Estimates of linkage disequilibrium and effective population size in rainbow trout

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

“…Thus, the 566 loci remain candidates for adaptation to environmental variation and are valid targets for future studies. It should also be noted that despite querying the genome at almost 20 000 SNP loci, this probably represents a relatively small survey of the possible linkage blocks within salmonid genomes (Rexroad & Vallejo ). It is possible that other regions of the genome associated with the environmental features investigated here remain to be identified.…”

Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers

“…LD, simply defined, is the nonrandom association of alleles at different loci. Previous studies generally considered r 2 = 0.10 or 0.25 as the critical value for the extent of LD analysis in aquaculture species (Guo et al ; Rexroad and Vallejo ). To describe the relationship between r 2 and genetic distance, two methods of establishing critical r 2 values were investigated.…”

“…In recent years, a number of investigations have studied the level of LD in humans, domestic animals, and several important aquatic organisms, which may be helpful to design the strategy of association mapping (Farnir et al ; Conrad et al ; Du et al ). By genotyping 49 microsatellites, spanning four chromosomes, in 96 unrelated rainbow trout, Oncorhynchus mykiss , Rexroad and Vallejo () showed that LD (squared correlation coefficient r 2 ) between syntenic loci decayed rapidly at distances greater than 2 cM. By genotyping 307 single‐nucleotide polymorphisms (SNPs) and 146 microsatellites in 16 Atlantic salmon, Salmo salar , Moen et al () showed that r 2 dropped to half its maximum value (above baseline) within 15 cM, and r 2 values were higher than 0.2 above baseline for unlinked markers at distances less than 5 cM.…”

Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

“…To date, the most widely used measures of LD between two loci are r 2 and Lewontin's 103 et al, 2017), rainbow trout (Rexroad and Vallejo, 2009;Vallejo et al, 2018), coho 116 salmon (Barria et al, 2018a) and Atlantic salmon (Barria et al, 2018c;Gutierrez et al, 117 2015;Hayes et al, 2006;Kijas et al, 2016). However, to date there is scarce 118 information about population genomic structure and LD in farmed Nile tilapia assessed 119 by the use of dense SNP panels.…”