Staff Publications

Staff Publications

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

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

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

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Identification of metabolites involved in heat stress response in different tomato genotypes
Paupière, Marine J. - \ 2017
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Arnaud Bovy; Yury Tikunov. - Wageningen : Wageningen University - ISBN 9789463431842 - 168
solanum lycopersicum - tomatoes - genotypes - heat stress - heat tolerance - pollen - metabolomes - metabolites - metabolomics - tomaten - genotypen - warmtestress - hittetolerantie - stuifmeel - metabolomen - metabolieten - metabolomica

Tomato production is threatened by climate change. High temperatures lead to a decrease of fruit set which correlates with a decrease of pollen fertility. The low viability of tomato pollen under heat stress was previously shown to be associated with alterations in specific metabolites. In this thesis, we used untargeted metabolomics approaches to broaden the identification of metabolites affected by heat stress. We assessed the suitability of pollen isolation methods for metabolomics analysis and considered the pitfalls for our further analysis. We explored the developmental metabolomes of pollen and anthers of different tomato genotypes under control and high temperature conditions and identified that microsporogenesis is a critical developmental stage for the production of mature and fertile pollen grain under heat stress. Several metabolites were putatively associated with tolerance to high temperature such as specific flavonoids, polyamines and alkaloids. These metabolites can be further used as markers in breeding programs to develop new genotypes tolerant to high temperatures.

Invloed van gewassen op bodemkwaliteit: Variatie tussen genotypen : een verkennende literatuurstudie voor ruwvoedergewassen
Wiel, Clemens C.M. van de; Linden, Gerard van der; Sukkel, Wijnand - \ 2017
Wageningen : Wageningen Plant Research (Rapport / Wageningen Plant Research 668) - 17
voederplanten - ruwvoer (forage) - bodemkwaliteit - genotypen - fodder plants - forage - soil quality - genotypes
Gewassen beïnvloeden de bodem waarop ze geteeld worden. In deze verkennende literatuurstudie is onderzocht wat er bekend is over variatie tussen verschillende genotypen/plantenrassen met betrekking tot hun effect op bodemkwaliteit voor een aantal ruwvoedergewassen, in het bijzonder Maïs (Zea mays), Engels raaigras (Lolium perenne) en Witte klaver (Trifolium repens). Dergelijke variatie zou mogelijkheden kunnen bieden om via veredeling en het inzetten van specifieke rassen de bodemkwaliteit te verbeteren. Er is betrekkelijk weinig onderzoek vanuit deze invalshoek gedaan. De focus van de studie was gericht op variatie in wortelarchitectuur, en wortelexudatie en wortelafsterving/nieuwvorming in relatie tot het organische stof gehalte en beschikbaarheid van nutriënten, en de bodem biota, met name mycorrhiza.
Development and application of a 20K SNP array in potato
Vos, Peter - \ 2016
Wageningen University. Promotor(en): Richard Visser; Fred van Eeuwijk, co-promotor(en): Herman van Eck. - Wageningen : Wageningen University - ISBN 9789462579569 - 166
solanum tuberosum - potatoes - genotypes - single nucleotide polymorphism - data analysis - plant breeding - linkage disequilibrium - genome analysis - tetraploidy - aardappelen - genotypen - gegevensanalyse - plantenveredeling - verstoord koppelingsevenwicht - genoomanalyse - tetraploïdie

In this thesis the results are described of investigations of various application of genome wide SNP (single nucleotide polymorphism) markers. The set of SNP markers was identified by GBS (genotyping by sequencing) strategy. The resulting dataset of 129,156 SNPs across 83 tetraploid varieties was used directly to map traits, but also as a basis for the development of a 20K SNP array in Potato (Solanum tuberosum L.). Subsequently this array, named SolSTW, was used to collect genotypic data from 569 potato genotypes. This dataset offered insight in the breeding history of potato, population structure, linkage disequilibrium (LD) and the potential of GWAS (genome wide association studies) in potato.

In Chapter 2 we describe to development of the SolSTW 20K Infinium SNP array. One third of the SNPs on this array originate from the well-known SolCAP 8303 SNP array. The other SNPs are a subset from a targeted re-sequencing project of 83 tetraploid potato varieties. Because of the high SNP density in potato only a limited number of SNPs is suitable for assay development on a SNP array. An obvious outcome is that flanking SNPs contribute to assay failure, particularly for assays with SNPs located in introns. We used fitTetra software to cluster the distribution of captured signals of each marker into the expected five genotypic classes (nulliplex, simplex, duplex, triplex, quadruplex), resulting in a dataset with 14,530 SNP markers. Subsequently the genotypic data obtained with the SolSTW array was used to characterize a set of 569 potato varieties, advanced breeding clones and progenitors. This resulted in the identification of several footprints of potato breeding. Firstly SNPs were dated i.e. the year of market release of the first variety showing polymorphism for a SNP locus is an indication of the ancestry of a SNP. In such a way we identified SNPs with an ancestry tracing back to heirloom varieties, and SNPs (post-1945 SNPs) tracing back to wild species used in modern introgression breeding. Secondly, the changes in allele frequency were calculated over time. Most SNPs show a relative stable allele frequency over time, and very limited genetic variation is removed from the gene-pool of potato i.e genetic erosion is almost absent. Therefore we conclude that 100 years of breeding has not been able to get rid of non-beneficial genetic variation. Only a limited number of SNPs show a rapid increased in allele frequency, which can be explained by positive selection for disease resistance by breeders, or the more frequent use of several founders.

Better understanding of the genome wide decay of Linkage Disequilibrium (LD) and population structure offers relevant knowledge to perform and interpret the results of a genome wide association study (GWAS) (Chapter 3). Linkage disequilibrium (LD) is a complex phenomenon, and the influence of the factors shaping LD in tetraploids is hardly studied. Therefore we used simulated data to disentangle and therewith understand often-confounded factors underlying LD-decay. We simulated datasets differing in number of haplotypes in a population, and differing in percentage of haplotype specific SNPs. In these simulations we observed that the choice of an estimator of LD-decay has a major effect on the outcome of an LD-decay estimate, while the true LD-decay remains the same. Based on the simulation we conclude that a 90% percentile and a so-called D1/2 (the distance where 50% of the initial LD is decayed) performed best to estimate and compare LD-decay in potato. To understand the various aspects of LD-decay in the variety panel of 537 varieties, the panel was subdivided in several groups based on the age of a variety and the population structure groups. This resulted in the identification of LD-decay over time, i.e in relatively young varieties the average size of the LD-blocks is smaller. The differences between subpopulations were smaller and are most likely the effect of the population structure. We also observed that there are very long LD-blocks caused by introgression breeding and that different a priori MAF-thresholds also can influence the outcome of LD-decay estimation.

Having both LD-decay and population structure defined a genome wide association study (GWAS) was conducted (Chapter 4). For this purpose α-solanine and α-chaconine were measured in potato tubers. Subsequently the sum of both (total SGA) and the ratio between the two were used to discover QTLs for these traits in a GWAS. Additionally we used three bi-parental populations to validate the GWAS results. Total SGA content was confounded with population structure and therefore it was difficult to explain all phenotypic variation with SNP markers. Two QTLs (Sgt1.1 and Sgt11.1) were identified which could be validated in one of the segregating populations. The ratio between α-solanine and α-chaconine was not confounded with population structure, resulted in the identification of two major-effect QTLs (Sgr7.1 & Sgr8.1) located near the candidate genes SGT1 and SGT2, which are known for being responsible in the final steps towards either α-solanine or α-chaconine. The QTL Sgr8.1 could be validated, however similar phenotypes were explained by different haplotypes in two populations. We show that population structure, low frequent alleles and genetic heterogeneity may explain to some degree the missing heritability in GWAS in potato.

In Chapter 5 we describe how the method of graphical genotyping, which is widely used in diploid bi-parental populations, can be applied in a variety panel of tetraploid varieties. We show that a few discrete filtering steps in Excel can be used to display patterns that are visual representations of introgression segments and the locations of historical recombination events. Using this method we identified introgression segments from Solanum vernei including the Gpa5 locus on chromosome 5 and Solanum stoloniferum introgression segment including a gene involved in resistance to Potato Virus Y on chromosome 11. This method requires that the haplotypes that cause the phenotypic effect have to be identical by descent (IBD).

In the final chapter 6 the results of chapter 2 to 5 are discussed. We look forward on how our results can be used in future research and applied in marker-assisted breeding. Additionally some new GWAS results are presented for tuber flesh colour, foliage maturity and resistance to Globodera pallida pathotype 3.

Horsegene database: an efficient and secure way to store and share phenotypes and genotypes between researchers
Velie, B.D. ; Shrestha, M. ; Schurink, A. ; Ducro, B.J. ; Buys, N. ; lindgren, G. - \ 2015
phenotypes - genotypes - horsegene database
Using reliable state-of-the-art genomic technologies to identify genetic markers for heritable diseases in harses, the Horsegene co.nsortium, comprised of both research institutions and industry partners, aimed to provide a genetic alternative to traditional breeding methods. Funded by the EU's Seventh Framework Programme, this collaboration brought together the efforts of multiple European research groups that had been werking independently on the
genetics of disease susceptibility in harses for many years. As a result, a database capable of securely and efficiently storing phenotypic and genotypic information for harses was developed in order to better facilitate the sharing of information between researcher partners. Here we describe the Horsegene Database functionality and comment on its value and potential application outside of the Horsegene consortium. The database is capable of housing unlimited pedigree and phenotype data as well as genotype data from multiple array platforms. Uploading to the database requires a researcher to be a registered user and although the database requires files to be in a specific format, file alteration is minimal and a file format guide is provided. Once uploaded, the majority of data is not viewable or downloadable to anyone except these responsible for m~intaining the functionality of the database. However, genera! information (animal ids changed to prevent identification of any
individual) can be viewed via the Horsegene Database web interface. The web interface displays information on breed, birthdate, disease phenotype(s) (e.g.
OC=unaffected; IBH=affected; CPL=unaffected), and the genotyping platforms available for each individual. In addition, information on the principal investigator (PI) and institution associated with each animal is provided. This information can then be used to search for individuals expressing a specific disease, certain breeds, or individuals with genotypes from a specific array platform. Registered users then have the option to tick boxes for any individual
or group of individuals in which they would like to request data. The web interface then automatically sends an email request to the Pl(s) .associated with those individuals and the Pl(s) has the option to grant or deny the request. lf granted, the registered user receives an email that contains information on their time-restricted download access of information corresponding only the individuals they requested . The security and simplicity of the Horsegene Database is an ideal way for institutions both within and outside the Horsegene consortium to collaborate and share data in the future. Adoption of the Horsegene Database by research institutions from outside the Horsegene
consortium would not only make collaborations between institutions more probable, but it is also likely to increase the power of heritable disease studies in the future.
Evaluation of two commercial, rapid, ELISA kits testing or scrapie in retro-pharyngeal lymph nodes in sheep
Kittelberger, R. ; McIntuyre, L. ; Watts, S. ; MacDiarmid, S. ; Hannah, M.J. ; Jenner, J. ; Bueno, R. ; Swainsbury, R. ; Langeveld, J.P.M. ; Keulen, L.J.M. van; Zijderveld, F.G. van; Wemheuer, W.M. ; Richt, J.A. ; Sorenson, S.J. ; Pigott, C.J. ; O'Keefe, J.S. - \ 2014
New Zealand Veterinary Journal 62 (2014)6. - ISSN 0048-0169 - p. 343 - 350.
natural scrapie - prion protein - immunohistochemical detection - new-zealand - prp - accumulation - diagnosis - genotypes - tissues - brain
AIMS: To estimate the number of cases of scrapie that would occur in sheep of different prion protein (PrP) genotypes if scrapie was to become established in New Zealand, and to compare the performance of two commercially available, rapid ELISA kits using ovine retro-pharyngeal lymph nodes (RLN) from non-infected and infected sheep of different PrP genotypes. METHODS: Using published data on the distribution of PrP genotypes within the New Zealand sheep flock and the prevalence of cases of scrapie in these genotypes in the United Kingdom, the annual expected number of cases of scrapie per genotype was estimated, should scrapie become established in New Zealand, assuming a total population of 28 million sheep. A non-infected panel of RLN was collected from 737 sheep from New Zealand that had been culled, found in extremis or died. Brain stem samples were also collected from 131 of these sheep. A second panel of infected samples comprised 218 and 117 RLN from confirmed scrapie cases that had originated in Europe and the United States of America, respectively. All samples were screened using two commercial, rapid, transmissible spongiform encephalopathy ELISA kits: Bio-Rad TeSeE ELISA (ELISA-BR), and IDEXX HerdChek BSE-Scrapie AG Test (ELISA-ID). RESULTS: If scrapie became established in New Zealand, an estimated 596 cases would occur per year; of these 234 (39%) and 271 (46%) would be in sheep carrying ARQ/ARQ and ARQ/VRQ PrP genotypes, respectively. For the non-infected samples from New Zealand the diagnostic specificity of both ELISA kits was 100%. When considering all infected samples, the diagnostic sensitivity was 70.4 (95% CI=65.3-75.3)% for ELISA-BR and 91.6 (95% CI=88.2-94.4)% for ELISA-ID. For the ARQ/ARQ genotype (n=195), sensitivity was 66.2% for ELISA-BR and 90.8% for ELISA-ID, and for the ARQ/VRQ genotype (n=107), sensitivity was 81.3% for ELISA-BR and 98.1% for ELISA-ID. CONCLUSIONS: In this study, the ELISA-ID kit demonstrated a higher diagnostic sensitivity for detecting scrapie in samples of RLN from sheep carrying scrapie-susceptible PrP genotypes than the ELISA-BR kit at comparable diagnostic specificity.
Feather pecking and monoamines - a behavioral and neurobiological approach
Kops, M.S. - \ 2014
Wageningen University; Utrecht University. Promotor(en): B. Olivier; O. Güntürkün, co-promotor(en): S.M. Korte; Liesbeth Bolhuis. - Utrecht, The Netherlands : Utrecht University - ISBN 9789039361283 - 172
pluimveehouderij - hennen - verenpikken - diergedrag - dierenwelzijn - pluimvee - diergezondheid - dierlijke productie - serotonine - dopamine - fenotypen - genotypen - neurotransmitters - invloeden - poultry farming - hens - feather pecking - animal behaviour - animal welfare - poultry - animal health - animal production - serotonin - phenotypes - genotypes - influences
Severe feather pecking (SFP) remains one of the major welfare issues in laying hens. SFP is the pecking at and pulling out of feathers, inflicting damage to the plumage and skin of the recipient. The neurobiological profile determining the vulnerability of individual hens to develop into a severe feather pecker is unknown, although brain monoamines such as serotonin (5-HT) and dopamine (DA) seem to play a role. Previous studies related lower 5-HT and DA turnover ratios to an increased risk to develop SFP.In this thesis, monoamine levels in brain areas involved in emotional regulation and motor control were compared between phenotypically and genetically selected high and low feather peckers at different ages. It was found that adult high feather peckers had higher monoaminergic activity (lower metabolite levels and/or turnover ratios) in comparison to low feather peckers, which is in contrast with results on young hens. Differences were seen in several brain areas, namely the dorsal thalamus, medial striatum, amygdala, caudocentral nidopallium, and the somatomotor arcopallium, but to a lesser extend or not in the caudolateral nidopallium and the hippocampus. To investigate the exact neurobiological mechanism behind severe feather pecking further extracellular levels of 5-HT and DA and their metabolites were measured by in vivo microdialysis. Up till now, microdialysis has only been executed in young chickens, but this thesis describes the first microdialysis study performed in adult laying hens. It was found that adult severe feather peckers had a higher baseline release of 5-HT in the caudal nidopallium, a large associative area in the chicken’s forebrain. This result could not be explained by the amount of 5-HT presynaptically stored, as both high and low SFP lines displayed a similar 5-HT release after d-fenfluramine administration. This confirms that genetic selection on SFP has altered the serotonergic system in feather pecking-phenotypes. With clear phenotypic and genotypic differences in brain areas related to emotional regulation and motor control, it can be assumed that brain deficits at a young age increase an individual’s vulnerability to stressful environmental changes, which is associated with the prevalence of SFP later in life. The cause of the inversion of neurochemical patterns in young and adult high and low feather pecking hens remains to be elucidated. Perhaps this inversion is caused by development itself. On the other hand, higher behavioral patterns (SFP and other types of allopecking) observed in the high feather pecking chickens might have influenced the monoaminergic activity since the brain influences behavior and vice versa. Altogether, this thesis demonstrates the importance of considering the impact of genetic selection and also environmental conditions on brain neurotransmission and with that, on the vulnerability of individual chickens to develop SFP. Both the serotonergic and dopaminergic systems are involved in the development of SFP. With SFP being a multifactorial problem both genotype and phenotype have to be taken into account. Furthermore, in vivo microdialysis is a valuable approach to investigate why individual laying hens start SFP. This will lead to further understanding and ultimately in the reduction of SFP.
The potential of genomic selection to support local breed conservation
Calus, Mario - \ 2014
animal breeding - genotypes - phenotypes - genetic variance - genomics - genetic correlation - irish republic - beef cows - animal genetic resources - breeds
Plant density affects light interception and yield in cotton grown as companion crop in young jujube plantations
Zhang, D. ; Zhang, L. ; Liu, Jianguo ; Han, S. ; Wang, Q. ; Evers, J.B. ; Liu, Jun ; Werf, W. van der; Li, L. - \ 2014
Field Crops Research 169 (2014). - ISSN 0378-4290 - p. 132 - 139.
radiation-use efficiency - agroforestry systems - relay intercrops - leaf senescence - photosynthesis - competition - components - sunflower - genotypes - nitrogen
Tree-crop mixturesmayincreaseyieldandrevenueespeciallyduringtheearlyyearsoftreeplantations. Jujube isgrownwidelyinChinafortheirfruits,andcottonisgainingpopularityasanunderstorycropin young jujubeplantations.Thereisaneedforinformationonproductivityandoptimalplantingdensities of cottoninthesemixedsystems.Fieldexperimentswerecarriedoutin2012and2013inHetian,Xinjiang, China. Threecottonplantdensities(13.5,18.0and22.5plantsm-2) weretestedin6–7yearsoldjujube plantations, inwhichthecottonwasgrownina6m-widespacebetweenthetreerows.Cottonleafarea index increasedbutplantheightdecreasedwithplantdensity.Cottonlightinterceptionincreasedwith density, butatearlyandmid-season,thedifferenceinlightinterceptionbetween18.0and22.5plantsm-2 was onlymarginal.Increasingplantdensitymodifiedthedistributionpatternofthelightwithinthe canopy, thusaffectedoverallcottonlightinterceptionanduseefficiency.Thehighestyieldandlight use efficiencyofcottonwereachievedat18.0plantsm-2. Spatialdistributionsoflightintensitiesand extinction coefficientswereaffectedbytheshadingofjujubetreeswithinthecottoncanopyinthe intercrop. Jujubegrowth,yieldandlightutilizationwerenotsignificantlyaffectedbycottonplantdensity. We concludethattheproductivityandlightutilizationofcottoninjujube-cottonintercroppingcanbe increased byoptimizingcottonplantdensity.
Selection for niche differentiation in plant communities increases biodiversity effects
Zuppinger-Dingley, D. ; Schmid, B. ; Petermann, J.S. ; Yadav, V. ; Deyn, G.B. de; Flynn, D.F.B. - \ 2014
Nature 515 (2014). - ISSN 0028-0836 - p. 108 - 111.
diversity-productivity relationships - grassland experiment - species-diversity - evolution - genotypes - richness
In experimental plant communities, relationships between biodiversity and ecosystem functioning have been found to strengthen over time1, 2, a fact often attributed to increased resource complementarity between species in mixtures3 and negative plant–soil feedbacks in monocultures4. Here we show that selection for niche differentiation between species can drive this increasing biodiversity effect. Growing 12 grassland species in test monocultures and mixtures, we found character displacement between species and increased biodiversity effects when plants had been selected over 8 years in species mixtures rather than in monocultures. When grown in mixtures, relative differences in height and specific leaf area between plant species selected in mixtures (mixture types) were greater than between species selected in monocultures (monoculture types). Furthermore, net biodiversity and complementarity effects1, 2 were greater in mixtures of mixture types than in mixtures of monoculture types. Our study demonstrates a novel mechanism for the increase in biodiversity effects: selection for increased niche differentiation through character displacement. Selection in diverse mixtures may therefore increase species coexistence and ecosystem functioning in natural communities and may also allow increased mixture yields in agriculture or forestry. However, loss of biodiversity and prolonged selection of crops in monoculture may compromise this potential for selection in the longer term.
Host genetic heterozygosity and age are important determinants of porcine circovirus type 2 disease prevalence in European wild boar
Goedbloed, D.J. ; Hooft, W.F. van; Megens, H.J.W.C. ; Bosch, T. ; Lutz, W. ; Wieren, S.E. van; Ydenberg, R.C. ; Prins, H.H.T. - \ 2014
European Journal of Wildlife Research 60 (2014)5. - ISSN 1612-4642 - p. 803 - 810.
respiratory syndrome virus - sus-scrofa - domestic pigs - infection - resistance - population - reproduction - replication - parvovirus - genotypes
Emerging and zoonotic diseases are important challenges for veterinary and public health. It is therefore a key issue to assess the relative importance of various factors for disease dynamics and to understand the mechanisms behind these factors and interactions. Here, we evaluate the influence of a number of demographic and genetic factors on porcine circovirus type 2 (PCV2) antibody prevalence in the European wild boar (Sus scrofa). We measured PCV2 blood serum antibody levels of 462 randomly sampled wild boars from a cross-border area in the Netherlands and western parts of Germany in a 3-year period. These samples were also genotyped using a randomly selected genome-wide 351 SNP assay. Generalized linear mixed model analysis shows that wild boar PCV2 antibody status is determined by age and genetic heterozygosity, with an idiosyncratic influence of the year of sampling. In contrast, sex, population membership and domestic hybrid status did not significantly affect PCV2 antibody status. The observed positive relationship between PCV2 antibody status and age is most likely caused by cumulative exposure and PCV2-typical intracellular hiding behaviour. The observed positive relationship between wild boar genetic heterozygosity and PCV2 antibody status could be attributed to disappearance of relatively inbred (low-heterozygosity) individuals. This finding suggests that PCV2 can act as a selective force in wild boar populations and that disease mortality can be mediated by host heterozygosity. © 2014 Springer-Verlag Berlin Heidelberg.
Linkages between plant traits and soil ecology in the rhizosphere and through litter decomposition
Brolsma, K.M. - \ 2014
Wageningen University. Promotor(en): Ellis Hoffland, co-promotor(en): Ron de Goede. - Wageningen : Wageningen University - ISBN 9789462571068 - 112
bodemecologie - rizosfeer - ligstro - decompositie - wortels - bodembiologie - nematoda - solanum tuberosum - globodera pallida - biofumigatie - genotypen - soil ecology - rhizosphere - litter - decomposition - roots - soil biology - biofumigation - genotypes
Environmental regulation of seed performance
He, H. - \ 2014
Wageningen University. Promotor(en): Harro Bouwmeester; J.C.M. Smeekens, co-promotor(en): Henk Hilhorst; Leonie Bentsink. - Wageningen University : Wageningen University - ISBN 9789462570337 - 185
arabidopsis - zaden - kiemrust - zaadkieming - milieueffect - genetica - genotypen - temperatuur - seeds - seed dormancy - seed germination - environmental impact - genetics - genotypes - temperature

The seed stage is an essential episode in the life cycle of higher plants. The environmental cues that seeds experience during their development are important components of their life history. The parental environment, from pre-fertilization until seed dispersal affects performance of the dry mature seed and, therefore, affects the life cycle of the next generation. The evolutionary response to environmental perturbations has resulted in genetic changes in order to increase the fitness of the population, which is called ‘adaptation’. The aims of this study were to increase our understanding of how environments regulate seed performance, both on the long term, i.e. through adaptation of seed performance traits to local conditions and on the short term, i.e. by acclimation of plants to different seed maturation environments.

Factors influencing casein micelle size in milk of individual cows: Genetic variants and glycosylation of k-casein
Bijl, E. ; Vries, R.F.M. de; Valenberg, H.J.F. van; Huppertz, T. ; Hooijdonk, A.C.M. van - \ 2014
International Dairy Journal 34 (2014)1. - ISSN 0958-6946 - p. 135 - 141.
protein-composition - bovine-milk - liquid-chromatography - electrophoresis - polymorphism - coagulation - genotypes - pattern - cattle
The average casein micelle size varies widely between milk samples of individual cows. The factors that cause this variation in size are not known but could provide more insight into casein micelle structure and into the physiology of casein micelle formation. The objective of this research was therefore to determine factors that influence average casein micelle size in milk from individual cows. Average casein micelle size of milk samples was associated with the A and B genetic variants of k-casein, and differences in concentration of glycosylated k-casein as a fraction of total milk protein. Milk samples with a low average casein micelle size were associated with the B variant of k-casein and a higher relative concentration of glycosylated k-casein, compared with milk samples with a high average casein micelle size. Differences observed may be attributed to the effect of glycosylated k-casein groups on casein micelle formation in the mammary gland.
The ideal hen for organic and free range systems
Maurer, V. ; Amsler, Z. ; Zeltner, E. ; Leenstra, F.R. ; Niekerk, T.G.C.M. van; Reuvekamp, B.F.J. ; Bestman, M.W.P. ; Verwer, C.M. ; Sambeek, F. ; Galea, F. - \ 2014
pluimveehouderij - biologische landbouw - huisvesting van kippen - hennen - scharrelhouderij - genotypen - diergezondheid - poultry farming - organic farming - chicken housing - hens - free range husbandry - genotypes - animal health
The aim of LowInputBreeds is to develop a system to evaluate layer genotypes in free range and organic systems and to optimise the management of those systems.
The cocoa mirid (Hemiptera: Miridae) problem: evidence to support new recommendations on the timing of insecticide application on cocoa in Ghana
Adu-Acheampong, R. ; Jiggins, J. ; Huis, A. van; Cudjoe, A.R. ; Johnson, V. ; Sakyi-Dawson, O. ; Ofori-Frimpong, K. ; Nyarko Eku-X, N. ; Quarshie, E.T.N. - \ 2014
International Journal of Tropical Insect Science 34 (2014)1. - ISSN 1742-7584 - p. 58 - 71.
genotypes - africa - farm
The government’s cocoa spraying gangs in Ghana treat about two million hectares of the crop against black pod disease and mirids, the key insect pests of cocoa in West Africa, each August through to December, based on recommendations issued in the 1950s. A few cocoa farmers use additional pesticides.We studied the temporal distribution of two important mirid species, Distantiella theobroma (Dist.) and Sahlbergella singularis *E-mail: r.aduacheampong@yahoo.co.uk International Journal of Tropical Insect Science Vol. 34, No. 1, pp. 58–71, 2014 doi:10.1017S1742758413000441q icipe 2014 Hagl., in 1991, 1999, 2003 and 2012 to determine the appropriate timing for the application of controlmeasures in current farming systems. There was a significant correlation between mirid abundance and pod availability on trees, as well as the number of basal shoots and the cocoa variety grown. Mirid populations peaked between January and April and from September to October. Surveys (interviews and focus group discussions involving over 300 farmers in 33 cocoa-growing districts) on pesticide use, sources of recommendations, and perceived successes and failures of current cocoa pest treatments suggested that the 1950 recommendations on the timing of insecticide application need revising.
Toprunderen door genomische kennis
Veerkamp, R.F. ; Calus, M.P.L. ; Roos, S. de; Geus, B. de - \ 2014
V-focus 2014 (2014)1. - ISSN 1574-1575 - p. 30 - 31.
rundveehouderij - dierveredeling - dierenwelzijn - duurzame veehouderij - duurzame ontwikkeling - bedrijfsresultaten in de landbouw - dna - genotypen - dierlijke productie - tracking en tracing - cattle husbandry - animal breeding - animal welfare - sustainable animal husbandry - sustainable development - farm results - genotypes - animal production - tracking and tracing
Met de introductie van genomics is het mogelijk om op basis van DNA-testen te voorspellen wat de genetische waarde van een dier in de populatie is. Breed4Food, een samenwerking van vier private partijen en Wageningen UR, wil de kennis over genomische informatie versnellen en samen delen. Dit artikel beschrijft de activiteiten, die worden opgepakt voor de rundveehouderij.
Haptoglobin phenotype prevalence and cytokine profiles during plasmodium falciparum infection in Dogon and Fulani ethnic groups living in Mali
Perdijk, O. ; Arama, C. ; Giusti, P. ; Maiga, B. ; Troye-Blomberg, M. ; Dolo, A. ; Doumbo, O. ; Persson, J.O. ; Bostrom, S. - \ 2013
Malaria Journal 12 (2013). - ISSN 1475-2875
hemoglobin scavenger receptor - severe malaria - soluble cd163 - west-africa - children - susceptibility - polymorphism - association - genotypes - ahaptoglobinemia
Background The Fulani are known to have a lower parasitaemia and less clinical episodes of malaria as compared to the Dogon sympatric ethnic group, living in Mali. Higher circulating malaria-specific antibody titers and increased pro-inflammatory cytokine levels have been shown in Fulani individuals. Several studies have tried to link haptoglobin (Hp) phenotypes with susceptibility to malaria, but without consensus. This study investigated the role of Hp phenotypes and cytokine levels in Dogon and Fulani during asymptomatic Plasmodium falciparum infection. Methods Two different cohorts were combined in this study: a 2008 cohort with 77 children aged between two and ten years and a 2001 cohort, with 82 children and adults, aged between 11 and 68 years. Hp phenotypes in plasma were measured by Western Blot. Circulating levels of sCD163, IL-6, IL-10, IFN-¿ and TNF were measured by ELISA. Multiple regression analysis was performed to associate Hp phenotypes with cytokine profiles. In addition, in vitro stimulation of peripheral blood mononuclear cells (PBMCs) with Hp:Hb complexes was performed and cytokine release in corresponding supernatants were measured using cytometric bead array. Results The results revealed a higher Hp2-2 phenotype prevalence in the Fulani. The Hp2-2 phenotype was associated with a higher susceptibility to P. falciparum infection in Dogon, but not in Fulani. In concordance with previous studies, Fulani showed increased inflammatory mediators (IL-6, IFN-¿) and additionally also increased sCD163 levels compared to Dogon, irrespective of infection. Furthermore, infected individuals showed elevated sCD163 levels compared to uninfected individuals, in both Fulani and Dogon. Multiple regression analysis revealed that the Hp1-1 phenotype was associated with higher levels of TNF and IFN-¿, as compared to the Hp2-2 phenotype. In vitro stimulation of PBMCs with Hb:Hp1-1 complexes resulted in a pro-inflammatory cytokine profile, whilst stimulation with Hb:Hp2-2 complexes showed a more balanced profile. Conclusions Ethnicity might be an important confounder on the Hp phenotype-dependent susceptibility to malaria and future studies could consider taking this into account when designing new immunological studies. Although, the relatively small sample size used in this study warrens for precautions in the interpretation of the data and these findings should ideally be validated in a bigger cohort.
Sweet sorghum performance under irrigated conditions in northwest China : Biomass and its partitioning in inbred and hybrid cultivars at two nitrogen levels
Fan, F. ; Spiertz, J.H.J. ; Han, L.P. ; Liu, Z.X. ; Xie, G.H. - \ 2013
Research on Crops 14 (2013)2. - ISSN 0972-3226 - p. 459 - 470.
bicolor-l. moench - water-use efficiency - ethanol-production - harvest time - raw-material - yield - sugar - growth - crop - genotypes
Effects of cultivar choice and nitrogen supply on biomass yield and dry matter partitioning of sweet sorghum [Sorghum bicolor (L.) Moench] were studied under irrigated conditions in the arid temperate climate of north-west China. Two hybrid cultivars, Zaoshu-1 (ZS 1) and Chuntian-2 (CT 2), and two inbred cultivars, Rio and Lvneng-3 (LN 3) were grown in a field trial at two nitrogen fertilizer levels (0 and 150 kg/ha of N) in Urumchi (43°01'N, 88°37'E). Hybrid cultivars produced much higher aboveground dry biomass yields, amounting to on an average 27.2 t/ha than inbred cultivars with on an average 24.3 t/ha. Crop growth rates amounted to 30.8 g/m2/day on an average during the period from elongation to heading as well as from heading to maturity, however; the growth rates of the inbred cultivars slowed down after heading, while those of the hybrids still increased. Inbred cultivar Rio had the highest plant height (328 cm) and stem dry weight (16.5 t/ha). Average grain yield was 11.2 and 5.5 t/ha for hybrids and inbreds, respectively. Partitioning of dry matter differed between the inbred cultivars, but did not for the hybrids. Application of fertilizer nitrogen resulted in a higher plant height, stem dry biomass, dry biomass of leaves and aboveground biomass in inbred and hybrid cultivars. In conclusion, hybrid and inbred cultivars of sweet sorghum performed well in the environment of north-west China when irrigated. Biomass and grain yields of hybrids turned out to be higher than those of inbreds.
Grain filling, starch degradation and feeding value of maize for ruminants
Ali, M. - \ 2013
Wageningen University. Promotor(en): Paul Struik; Wouter Hendriks, co-promotor(en): John Cone. - Wageningen : Wageningen UR - ISBN 9789461738196 - 177
maïs - zea mays - groeifasen, rijp - genotypen - zetmeelvertering - pensvertering - voedingswaarde - herkauwersvoeding - korrels (granen) - maïskuilvoer - kuilvoerbereiding - gewasfysiologie - voedingsfysiologie - maize - maturity stage - genotypes - starch digestion - rumen digestion - nutritive value - ruminant feeding - kernels - maize silage - silage making - crop physiology - nutrition physiology

Keywords; Maize (Zea mays L), Genotypes, Grain filling, Growth temperature, Kernels, Gas production, Starch degradation, Oven-drying, Silage, Ensiling temperature, Ensiling duration, Feeding value, Lactating cows

Maize (Zea mays L.) is a major component in the ration of dairy cows in many parts of the world. The currently increasing economic importance of maize has highlighted the need to determine its nutritional value, and to assess the factors influencing its nutritive value. Genotypic make-up (especially differences in starch and endosperm), growing conditions, maturity stage at harvest, and post handling processes, like oven-drying, can influence nutritive value of maize kernels. Similarly, ensiling temperature and duration can affect feeding value of maize silage. This thesis is divided into three parts; the first aim was to characterize the dry matter (starch) accumulation of maize different genotypes in different environments under controlled (glasshouse) and on different locations (sand and clay) in field conditions. Maize genotypes used were different in starch structure and composition, and in type of endosperm. Starch structure refers to amylose and amylopectin; and composition refers to their proportions, whereas type of endosperm defines levels of vitreousness. The vitreousness is the ratio of vitreous (hard) to floury (soft) endosperm. Six maize genotypes, differing in amylose content and vitreousness, were grown under three contrasting day/night temperature regimes during grain filling and harvested at different maturity stages from two greenhouse experiments. Similar investigations were carried on another set of genotypes grown on sandy and clay soils and with different sowing times under field conditions. Water contents and dry matter (starch) accumulation were significantly influenced by growth temperature, genotype, soil type and sowing time (P<0.0001). The second aim of thesis was to establish a relationship between rumen in vitro starch degradation (feeding value) of maize kernels and different factors, like genotype, growth temperature during grain filling, and maturity stage. Oven-dried kernels of six maize genotypes, from the two greenhouse experiments mentioned before were investigated. Starch content was measured using an enzymatic method and the gas production technique was used to assess starch degradation in rumen fluid of dairy cows. The extent of starch degradation at different incubation times was calculated from measured gas production data (6, 12 and 20 h, respectively) and a published equation. At each maturity stage, whole kernel and starch degradation in rumen fluid depended on the genotype (P<0.0001), growing conditions (P<0.0001), starch content (P<0.0001) and starch amount (P<0.0001) in the kernels. The same but fresh (not oven-dried) maize kernel samples were investigated using gas production technique to determine the impact of oven-drying on rumen in vitro starch degradation of maize kernels. Oven-drying significantly (P<0.0001) influenced the rumen in vitro starch degradation in maize kernels various incubation times, with more starch being degraded in the fresh than in the oven-dried maize kernels, although the differences were small. There was a consistent and highly significant (P<0.009 to 0.0002) interaction between oven-drying and genotype, with the high-amylose genotype showing larger effects of oven-drying than the other genotypes. The third aim of thesis was to investigate effect of ensiling temperature and duration on feeding value of maize silage. Samples of maize whole plants (dry matter 33%) were collected from the medium vitreous endosperm cultivar, grown in different seasons on sandy soils. Maize plants were chopped and ensiled in mini silos at three different temperatures. Samples from the silos were taken after 0 (not ensiled, i.e. control), 4, 8 and 16 weeks of ensiling. The gas production technique was used to evaluate the influence of the ensiling temperature and duration of ensiling on the degradation of the fresh ground silage samples in rumen fluid. The final pH of the silages and the gas production was significantly influenced by ensiling temperature in both seasons (P<0.0001). Gas production and pH decreased with an increase in ensiling duration (P<0.0001). The relationship between pH and gas production was quadratic and depended on the ensiling temperature (P<0.002). It was found that ensiling temperature and ensiling duration determine the rate of change and final pH, and play a significant role in feeding value of maize silage. The finding of thesis can be used to determine the exact feeding value of maize kernels and silage, and also can be used as a tool to revise the current feeding evaluation systems i.e. shift from oven-dried to fresh samples.

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.

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