title: Estimates of linkage disequilibrium and effective population size in rainbow trout.
abstract: BACKGROUND
  The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To date the extent of LD has been characterized for humans and several agriculturally important livestock species but not for rainbow trout.
  
  
  RESULTS
  We observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures.
  
  
  CONCLUSIONS
  Our results indicate that large numbers of markers, more than are currently available for this species, will be required to enable the use of genome-wide integrated mapping approaches aimed at identifying genes of interest in rainbow trout.
authors.affiliation: USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia 25430, USA. caird.rexroadiii@ars.usda.gov
authors.forename: Caird E
authors.initials: CE
authors.lastname: Rexroad
authors.forename: Roger L
authors.initials: RL
authors.lastname: Vallejo
mesh_terms: D000818:Animals; D002875:Chromosomes; D005260:Female; D005819:Genetic Markers; D015810:Linkage Disequilibrium; D008297:Male; D018895:Microsatellite Repeats; D017686:Oncorhynchus mykiss / Q000235:genetics*; D011156:Population Density
chemical_list: D005819:Genetic Markers