The role of Mallard (Anas platyrhynchos) in the spread of avian influenza: genomics, population genetics, and flyways
Kraus, R.H.S. - \ 2011
Wageningen University. Promotor(en): Herbert Prins; Ron Ydenberg, co-promotor(en): Pim van Hooft. - [S.l.] : S.n. - ISBN 9789461730282 - 143
aviaire influenzavirussen - aviaire influenza - anas platyrhynchos - ziekteoverdracht - vogeltrek - genomica - populatiegenetica - evolutionaire genetica - zoögeografie - bioveiligheid - ziekteoverzichten - epidemiologie - avian influenza viruses - avian influenza - anas platyrhynchos - disease transmission - bird migration - genomics - population genetics - evolutionary genetics - zoogeography - biosafety - disease surveys - epidemiology
Birds, in particular poultry and ducks, are a source of many infectious diseases, such as those caused by influenza viruses. These viruses are a threat not only to the birds themselves but also to poultry farming and human health, as forms that can infect humans are known to have evolved. It is believed that migratory birds in general play an important role in the global spread of avian influenza (AI). However, it is still debated how large this role precisely is and whether other modes of spread may be more important. The mallard (Anas platyrhynchos) is the world’s most abundant and well-studied waterfowl species. Besides being an important game and agricultural species, it is also a flagship species in wetland conservation and restoration. Waterfowl (Anseriformes: Anatidae) and especially ducks currently are the focal bird group in long distance dispersal of Avian Influenza in the wild, and the mallard has been identified as the most likely species to transport this virus.
In my thesis I report aspects of the biology of this important host species of AI by molecular ecological means. As molecular marker system I established a genome-wide set of more than 100,000 SNPs of which I developed a subset of 384 SNPs into an assay to genotype about 1,000 ducks. This subset was employed to study the evolutionary history and speciation processes in the Anas genus. Further investigations into the world-wide mallard population structure on a species level were based not only on this set of 384 SNPs but also on mitochondrial DNA sequences. Last but not last, I investigated an option of AI sampling and detection from duck faeces by technology that is safe from a biohazard perspective, and solves transportation issues related to cold chains.
The main results of my thesis include the development of a generally applicable improved analysis pipeline to develop genome-wide SNP sets for non-model organisms. Further, my results show that, from a migration system perspective, mallard flyways/populations can hardly be delineated from a biological point of view. Detailed phylogenetic, population genetic and coalescent analyses of a data set of samples spanning the whole northern hemisphere leads me to conclude that the only firm population boundaries that I can draw are between Eurasia and North America, within which panmixia is almost achieved. Mallards’ and other Anas-ducks’ whole continental to global distribution brings them together in sympatry. I can show that a combination of sympatric distribution, conflicting genetically determined and learned mate recognition mechanisms, and genomic compatibility between species helps to explain the long-standing puzzle of waterfowl hybridisation and introgression of genes from one duck species into another. Besides obvious management implications I propose that this fact can be part of the explanation why ducks are so well adaptable and successful, as well as why they show extraordinary abilities to withstand AI infections, or its consequences for health status.
Natuurlijk gedrag en behoeften van pekingeenden; van theorie naar praktijk = Natural behavior and requirements of Pekin ducks; from theory to practice
Krimpen, M.M. van; Ruis, M.A.W. - \ 2011
Wageningen : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 436) - 32
pluimveehouderij - eenden - anas platyrhynchos - huisvesting, dieren - diergedrag - literatuuroverzichten - pluimvee - diergezondheid - poultry farming - ducks - anas platyrhynchos - animal housing - animal behaviour - literature reviews - poultry - animal health
Wageningen UR Livestock Research is verzocht om aan de hand van een literatuurstudie na te gaan hoe welzijnsverbeteringen in de vleeseendenhouderij geïmplementeerd kunnen worden. Naast een samenvatting van relevante nationale en internationale literatuur met betrekking tot het welzijn van eenden, zijn in de rapportage ook de bevindingen opgenomen van een onlangs gehouden bijeenkomst in Cambridge, Engeland. De bijeenkomst had als doel de laatste kennis, ervaringen en inzichten omtrent het welzijn van pekingeenden uit te wisselen tussen Engeland en Nederland. Hierin was vooral veel aandacht voor de toepassing van open water en de visies van het beleid.
Bioinformatics' approaches to detect genetic variation in whole genome sequencing data
Kerstens, H.H.D. - \ 2010
Wageningen University. Promotor(en): Martien Groenen; Mari Smits. - [S.l. : S.n. - ISBN 9789085857808 - 182
bio-informatica - genomen - nucleotidenvolgordes - genetische variatie - varkens - kalkoenen - kippen - anas platyrhynchos - dierveredeling - genexpressieanalyse - single nucleotide polymorphism - marker assisted breeding - bioinformatics - genomes - nucleotide sequences - genetic variation - pigs - turkeys - fowls - anas platyrhynchos - animal breeding - genomics - single nucleotide polymorphism - marker assisted breeding
Current genetic marker repositories are not sufficient or even are completely lacking for most farm animals. However, genetic markers are essential for the development of a research tool facilitating discovery of genetic factors that contribute to resistance to disease and the overall welfare and performance in farm animals.
By large scale identification of Single Nucleotide Polymorphisms (SNPs) and Structural Variants (SVs) we aimed to contribute to the development of a repository of genetic variants for farm animals. For this purpose bioinformatics data pipelines were designed and validated to address the challenge of the cost effective identification of genetic markers in DNA sequencing data even in absence of a fully sequenced reference genome.
To find SNPs in pig, we analysed publicly available whole genome shotgun sequencing datasets by sequence alignment and clustering. Sequence clusters were assigned to genomic locations using publicly available BAC sequencing and BAC mapping data. Within the sequence clusters thousands of SNPs were detected of which the genomic location is roughly known.
For turkey and duck, species that both were lacking a sufficient sequence data repository for variant discovery, we applied next-generation sequencing (NGS) on a reduced genome representation of a pooled DNA sample. For turkey a genome reference was reconstructed from our sequencing data and available public sequencing data whereas in duck the reference genome constructed by a (NGS) project was used. SNPs obtained by our cost-effective SNP detection procedure still turned out to cover, at intervals, the whole turkey and duck genomes and are of sufficient quality to be used in genotyping studies. Allele frequencies, obtained by genotyping animal panels with a subset our SNPs, correlated well with those observed during SNP detection. The availability of two external duck SNP datasets allowed for the construction of a subset of SNPs which we had in common with these sets. Genotyping turned out that this subset was of outstanding quality and can be used for benchmarking other SNPs that we identified within duck.
Ongoing developments in (NGS) allowed for paired end sequencing which is an extension on sequencing analysis that provides information about which pair of reads are coming from the outer ends of one sequenced DNA fragment. We applied this technique on a reduced genome representation of four chicken breeds to detect SVs. Paired end reads were mapped to the chicken reference genome and SVs were identified as abnormally aligned read pairs that have orientation or span sizes discordant from the reference genome. SV detection parameters, to distinguish true structural variants from false positives, were designed and optimized by validation of a small representative sample of SVs using PCR and traditional capillary sequencing.
To conclude: we developed SNP repositories which fulfils a requirement for SNPs to perform linkage analysis, comparative genomics QTL studies and ultimately GWA studies in a range of farm animals. We also set the first step in developing a repository for SVs in chicken, a relatively new genetic marker in animal sciences.