Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
| Autor: | Alain Vignal, Johan Elmberg, Richard P. M. A. Crooijmans, Martien A. M. Groenen, Robert H. S. Kraus, Hindrik H. D. Kerstens, Ning Li, Yinhua Huang, Jan J. van der Poel, Herbert H. T. Prins, Pim van Hooft |
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| Přispěvatelé: | Kraus, Robert HS, Resource Ecology Group, Wageningen University and Research [Wageningen] (WUR), Animal Breeding and Genomics Centre, Kristianstad University, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, State Key Laboratory for Agrobiotechnology, China Agricultural University (CAU) |
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
0106 biological sciences
Male [SDV]Life Sciences [q-bio] animal diseases markers 01 natural sciences Genome power Gene Frequency Biologiska vetenskaper base Genetics Expressed Sequence Tags 0303 health sciences evaluation biology genome snp anas platyrhynchos genotype correlation Chicken Genome Beijing Genome Institute Putative SNPs Domestic Duck Read Position conservation Chromosome Mapping virus diseases Biological Sciences PE&RC Ducks Female Biotechnology Research Article Anas animal structures lcsh:QH426-470 Genotype lcsh:Biotechnology Single-nucleotide polymorphism virus Animal Breeding and Genomics 010603 evolutionary biology Polymorphism Single Nucleotide DNA sequencing Evolution Molecular 03 medical and health sciences lcsh:TP248.13-248.65 ddc:570 map Animals Fokkerij en Genomica Genotyping Illumina dye sequencing 030304 developmental biology Sequence Analysis DNA biology.organism_classification Minor allele frequency lcsh:Genetics pathogenic avian influenza Wildlife Ecology and Conservation birds WIAS divergence Reference genome |
| Zdroj: | BMC Genomics BMC Genomics march (12, online), Non paginé. (2011) BMC Genomics, BioMed Central, 2011, 12, online (march), Non paginé. ⟨10.1186/1471-2164-12-150⟩ BMC Genomics, Vol 12, Iss 1, p 150 (2011) BMC Genomics, 12 BMC Genomics 12 (2011) |
| ISSN: | 1471-2164 |
| Popis: | Background Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs. |
| Databáze: | OpenAIRE |
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