The Impact of LD variation on the accuracy of genomic selection

In order to evaluate the effects of LD variance with different heritability on the accuracy of genomic selection present study was conducted in randomized computer simulation form through Visual Basic programming language. First, the effective population size of 100 individuals (50 male and 50 female) were simulated the population and this structure continued for 50 generations with random mating to establish linkage disequilibrium . Paternal and maternal haplotype of each individual formed randomly by using probability of recombination and regarding formation markers and not intended to limit the number of children for every person. After 50 generations of random mix, number of population was developed to 1,000 persons (500 males and 500 females) in 51st generation. The number of population remained unchanged for the next 15 generations (i.e. up to 65th generation).In each generation, males and females were randomly intercourse with each other to produce the next generation. . The generation of 51 to 55 have had phenotypic records and reference group (which phenotypic data were used to predict the effects of markers) formed and confirm that no records were phenotypic and genomic breeding values were predicted solely on the basis of genotypic data and Created a whole generation of 56 to 65.In all 9 Strategies (each of 10 replicates) to assess linkage disequilibrium on the prediction accuracy of genomic breeding values were tested values based on which different heritability were simulated./04 and measured with 0.05, 28 and 0.8 values and with different number of 10, 30 and 90 LD.The results showed that the more reference population is lengthened the more accuracy of estimation of genomic modified values is reduced from 55th to 65th generations but the accuracy of the number of LD (90) than 10 states and 30 LD with similar heritability has improved dramatically. On the other hand, the value of this accuracy with high heritability (0.6) is higher than moderate heritability (0.22) and low heritability (0.04) in number of similar LD in generations from 56 to 59.As a matter of fact, the results indicated that the amount of genomic breeding value estimation LD increases accuracy but the value of such increase strictly depends on the heritability

Keywords:

Accuracy of genomic selection , LD , heritability , Variance , reference population