Simultaneous effect of genomic selection and upgrade of alleles by Genomic Editing on quantitative traits improvement in dairy breeding programs

Abstract

Introduction: The present study aimed to compare the effect of upgrade of alleles by genome
editing was investigated on genomic variance, response to selection and coefficient of
inbreeding.
Materials & Methods: For this study, a population of dairy cattle was simulated based on over
ten generations with an effective size of 100 individuals in the base population. The genomic
structure was assumed consisting of 3 chromosomes with a length of 100 cM and On each
chromosome were located 1000 markers 2 allelic markers with a frequency of 0.5 and fifty
QTL double alleles, in random with equal frequency. Marker effects and variance components
were estimated using Bayes Lasso method and additive model. Then, upgrade of alleles was
performed on 5 and 10 bulls. In the first stage 1, then 20, 25 and 50 QTN was upgraded by
genome editing. The BGLR package in R software was used to estimate the additive effects
and variance component. In the next step, the mean inbreeding coefficient for GS+PAGE was
calculated and compared with the GS by PLINK software.
Results: The effect of upgrade alleles by genome editing was increased additive variance. With
1 QTNe was upgraded and inherited by next generation, additive variance relative to genome
selection increased by 0.139. The response to cumulative selection in GS+PAGE model in 5
bulls and 1, 20, 25 and 50 QTNe, increased by 0.07, 0.17, 0.29 and 0.31, respectively. With
increasing the number of QTNe, the inbreeding coefficient also increased slightly, but there
was no significant.
Conclusion: Genome editing improves the genetic variance of the population without
increasing inbreeding.