SNP marker detection and genotyping in tilapia.
Summary of "SNP marker detection and genotyping in tilapia."
We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.
Affiliation
Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, Wageningen, 6700 AH, The Netherlands.
Journal Details
This article was published in the following journal.
Name: Molecular ecology resources
ISSN: 1755-0998
Pages:
Links
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/22524158
- DOI: http://dx.doi.org/10.1111/j.1755-0998.2012.03144.x
Medical and Biotech [MESH] Definitions
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Detection of drugs that have been abused, overused, or misused, including legal and illegal drugs. Urine screening is the usual method of detection.
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Ascertaining of deception through detection of emotional disturbance as manifested by changes in physiologic processes usually using a polygraph.
Vaccines, Marker
Vaccines used in conjunction with diagnostic tests to differentiate vaccinated animals from carrier animals. Marker vaccines can be either a subunit or a gene-deleted vaccine.
Tilapia
A freshwater fish used as an experimental organism and for food. This genus of the family Cichlidae (CICHLIDS) inhabits Central and South America (one species extends north into Texas), West Indies, Africa, Madagascar, Syria, and coastal India.
Chorionic Gonadotropin, Beta Subunit, Human
The beta subunit of human CHORIONIC GONADOTROPIN. Its structure is similar to the beta subunit of LUTEINIZING HORMONE, except for the additional 30 amino acids at the carboxy end with the associated carbohydrate residues. HCG-beta is used as a diagnostic marker for early detection of pregnancy, spontaneous abortion (ABORTION, SPONTANEOUS); ECTOPIC PREGNANCY; HYDATIDIFORM MOLE; CHORIOCARCINOMA; or DOWN SYNDROME.
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