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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    We will mail you new results for this query: keywords==dna analysis
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Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)
Aslam, M.L. ; Bastiaansen, J.W.M. ; Elferink, M.G. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Blomberg, L.A. ; Fleischer, R.C. ; Tassell, C.P. van; Sonstegard, T.S. ; Schroeder, S.G. ; Groenen, M. ; Long, J.A. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
single-nucleotide polymorphisms - breast meat yield - linkage disequilibrium - evolutionary genomics - sequencing technology - body-composition - holstein cattle - farm-animals - dna analysis - chicken
Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey
Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation
McGregor, C.E. ; Treuren, R. van; Hoekstra, R. ; Hintum, T.J.L. van - \ 2002
Theoretical and Applied Genetics 104 (2002)1. - ISSN 0040-5752 - p. 146 - 156.
duplicate accessions - l. germplasm - dna analysis - rapd - identification - collection - rflp - ssr
The wild potato germplasm of the series Acaulia maintained at the Centre for Genetic Resources, The Netherlands, currently consists of 314 accessions. This collection comprises seed samples of the species Solanum acaule (ssp. acaule, ssp. aemulans, ssp. palmirense and ssp. punae) and Solanum albicans collected from South America. In order to validate taxonomic classification, to investigate the extent of redundancy and to study the distribution of genetic diversity across the collection area, the entire collection was analysed with two AFLP primer pairs on two plants per accession. Within the entire sample a total number of 130 polymorphic bands were scored for the two primer pairs. An UPGMA cluster analysis grouped the majority of plants according to the species and subspecies. A total number of 16 misclassifications were identified, including four cases that did not seem to belong to the series Acaulia. Two accessions were found to consist of plants of different AFLP clusters. AFLP data also allowed the taxonomic classification of the subspecies of 97 accessions that previously were described as S. acaule only. For 126 accessions the two individuals studied displayed identical AFLP profiles. Forty six of these 126 accessions shared their profiles with both or single plants of other accessions. These were all tested for identical profiles for a third primer pair, resulting in 15 duplication groups consisting of a total number of 22 accessions and 14 single plants. Analyses of molecular variance (AMOVA) were performed to examine the distribution of genetic variation. Comparison of geographic distances between the collection site of plants and the number of AFLP polymorphisms revealed no consistent relationship between geographic distance and genetic diversity. AFLP analysis appeared to be an efficient method to verify taxonomic classification and to identify redundancies in the wild germplasm of the series Acaulia. Implications of the results for the ex situ conservation of wild potato germplasm are discussed.
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