29 - 29.
tuinbouw - snijbloemen - glastuinbouw - consumentenpanels - smaakpanels - ornamentele waarde - veredelingsprogramma's - potplanten - tomaten - horticulture - cut flowers - greenhouse horticulture - consumer panels - taste panels - ornamental value - breeding programmes - pot plants - tomatoes
Wie beoordeelt beter wat mensen mooi of lekker vinden: specialisten of een panel van ‘gewone’ mensen, die de producten moeten kopen? In 25 jaar groeide een onderzoekspanel dat bijdroeg aan de verbetering van de smaak van tomaten uit tot het Bleiswijkse smaakpanel van Wageningen UR. Een dienstverlenend panel van zo’n 300 mensen, die inzetbaar zijn voor een scala aan smaaktesten. Kan dat smaakpanel ook worden ingezet voor de beoordeling van bloemen en planten?
Breeding program for indigenous chicken in Kenya
Ngeno, K. - \ 2015
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

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.

Indirect genetic effects for group-housed animals
Alemu, S.W. - \ 2015
University. Promotor(en): Johan van Arendonk, co-promotor(en): L.G. Janss; Piter Bijma; P. Berg. - Wageningen : Wageningen University - ISBN 9788793176713 - 228
nerts - pluimvee - groepshuisvesting - genetische effecten - sociaal gedrag - agressief gedrag - interacties - heritability - veredelingsprogramma's - statistische analyse - genetische parameters - selectief fokken - mink - poultry - group housing - genetic effects - social behaviour - aggressive behaviour - interactions - breeding programmes - statistical analysis - genetic parameters - selective breeding

ABSTRACT

Alemu, SW(2015) Indirect Genetic effects for Group-housed Animals. Joint PhD thesis between Aarhus University, Denmark and Wageningen University, the Netherlands.

Social interactions among individuals are common both in plants and animals. With social interactions, the trait value of an individual may be influenced by the genes of its interacting partners, a phenomenon known as indirect genetic effects (IGE). An IGE is heritable effect of an individual on trait values of another individual. A large body of literature has shown that social interactions can create addition heritable variation in both plants and animals, for both behavioural and production traits.

When IGE are estimated it is usually assumed that an individual interacts equally with all its group mates, irrespective of genetic relatedness. This assumption may not be true in mixed groups of kin and non-kin, where an individual may interact systematically different with kin and non-kin. Current IGE models ignore such systematically different interactions between kin and non-kin. Thus, the main aim of this thesis was to develop and apply statistical methods to estimate IGE when interactions differ between kin and non-kin.

Social interactions are important in mink that are kept in groups for the production of fur. Group housing of mink increases aggression behaviours, which is reflected by an increase in the number of bite marks on the pelts, and reduces the welfare of the animals. We estimated the genetic parameter for bite mark traits in group-housed mink, to investigate the prospects for genetic improvement of bite mark traits. We found that there are good prospects to produce mink that have a low level of biting. Finally, we further concluded that genetic parameter estimation for bite mark score should take into account systematic interactions due to sex or kin.

In this thesis we also investigated genomic selection for socially affected traits, considering survival time in two lines of brown egg layers showing cannibalistic behaviour. Despite the limited reference population of ~234 progeny tested sires, the accuracy of estimated breeding values (EBV) was ~35% higher for genomic selection compared with the parent average-EBV. We found that the response to genomic selection per year for line B1 was substantially higher than for the traditional breeding scheme, whereas for line BD response was slightly higher than for the traditional breeding scheme. In conclusion, genetic selection with IGE combined with marker information can substantially reduce detrimental social behaviours such as cannibalism in layers and biting in group-housed mink.

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
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 - social behaviour - body weight - variation - genetic effects - inbreeding - traits - genotype environment interaction - genetic variance - genetic improvement - breeding programmes - fish culture - malaysia

Abstract

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.

Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice
Calingacion, M.N. - \ 2015
University. Promotor(en): Robert Hall; M.A. Fitzgerald, co-promotor(en): Roland Mumm. - Wageningen : Wageningen University - ISBN 9789462572188 - 198
oryza sativa - rijst - rassen (planten) - cultivars - genetische diversiteit - gewaskwaliteit - aroma - geur en smaak - consumentenvoorkeuren - plantenveredeling - veredelingsprogramma's - rice - varieties - genetic diversity - crop quality - flavour - consumer preferences - plant breeding - breeding programmes

Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice

Mariafe N. Calingacion

Most rice breeding programs have focused on improving agronomic traits such as yield, while enhancing grain quality traits such as flavour and aroma, especially of non-fragrant rices, has not been given high priority. In this study, we utilised a multi-disciplinary approach to understand better quality traits of aroma and flavour in rice grains, and to determine whether good flavour in the grain could be combined with stress tolerant genotypes.

To understand what factors drive rice preferences, an extensive survey among members of the International Network for Quality Rice who are local experts in grain quality evaluation programs in 25 countries was conducted (Chapter 2). The objective was to identify the grain quality characteristics of the popular rice varieties in each region. Eighteen combinations of size and shape of the grain, amylose content (AC), gelatinisation temperature (GT) and fragrance were identified. These trait combinations reveal the complexity of consumer preferences. The two most popular combinations both have long and slender grains, while one has low amylose, low GT and is aromatic, and the other has intermediate AC and intermediate GT and is non-aromatic. Further evaluation of varieties having the same combination of grain quality traits showed that consumers readily identify differences between these varieties. For example, BRS Primavera and IR64 that are popular in Brazil and in the Philippines, respectively, have the same combination of all 18 traits, however, panellists of sensory evaluation can easily perceive differences in aroma and flavour of BRS Primavera and IR64. This emphasises that the current tools we have available to assess rice quality are unable to capture all the quality traits consumers are looking for in rice.

In Chapter 3, a novel multiplatform metabolomic and ionomic approach with genome-wide genotyping was utilised to investigate the effect of different nitrogen fertiliser regimes on the biochemical profile of three premium waxy rice varieties, Hom Nang Nouane (HNN), Kai Noi Leuanag (KNL) and Tha Sa No (TSN) from Lao PDR. The current tools used to phenotype grain quality such as GT, values from viscosity curves, and hardness and stickiness, were unable to differentiate between HNN, KNL and TSN either on the basis of nitrogen treatment nor genotype. However, metabolite profiling of metabolites and minerals followed by multivariate statistical methods readily separated the genotypes on each platform, and discriminatory compounds that were identified were relevant to consumers in terms of flavour, taste and nutrition. However, despite yield differences, nitrogen treatment did not significantly affect the overall metabolite and mineral profiles of the samples. Using 1536 single nucleotide polymorphism (SNP) loci, the Euclidean distance between each variety was calculated and compared to the distance between each variety for each metabolomic platform. Procrustes analysis was used to rotate and scale the variety mean scores on the metabolite principal components to give the best fit to the genetic principal coordinates. Comparing the triangles whereby each vertex of the triangle is a variety and the length of each side is equal to the scaled Euclidean distance, mineral elements, polar metabolites and volatile compounds all associate very well with the genetic distance between each variety. This study highlights that multiple metabolomic platforms are potential phenotyping tools to characterise rice quality in a comprehensive and efficient way, and in a way that provides data that is relevant to consumers.

To gain insights on the influence of water availability to the metabolomic profile of drought tolerant rice, two contrasting varieties, Apo and IR64, and a mapping population derived from them were extensively characterised in Chapters 4 and 5. Apo is drought tolerant but has unacceptable grain quality while IR64 is drought susceptible with premium grain quality. Apo and IR64 were grown under irrigated and drought conditions. Yield of Apo from both water conditions was higher than yield of IR64 under the same conditions. Moreover, metabolite profiling and sensory analysis showed that grains of Apo were not affected by drought conditions i.e. panellists perceived no difference in the aroma of Apo from both conditions and Principal Components Analysis (PCA) of the volatiles showed one cluster of Apo from both conditions. However, grains of IR64 formed two clusters based on water condition in the PCA and panellists were able to perceive ‘water-like metallic’ aroma in IR64 that was grown under drought conditions but this was not detected in grains from the irrigated treatment. This suggests that response to water stress in the metabolomic profile of the grain is variety dependent.

In Chapter 5, a mapping population derived from Apo and IR64 was grown, with the parents, under irrigated and drought conditions. The yield of more than half of the population was higher than the yield of Apo and IR64 under both irrigated and drought conditions; this indicates significant transgressive segregation. Using a dense linkage map based on genotyping by sequencing data, quantitative trait loci (QTL) analysis of drought stress identified one major QTL on chromosome 3 that is likely to be qDTY3.1 which was previously detected in a population derived from Apo as the drought tolerant parent. All the lines of the population carrying this QTL showed significantly higher yield under drought than those without it, indicating the potential importance of this QTL in drought tolerance.

Metabolite profiling and sensory analysis were also conducted in the grains of the population. More than a hundred volatiles were detected in the headspace of rice samples and PC1 and PC2 explained 55.6% of the variation in the metabolite profiles with many of the lines clustering in between the Apo and IR64 parent values. Six novel metabolite QTLs for volatile compounds were identified - 1 QTL was detected in chromosome 1 for 3,7-dimethyl-octen-1-ol, 1 QTL for hexanol in chromosome 2, and 4 QTLs for pentanol, hexanol, hexanal, and heptanone in chromosome 3. Interestingly, three lines were observed by the panellists to have similar aroma as IR64 while four lines were observed to have similar aroma as that perceived in Apo. Lines 20, 164 and 28 were perceived by the panellists to have high levels of corn, dairy and sweet aromatic features. Moreover, the yield of these 3 lines under both irrigated and drought conditions was similar to that of the Apo parent under the same conditions with Line 28 yielding the highest under drought and has the QTL associated with yield under drought on chromosome 3.

Finally, the potential of metabolomics as a phenotyping tool in characterising grain quality is further highlighted in Chapter 6. Combining metabolomics with high throughput genotyping and sensory analysis offers new breadth of approach in understanding grain quality of rice. Three lines identified that carry IR64 quality along with high yield in both irrigation and drought, are recommended to enter a rice breeding program at the stage of advanced replicated and multi-location testing. By using advanced tools of phenotyping and genotyping, with validation by sensory panels, these three advanced lines have been selected in just three years.

Blaarkopfokplan voor de toekomst : ras van het jaar
Oldenbroek, J.K. ; Faber, J.H. ; Wieringa, R. - \ 2014
Zeldzaam huisdier 39 (2014)4. - ISSN 0929-905X - p. 8 - 9.
rundvee - rundveeteelt - rundveerassen - groninger blaarkop - dierveredeling - fokkerijmethoden - veredelingsprogramma - cattle - cattle farming - cattle breeds - groningen white headed - animal breeding - animal breeding methods - breeding programmes
Eind 2013 heeft de SZH met de blaarkopbestuurders een strategiedag gehouden. Daaruit kwam onder meer naar voren dat er behoefte is aan een goed en doelgericht fokplan. Onlangs is de Landelijke (Fok)-Commissie begonnen het fokplan uit te werken.
Breeding strategies to make sheep farms resilient to uncertainty
Rose, I.J. - \ 2014
University. Promotor(en): Johan van Arendonk, co-promotor(en): Herman Mulder; J. Werf. - Wageningen : Wageningen University - ISBN 9789462570900 - 188
schapen - schapenhouderij - dierveredeling - veredelingsprogramma's - economische haalbaarheid - rentabiliteit - veerkracht - weiden - schapenvoeding - western australia - sheep - sheep farming - animal breeding - breeding programmes - economic viability - profitability - elasticity - pastures - sheep feeding

The sheep industry in Western Australian has had many challenges over the last 20 years which have caused sheep numbers to decline. This decline is because sheep farms are not resilient to uncertain pasture growth and commodity prices. One way to improve resilience and profitability of farming systems is through breeding of sheep. Therefore, this thesis had two aims; 1. Quantify the potential to select and breed sheep that are more resilient and 2. Quantify how sheep breeding can make farming systems more resilient. To determine if sheep can be bred to be resilient to varying pasture growth I investigated if live weight change is a heritable trait. I investigated live weight change in adult Merino ewes managed in a Mediterranean climate in Katanning in Western Australia. Live weight change traits were during mating and lactation. The heritability of live weight change was low to moderate. Therefore that live weight change could be a potential indicator trait for resilience to uncertain pasture growth. To include live weight change in a breeding goal, correlations with other traits are needed. I calculated the genetic correlations between live weight change during mating, pregnancy and lactation, and reproduction traits. Most genetic correlations were not significant, but genetically gaining live weight during mating in two-year old ewes and during pregnancy for three-year-old ewes improved reproduction. Therefore, optimised selection strategies can select for live weight change and reproduction simultaneously. To investigate optimal breeding programs to make sheep farms resilient to uncertain pasture growth and prices, I modelled a sheep farm in a Mediterranean environment. The economic value of seven traits in the breeding objective were estimated. Including variation in pasture growth and commodity prices decreased average profit and increased the economic value of all breeding goal traits compared to the average scenario. Economic values increased most for traits that had increases in profit with the smallest impact on energy requirements. I also compared optimal breeding programs for across 11 years for 10 regions in Western Australia with different levels of reliability of pasture growth. I identified two potential breeding goals, one for regions with low or high pasture growth reliability and one for regions with medium reliability of pasture growth. Regions with low or high reliability of pasture growth had similar breeding goals because the relationship between economic values and reliability of pasture growth were not linear for some traits. Therefore, farmers can customise breeding goals depending on the reliability of pasture growth on their farm.



A mutation breeding program to improve the quality of the oil crop Crambe abyssinica
Cheng, J. - \ 2014
University. Promotor(en): Richard Visser, co-promotor(en): Elma Salentijn; Robert van Loo. - Wageningen : Wageningen University - ISBN 9789461739629 - 180
crambe abyssinica - plantenveredeling - moleculaire veredeling - veredelingsprogramma's - mutaties - olieleverende planten - brandstofgewassen - biobased economy - plant breeding - molecular breeding - breeding programmes - mutations - oil plants - fuel crops
Since C. abyssinica is considered to be an ideal crop for industrial oil, further improving the value of crambe oil is of importance. The value of crambe oil can be improved by increasing the C22:1 content or reducing polyunsaturated fatty acids (PUFA). To improve crambe oil by a non-GM approach, a mutant population (12,480 lines) was established from the EMS-treated seeds of C. abyssinica cv. ‘Galactica’. Furthermore, the mutants in CaFAD2 were detected by 454-amplicon sequencing and Illumina sequencing.
Het Nederlands Groot-Yorkshire varken
Slaghuis, H. ; Oldenbroek, J.K. - \ 2014
Zeldzaam huisdier 39 (2014)2. - ISSN 0929-905X - p. 20 - 21.
varkensfokkerij - varkensrassen - zeldzame rassen - veredelingsprogramma's - fokwaarde - rassen (dieren) - pig breeding - pig breeds - rare breeds - breeding programmes - breeding value - breeds
De Bonte Bentheimer en het Nederlands landvarken hebben al de volle aandacht van de SZH. Maar verdient het Groot-Yorkshirevarken die aandacht ook niet? In de Nederlandse varkensfokkerij is dit ras indertijd gefokt voor de productie van slagersvarkens. In dit artikel wordt de geschiedenis van het Nederlands Groot-Yorkshirevarken op een rij gezet en aangegeven hoe het er nu voorstaat.
Snow shoes and sandals? : genetic aspects of heat stress sensitivity and sow reproduction
Bloemhof, S. - \ 2013
University. Promotor(en): Johan van Arendonk; I. Misztal, co-promotor(en): E.F. Knol; Liesbeth van der Waaij. - S.l. : s.n. - ISBN 9789461735881 - 173
zeugen - warmtestress - diergenetica - gevoeligheid - geslachtelijke voortplanting - voortplantingsvermogen - kritische temperatuur - hittetolerantie - selectief fokken - genetische correlatie - veredelingsprogramma's - varkensfokkerij - sows - heat stress - animal genetics - sensitivity - sexual reproduction - reproductive performance - critical temperature - heat tolerance - selective breeding - genetic correlation - breeding programmes - pig breeding

Globally the average size of pig herds are increasing and amount of labour spent per sow / finisher pig is decreasing. These changes require sows which need less management interventions. In addition to easier manageable sows modern genotypes will also need to be more adaptable considering that global temperatures are expected to increase and pork production is partially moving to warmer climates. The end result is that commercial pigs nowadays will potentially face more heat stress challenges during their productive lives.

In this thesis, a model was developed which was used to estimate upper critical temperatures for sows’ reproductive performance. Additionally the possibility to breed for reduced heat tolerance of sows was investigated. Therefore heritability for the random regression slope of farrowing rate against increasing temperature at day of insemination (= heat tolerance) and the genetic correlation between farrowing rate and heat tolerance was estimated.Commercial production pigs are crossbreds farmed all over the world. In contrast, selection is practiced mainly in temperate climates, in nucleus herds using purebred pigs. The success of genetic selection depends on how much genetic progress is realized in crossbred pigs. Within this thesis these genetic correlations for farrowing rate between purebreds and crossbreds were estimated.

Sow productivity depends on a number of related traits, such as ovulation rate, the number of litters per sow per year, the number of weaned piglets per sow per year, and the length of productive live. Traditionally pig breeding programs have improved sow productivity by increasing number weaned piglets per sow per year. To improve herd-level litters per sow per year a new trait was proposed called problem free sow production by parity, which incorporates the traits interval weaning first insemination, non-return rate, farrowing rate, and selection for next parity. Heritability of problem free sow production and genetic correlations with other sow production traits were estimated.

The main conclusion of this thesis was that it is possible to select for improved heat resistance in addition to improved commercial production levels in commercial pigs. However, genetic correlation between production in temperate and hot climates is high. This high correlation implies that, within-line, pigs with the best performance in a hot climate will be the best in temperate climate too. Most important for the success of a pig breeding program is to define appropriate breeding goals which are based on the environment(s) that market pigs are expected to perform in. The overall data collection for the genetic evaluation needs to be done in those specific environments and this will favour pigs which are able to produce over more than one specific environment.

Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)
Trong, T.Q. - \ 2013
University. Promotor(en): Johan van Arendonk, co-promotor(en): Hans Komen. - S.l. : s.n. - ISBN 9789461735447 - 176
oreochromis niloticus - selectief fokken - veredelingsprogramma's - genetische parameters - voortplantingskenmerken - kuitschieten - voortplantingspotentieel - vruchtbaarheid - heritability - genotype-milieu interactie - groeitempo - dierveredeling - visteelt - aquacultuur - selective breeding - breeding programmes - genetic parameters - reproductive traits - spawning - fecundity - fertility - genotype environment interaction - growth rate - animal breeding - fish culture - aquaculture

The aim of this thesis was to optimise the selective breeding program for Nile tilapia in the Mekong Delta region of Vietnam. Two breeding schemes, the “classic” BLUP scheme following the GIFT method (with pair mating) and a rotational mating scheme with own performance selection and natural group spawning, were investigated. In the latter scheme, the aim was to mimic natural spawning conditions of Nile tilapia to reduce the time for family production; however reconstruction of pedigrees using DNA markers to monitor inbreeding is required. Parental assignment using microsatellites and SNPs showed that exclusion- and likelihood-based methods are equally good for parental assignment, provided that good marker sets with high exclusion power, such as SNPs, are available and that all parents are sampled. Prolonged family production is problematic in BLUP breeding value estimation and could be a consequence of selection for harvest weight in Nile tilapia. Using a natural mating design with single males mated to multiple females in groups, 85% of the successful spawns were collected within 20 days. Genetic correlations between harvest weight and spawning success ranged from 0.48 to 0.52, provided that the mating period is limited to 20-32 days. We conclude that Nile tilapia favour mating in groups, and that selection for harvest weight in GIFT should improve spawning success of Nile tilapia. Moreover, harvest weight and body weight at spawning have favourable genetic correlations with number of eggs, relative fecundity, and number of swim-up fry, which are the desired characteristics for Nile tilapia seed production. High-input cages and low-input ponds are the dominant production systems for tilapia in the Mekong Delta. We show that selection in nucleus ponds will produce desired correlated responses in Nile tilapia grown in river-cages. Moreover, they are expected to develop a more rotund and thicker body shape at the same length compared to fish grown in ponds. In conclusion, we recommend the use of the ‘single male, multiple females’ mating as this will reduce the generation interval by 2 months, thereby increasing genetic gain by about 20%. A rotational mating scheme, with at least 4 cohorts, can be incorporated into the GIFT selection scheme to further reduce inbreeding, to estimate pond effects and to secure the breeding material. Finally, a reliable multiplier system is important to sustain the current Nile tilapia breeding program, which can provide sufficient improved fry (>50 million per year) for the whole Mekong Delta Nile tilapia production.

Potato quality traits: variation and genetics in Ecuadorian potato landraces
Cuesta Subía, X. - \ 2013
University. Promotor(en): Richard Visser, co-promotor(en): Ben Vosman; Christian Bachem. - S.l. : s.n. - ISBN 9789461734945 - 197
solanum tuberosum - solanum - aardappelen - landrassen - wilde verwanten - kwaliteit - ideotypen - genetische variatie - kwantitatieve kenmerken - veredelingsprogramma's - plantenveredeling - genetische bronnen van plantensoorten - ecuador - potatoes - landraces - wild relatives - quality - ideotypes - genetic variation - quantitative traits - breeding programmes - plant breeding - plant genetic resources
One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction
Sae-Lim, P. - \ 2013
University. Promotor(en): Johan van Arendonk, co-promotor(en): Hans Komen; A. Kause. - S.l. : s.n. - ISBN 9789461734648 - 200
regenboogforel - dierveredeling - veredelingsprogramma's - genotype-milieu interactie - optimalisatie - kenmerken - genetische winst - selectief fokken - simulatie - visteelt - aquacultuur - rainbow trout - animal breeding - breeding programmes - genotype environment interaction - optimization - traits - genetic gain - selective breeding - simulation - fish culture - aquaculture

Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.

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