Staff Publications

Staff Publications

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    '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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    Estimation of litter size variability phenotypes in Large White sows
    Dobrzański, Jan ; Mulder, Han A. ; Knol, Egbert F. ; Szwaczkowski, Tomasz ; Sell-Kubiak, Ewa - \ 2020
    Journal of Animal Breeding and Genetics (2020). - ISSN 0931-2668
    pigs - reproductive traits - total number born - trait's variation

    The objective of this study was to obtain new phenotypes of phenotypic variability for the total number born (TNB) in pigs using the residual variance of TNB. The analysis was based on 246,799 Large White litter observations provided by Topigs Norsvin. Three animal models were used to obtain estimates of residual variance for TNB: the basic model (BM) containing fixed effects of farm–year and season and random effects of animal and permanent environmental sow, the basic model with an additional fixed effect of parity (BMP) and a random regression model (RRM). The within-individual variance of the residuals was calculated and log-transformed to obtain three new variability traits: LnVarBM, LnVarBMP and LnVarRRM. Then, (co)variance components, heritability, the genetic coefficient of variation at the standard deviation level (GCVSDe) and genetic correlations between the three LnVar's and between the LnVar's and mean total number born (mTNB) were estimated with uni-, bi- and trivariate models. Results indicated that genetically LnVar's are the same trait and are positively correlated with the mTNB (~0.60). Thus, both traits should be included in breeding programmes to avoid an increase in TNB variability while selecting for increased TNB. Heritability of the LnVar's was estimated at 0.021. The GCVSDe for LnVar's showed that a change of 8% in residual standard deviation of TNB could be obtained per generation. Those results indicate that phenotypic variability of litter size is under genetic control, thus it may be improved by selection.

    Superfetation reduces the negative effects of pregnancy on the fast-start escape performance in live-bearing fish
    Fleuren, Mike ; Leeuwen, Johan L. van; Pollux, Bart J.A. - \ 2019
    Proceedings of the Royal Society. B: Biological Sciences 286 (2019)1916. - ISSN 0962-8452 - 1 p.
    biomechanics - C-start - evolution - Poeciliidae - reproductive traits - viviparity

    Superfetation, the ability to simultaneously carry multiple litters of different developmental stages in utero, is a reproductive strategy that evolved repeatedly in viviparous animal lineages. The evolution of superfetation is hypothesized to reduce the reproductive burden and, consequently, improve the locomotor performance of the female during pregnancy. Here, we apply new computer-vision-based techniques to study changes in body shape and three-dimensional fast-start escape performance during pregnancy in three live-bearing fishes (family Poeciliidae) that exhibit different levels of superfetation. We found that superfetation correlates with a reduced abdominal distension and a more slender female body shape just before parturition. We further found that body slenderness positively correlates with maximal speeds, curvature amplitude and curvature rate, implying that superfetation improves the fast-start escape performance. Collectively, our study suggests that superfetation may have evolved in performance-demanding (e.g. high flow or high predation) environments to reduce the locomotor cost of pregnancy.

    Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy
    Bergh, Erik van den - \ 2017
    Wageningen University. Promotor(en): M.E. Schranz; Y. van de Peer. - Wageningen : Wageningen University - ISBN 9789463431705 - 106
    capparaceae - genomics - polyploidy - evolution - genomes - reproductive traits - flowers - colour - glucosinolates - genetic variation - biosystematics - taxonomy - identification - capparaceae - genomica - polyploïdie - evolutie - genomen - voortplantingskenmerken - bloemen - kleur - glucosinolaten - genetische variatie - biosystematiek - taxonomie - identificatie

    As more and more species have been sequenced, evidence has been piling up for a fascinating phenomenon that seems to occur in all plant lineages: paleopolyploidy. Polyploidy has historically been a much observed and studied trait, but until recently it was assumed that polyploids were evolutionary dead-ends due to their sterility. However, many studies since the 1990’s have challenged this notion by finding evidence for ancient genome duplications in many genomes of current species. This lead to the observation that all seed plants share at least one ancestral polyploidy event. Another polyploidy event has been proven to lie at the base of all angiosperms, further signifying the notion that ancient polyploidy is widespread and common. These findings have led to questions regarding the apparent disadvantages that can be observed in a first generation polyploid. If these disadvantages can be overcome however, duplication of a genome also presents an enormous potential for evolutionary novelty. Duplicated copies of genes are able to acquire changes that can lead to specialization of the duplicated pair into two functions (subfunctionalization) or the development of one copy towards an entirely new function (neofunctionalization).

    Currently, most research towards polyploidy has focused on the economically and scientifically important Brassicaceae family containing the model plant Arabidopsis thaliana and many crops such as cabbage, rapeseed, broccoli and turnip. In this thesis, I lay the foundations for the expansion of this scope to the Cleomaceae, a widespread cosmopolitan plant family and a sister family of Brassicaceae. The species within Cleomaceae are diverse and exhibit many scientifically interesting traits. They are also in a perfect position phylogenetically to draw comparisons with the much more studied Brassicaceae. I describe the Cleomaceae and their relevance to polyploid research in more detail in the Introduction. I then describe the important first step towards setting up the genetic framework of this family with the sequencing of Tarenaya hassleriana in Chapter 1.

    In Chapter 2, I have studied the effects of polyploidy on the development of C4 photosynthesis by comparing the transcriptome of C3 photosynthesis based species Tarenaya hassleriana with the C4 based Gynandropsis gynandra. C4 photosynthesis is an elaboration of the more common C3 form of photosynthesis that concentrates CO2 in specific cells leading to decreased photorespiration by the RuBisCO and higher photosynthetic efficieny in low CO2 environments. I find that polyploidy has not led to sub- or neofunctionalization towards the development of this trait, but instead find evidence for another important phenomenon in postpolyploid evolution: the dosage balance hypothesis. This hypothesis states that genes which are dependent on specific dosage levels of their products will be maintained in duplicate; any change in their function would lead to dosage imbalance which would have deleterious effects on their pathway. We show that most genes involved in photosynthesis have returned to single copy in G. gynandra and that the changes leading to C4 have mostly taken place at the expression level confirming current assumptions on the development of this trait.

    In Chapter 3, I have studied the effects of polyploidy on an important class of plant defence compounds: glucosinolates. These compounds, sometimes referred to as ‘mustard oils’, play an important role in the defence against herbivores and have radiated widely in Brassicaceae to form many different ‘flavors’ to deter specific herbivores. I show that in Cleomaceae many genes responsible for these compounds have benefited from the three rounds of polyploidy that T. hassleriana has undergone and that many duplicated genes have been retained. We also show that more than 75% is actively expressed in the plant, proving that the majority of these duplications has an active function in the plant.

    Finally, in Chapter 4 I investigate a simple observation made during experiments with T. hassleriana in the greenhouse regarding the variation in flower colour between different individuals: some had pink flowers and some purple. Using LC-PDA mass spectrometry we find that the two colours are caused by different levels of two anthocyanin pigments, with cyanidin dominating in the purple flowers and pelargonidin being more abundant in pink flowers. Through sequence comparison and synteny analysis between A. thaliana and T. hassleriana we find the orthologs of the genes involved in this pathway. Using a Genotyping by Sequencing method on a cross between these two flower colours, we produce a collection of SNP markers on the reference genome. With these SNPs, we find two significant binary trait loci, one of which corresponds to the location of the F3’H ortholog which performs the conversion of a pelargonidin precursor to a cyanidin precursor.

    In the General Conclusion, I combine all findings of the previous chapters and explain how they establish part of a larger species framework to study ancient polyploidy in angiosperms. I then put forth what these findings can mean for possible future research and the directions that are worth to be explored further.

    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.

    A genome-wide association study reveals a novel candidate gene for sperm motility in pigs
    Diniz, D.B. ; Lopes, M.S. ; Broekhuijse, M.L.W.J. ; Lopes, P.S. ; Harlizius, B. ; Guimaraes, S.E.F. ; Duijvesteijn, N. ; Knol, E.F. ; Silva, F.F. - \ 2014
    Animal Reproduction Science 151 (2014)3-4. - ISSN 0378-4320 - p. 201 - 207.
    assisted semen analysis - linkage disequilibrium - reproductive traits - fertility - boar - quality - casa - expression - parameters - selection
    Sperm motility is one of the most widely used parameters in order to evaluate boar semen quality. However, this trait can only be measured after puberty. Thus, the use of genomic information appears as an appealing alternative to evaluate and improve selection for boar fertility traits earlier in life. With this study we aimed to identify SNPs with significant association with sperm motility in two different commercial pig populations and to identify possible candidate genes within the identified QTL regions. We performed a single-SNP genome-wide association study using genotyped animals from a Landrace-based (L1) and a Large White-based (L2) pig populations. For L1, a total of 602 animals genotyped for 42,551 SNPs were used in the association analysis. For L2, a total of 525 animals genotyped for 40,890 SNPs were available. After the association analysis, a false discovery rate q-value
    Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression
    Bosse, M. ; Megens, H.J.W.C. ; Frantz, L.A.F. ; Madsen, O. ; Paudel, Y. ; Duijvestein, N. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2014
    Nature Communications 5 (2014). - ISSN 2041-1723 - 8 p.
    hydrocarbon dioxin receptor - recent positive selection - haplotype structure - molecular characterization - reproductive traits - domestic pig - wide snp - evolution - models - polymorphisms
    The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the ¿AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds.
    Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)
    Trong, T.Q. - \ 2013
    Wageningen 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 - oreochromis niloticus - selective breeding - breeding programmes - genetic parameters - reproductive traits - spawning - fecundity - fertility - heritability - 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.

    Effects of milk fat composition, DGAT1, and SCD1 on fertility traits in Dutch Holstein cattle
    Demeter, R.M. ; Schopen, G.C.B. ; Oude Lansink, A.G.J.M. ; Meuwissen, M.P.M. ; Arendonk, J.A.M. van - \ 2009
    Journal of Dairy Science 92 (2009)11. - ISSN 0022-0302 - p. 5720 - 5729.
    genetic-parameters - reproductive traits - italian holsteins - acid-composition - dairy-products - genome scan - bovine-milk - rat ovary - polymorphism - desaturase
    Recently, selective breeding was proposed as a means of changing the fatty acid composition of milk to improve its nutritional quality. Before implementing such breeding objectives, effects on other economically important traits should be investigated. The objectives of this study were to examine 1) the effect of milk fat composition, and 2) the effect of polymorphisms of DGAT1 and SCD1 genes on female fertility in commercial Dutch Holstein-Friesian cattle. Data on 1,745 first-lactation cows were analyzed by fitting linear mixed models. We found that higher concentrations of trans fatty acids within total milk fat negatively affected reproductive performance. Furthermore, results suggested a potential effect of the DGAT1 polymorphism on nonreturn rates for insemination 28 and 56 d after the first service. Our results can be used to assess the correlated effects of breeding for improved milk fat composition on reproduction, thereby allowing for better evaluation of breeding programs before implementation
    A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore ( Bos indicus) beef cattle
    Rosa, A.J.M. ; Bijma, P. ; Oliveira, H.N. ; Lobo, R.B. ; Arendonk, J.A.M. van - \ 2007
    Genetics and Molecular Biology 30 (2007)3. - ISSN 1415-4757 - p. 552 - 559.
    quantitative trait loci - bovine preimplantation embryos - genetic-linkage map - dairy-cattle - breeding schemes - reproductive traits - outbred population - multistage selection - efficient production - single blastomere
    We used deterministic simulation of four alternative multiple ovulation and embryo manipulation (MOET) closed nucleus schemes to investigate the benefits of using marker-assisted selection (MAS) of Nellore (Bos indicus) beef cattle embryos prior to transplantation to reduce the age at first calving (AFC). We found that MAS resulted in increased genetic gain as compared to selection without AFC quantitative trait loci (AFC-QTL) information. With single-stage selection the genetic response (GR) increased as follows: GR = 0.68% when the AFC-QTL explained 0.02 of the AFC additive genetic variance (s2A); GR = 1.76% for AFC-QTL explaining 0.05 s2A; GR = 3.7% for AFC-QTL explaining 0.1 s2A; and GR = 55.76% for AFC-QTL explaining 0.95 s2A. At the same total selected proportion, two-stage selection resulted in less genetic gain than single stage MAS at two-years of age. A single stage selection responses of > 95% occurred with pre-selected proportions of 0.4 (0.1 s2A explained by AFC-QTL), 0.2 (0.3 s2A explained by AFC-QTL) and 0.1 (0.5 s2A explained by AFC-QTL), indicating that the combined use of MAS and pre-selection can substantially reduce the cost of keeping recipient heifers in MOET breeding schemes. When the number of recipients was kept constant, the benefit of increasing embryo production was greater for the QTL explaining a higher proportion of the additive genetic variance. However this advantage had a diminishing return especially for QTL explaining a small proportion of the additive genetic variance. Thus, marker assisted selection of embryos can be used to achieve increased genetic gain or a similar genetic response at reduced expense by decreasing the number of recipient cows and number of offspring raised to two-years of age.
    Economic values for traits in breeding objectives for sheep in the tropics: impact of tangible and intangible benefits
    Kosgey, I.S. ; Arendonk, J.A.M. van; Baker, R.L. - \ 2004
    Livestock Production Science 88 (2004)1-2. - ISSN 0301-6226 - p. 143 - 160.
    accelerated lambing system - litter size - reproductive traits - genetic-parameters - small ruminants - ewes - derivation - livestock - survival - weights
    In traditional management systems in the tropics, sheep constitute a source of easily convertible capital for financing purposes and insurance, a means of cultural and ceremonial functions, and a source of prestige, meat, manure and skins. In this study, breeding objectives were derived for an indigenous tropical sheep breed under pastoral production. Economic values were calculated for five situations: (i) base accounting for both tangible and intangible roles of sheep; (ii) accounting for manure, skins and intangible roles; (iii) accounting for 20% of animals sold, insurance, manure and skins; (iv) accounting for intangible roles only; and (v) accounting for tangible roles only. Sensitivity analysis to different levels of financing and insurance benefit factors, reproduction, survival and live weight traits was performed for the situation accounting for both tangible and intangible roles, and with a constant number of ewes. The economic value for a trait considered in a particular situation was calculated from the difference between the average performance level of the trait before and after incrementing it by one unit. The traits considered were litter size, lambing frequency, pre-weaning and post-weaning lamb survival to 12 months, ewe survival, 12-month lamb live weight, mature ewe live weight, consumable meat and kg manure dry matter sold ewe(-1) year(-1). Genirally, in descending order of the profits and economic values, the situations studied ranked as follows: (i), (v), (iii), (ii) and (iv). For the base situation, financing and insurance benefits accounted for 13% and 6% of the total revenues, respectively. Situation (v) had a profit that was about 35% lower relative to situation (i). In terms of genetic standard deviations, the economic values (US$ ewe(-1) year(-1)) for the base situation were: 2.81 for litter size, 6.40 for lambing frequency, 0.02 for pre-weaning survival, 0.03 for post-weaning survival, 0.05 for ewe survival, 1.81 for 12-month lamb live weight, 0.43 for mature ewe live weight, 0.09 for consumable meat and 0.01 for kg manure dry matter sold (ewe(-1) year(-1)). The economic values indicate that litter size, lambing frequency and 12-month lamb live weight are likely to be important traits in pastoral production. Sensitivity analysis showed that future economic values for all the traits considered, except kg manure dry matter sold ewe(-1) year(-1), might change depending on levels of intangible benefit factors. Ewe survival and mature ewe live weight were not responsive to changes in reproductive traits, and pre- and post-weaning traits, and vice versa. It is concluded that it is necessary to include the intangible roles of sheep in tropical breeding programmes. (C) 2003 Elsevier B.V. All rights reserved.
    Voortplanting bij de boommarter Martes martes in Nederland
    Broekhuizen, S. ; Müskens, G.J.D.M. - \ 2000
    Lutra 43 (2000). - ISSN 0024-7634 - p. 205 - 214.
    martes - martes martes - voortplanting - voortplantingskenmerken - nederland - populatie-ecologie - populatiebiologie - martes - martes martes - reproduction - reproductive traits - population ecology - netherlands - population biology
    Het stadium van voortplantingskenmerken bij boommarters is bestudeerd bij boommarters die in het verkeer waren doodgereden
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