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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #175131


item Rexroad, Caird

Submitted to: World Aquaculture Society Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2004
Publication Date: 3/1/2004
Citation: Stewart, A., Dailey, R., Rexroad Iii, C.E. 2004. Identification and use of polymorphic markers in rainbow trout. World Aquaculture Society Meeting. March 1 - 5, 2004 Honolulu, Hawaii.

Interpretive Summary:

Technical Abstract: Microsatellites are short tandem repeats of 2-6 base pairs commonly located in non-coding regions of DNA. Due to variability in number of tandem repeats, microsatellites are highly polymorphic. Analysis of patterns of microsatellites within an individual is referred to as genotyping, which is used in forensic and paternity cases. Microsatellite identification and analysis in rainbow trout are necessary to identify strains and to use marker-assisted selection to develop genetically superior strains for aquaculture. Microsatellite analysis can be used to determine evolutionary significant units in wild or released populations, and in cases of poaching and illegal importation. This study identified and used polymorphic microsatellites to examine variation in U. S. rainbow trout strains. Plasmid DNA samples isolated from clones in microsatellite-enriched libraries (Genetic Identification Services, Chatsworth, CA) were subjected to DNA sequencing. Markers containing adequate flanking sequences were used to generate polymerase chain reaction (PCR) primers. PCR was performed using genomic DNA isolated from fin tissue of six strains of rainbow trout. Products were electrophoresed on a 3.0% agarose gel. Bands that could be resolved were sized, and polymorphism was determined by variations in the length (in basepairs, bp). For fragment analysis, genomic DNA was isolated from 10 individuals from 10 strains, and PCR was performed with 5' fluorescently-labeled primers. Products were electrophoresed on an ABI 310 Genetic Analyzer; data was analyzed with Gene Scan and GenoTyper software. Due to semi-tetraploid condition of rainbow trout, up to 4 alleles were expected for each locus. From identification of 56 microsatellites, 39 were polymorphic. Future experiments will use these markers to develop an identification panel capable of distinguishing U. S. trout strains and to form high-resolution linkage maps that will be used to identify and locate markers that affect production trait differences. Estimated size (bp) from agarose gels of 3 representative microsatellite markers from one individual from each of 6 rainbow trout strains Marker Hot Creek Swanson Arlee Clearwater OSU Wytheville OMM1445 165 175 169 173 167 189 OMM1491 169 169 187 171 172 187/172* OMM1478 253/214* 253/220* 242/208* 253/204* 274/214* 274 *Heterozygous Fragment analysis (bp) of marker OMM1445 with 10 individuals from Wytheville strain Allele 1 94 94 94 94 94 94 94 94 94 94 2 117 121 121 121 117 121 125 117 121 121 3 125 125 125 - 125 125 - 125 125 125