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.

Figure 1

Decline of linkage disequilibrium (r²) with distance (recombination rate in Morgans) for chromosomes 13, 14, 17 and Sex. The estimates of r² for pairs of markers were adjusted for experimental sample size 1/n, were n is the chromosome sample size (n = 192). The predicted LD value plot (filled non-linear curve) was estimated fitting the equation LD_ij = 1/(1+kb_jd_ij)+e_ij performing non-linear modeling with JMP^® Genomics 3.1 (SAS Institute Inc., Carey, NC, 2007). Here, LD_ij is the observed LD for marker pair i in chromosome j, d_ij is the distance in Morgans for marker pair i in chromosome j, b_j is the estimate of effective population size for chromosome j, and the constant k = 2 for sex chromosome and k = 4 for autosomes.

Figure 2

Proportion of markers pairs with significant extent of LD (r² ≥ 0.25). All marker pairs were evaluated in addition to pairwise combinations of all non-syntenic loci.