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Putative SNPs (putative + snp)
Selected AbstractsA gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannameiANIMAL GENETICS, Issue 3 2010Z.-Q. Du Summary Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r2), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r2 increased with decreasing inter-marker distance from ,80 cm, and increased more rapidly from ,30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits. [source] BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmonANIMAL GENETICS, Issue 1 2010S. Lorenz Summary A better understanding of the genotype,phenotype correlation of Atlantic salmon is of key importance for a whole range of production, life history and conservation biology issues attached to this species. High-density linkage maps integrated with physical maps and covering the complete genome are needed to identify economically important genes and to study the genome architecture. Linkage maps of moderate density and a physical bacterial artificial chromosome (BAC) fingerprint map for the Atlantic salmon have already been generated. Here, we describe a strategy to combine the linkage mapping with the physical integration of newly identified single nucleotide polymorphisms (SNPs). We resequenced 284 BAC-ends by PCR in 14 individuals and detected 180 putative SNPs. After successful validation of 152 sequence variations, genotyping and genetic mapping were performed in eight salmon families comprising 376 individuals. Among these, 110 SNPs were positioned on a previously constructed linkage map containing SNPs derived from expressed sequence tag (EST) sequences. Tracing the SNP markers back to the BACs enabled the integration of the genetic and physical maps by assigning 73 BAC contigs to Atlantic salmon linkage groups. [source] Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and qualityANIMAL GENETICS, Issue 4 2009J. L. Williams Summary A large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome-wide. Sequence-tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 individuals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast. Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed. [source] Joint Identification of Multiple Genetic Variants via Elastic-Net Variable Selection in a Genome-Wide Association AnalysisANNALS OF HUMAN GENETICS, Issue 5 2010Seoae Cho Summary Unraveling the genetic background of common complex traits is a major goal in modern genetics. In recent years, genome-wide association (GWA) studies have been conducted with large-scale data sets of genetic variants. Most of those studies have relied on single-marker approaches that identify single genetic factors individually and can be limited in considering fully the joint effects of multiple genetic factors on complex traits. Joint identification of multiple genetic factors would be more powerful and would provide better prediction on complex traits since it utilizes combined information across variants. Here we propose a multi-stage approach for GWA analysis: (1) prescreening, (2) joint identification of putative SNPs based on elastic-net variable selection, and (3) empirical replication using bootstrap samples. Our approach enables an efficient joint search for genetic associations in GWA analysis. The suggested empirical replication method can be beneficial in GWA studies because one can avoid a costly, independent replication study while eliminating false-positive associations and focusing on a smaller number of replicable variants. We applied the proposed approach to a GWA analysis, and jointly identified 129 genetic variants having an association with adult height in a Korean population. [source] Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannaiAQUACULTURE RESEARCH, Issue 14 2009Haigang Qi Abstract Although single nucleotide polymorphisms (SNPs) are important resources for population genetics, pedigree analysis and genomic mapping, such loci have not been reported in Pacific abalone so far. In this study, a bioinformatics strategy was adopted to discover SNPs within the expressed sequences (ESTs) of Pacific abalone, Haliotis discus hannai, and furthermore, polymerase chain reaction direct sequencing (PCR-DS) and allele-specific PCR (AS-PCR) were used for SNPs detection and genotype scoring respectively. A total of 5893 ESTs were assembled and 302 putative SNPs were identified. The average density of SNPs in ESTs was 1%. Fifty-two sets of sequencing primers were designed from SNPs flanking ESTs to amplify the genomic DNA, and 13 could generate products of expected size. Polymerase chain reaction direct sequencing of the amplification products from pooled DNA samples revealed 40 polymorphic SNP loci. Using a modified tetra-primer AS-PCR, seven mitochondrial and six nuclear SNPs were typed and characterized among 37 wild abalones. In conclusion, it is feasible to discover SNPs from number limited ESTs and the AS-PCR as a simple, robust and reliable assay could be a primary method for small- and medium-scale SNPs detection in abalones as well as other non-model organisms. [source] | ||||||||||