Evaluation of frequency of the favorable allele of major gene under overlapping and discrete generation: A study based on simulation

Document Type : Research Paper

Authors

• Maysam Latifi ¹
• Yousef Naderi ²

¹ Collage of Agriculture, Department of Animal Science, University of Kurdistan, Kurdistan, Iran.

² Department of Animal Science, Astara Branch, Islamic Azad University, Astara, Iran

Abstract

Keywords

• Selection designs
• Genetic gain
• Accuracy of prediction

Main Subjects

• Animal Breeding and Genetics

Extended Abstract

Introduction

Choosing an appropriate selection strategy for genetic enhancement and stabilizing of a favorite major gene`s allele is very important. Objective of this research was to evaluate the fixation selection designs for favorable major gene allele related to multiple births  trait under scenarios of overlapping and discrete generations using simulation in a sheep population. Selection scenarios were based on random selection (RND, estimated breeding value (EBV), and, phenotype (PHEN) . Genetic progress, evaluation accuracies, inbreeding rate, and the frequency of the desired allele were evaluated and compared after ten generations of selection in two scenarios.

Materials and methods

QMSim software (Sargolzaei & Schenkel, 2009) was used to simulate a sheep population. First, a historical population with an effective size of 1000 animals, including 500 male and 500 female was created. These animals were randomly mated for 1000 generations. Then, from the last generation of the historical population, 50 male and 500 female were selected based on estimated breeding value (EBV), phenotypic value (PHEN) and random (RND) and crossed for ten generations. Next, a sex-limited trait with heritability of 0.1 and a genome consisting of 26 chromosomes, each with the length of one Morgan. was simulated. It assumed that 60% of the additive genetic variance of this trait was polygenic and the remaining 40% was assigned to a QTL. This QTL was assigned as a major gene on one of the chromosomes. QTL effect was simulated from gamma distribution with parameter 0.4 and phenotypic variance of the one. The initial frequency of the desired allele of this major gene (QTL) in the zero generation was considered to be 0.1. Two selection scenarios of overlapping and discrete generations were applied to  investigate the effect of selection programs on increasing desired allele  frequency, genetic progress and average inbreeding rate after ten generations of selection. Furthermore, 20% of the above phenotypes were considered as twin and the remaining 80% as single birth in order to create the threshold phenotypes for this  trait.                                                                

Results and discussion             

The genetic improvement based on EBV, PHEN and RND in the scenario of no generation interference was 8, 23 and 26% higher than corresponding values in the generation interference scenario.  The accuracy of the evaluation in the generation interference and the absence of generation interference scenarios for the EBV, PHEN, and RND selected design were 0.87, 0.66, and 0.54, and 0.89, 0.69, and 0.55, respectively. With increasing selection intensity, the evaluation accuracy increased in both scenarios. According to the results of this research, if the goal is to increase the desired frequency of the major gene in native breeds, it is suggested to use the scenario of no generation interference and EBV selection plan to stabilize the desired allelic frequency of the major gene. The average inbreeding coefficient in the selected designs of EBV, PHEN and RND in the scenario of no generation interference were higher by 0.01, 0.023 and 0.029, respectively, compared to the generation interference scenario. In case of generation interference, parents are selected from different generations, and as a result, the structure of the pedigree becomes more heterogeneous, thus reducing inbreeding.                                                                                                                                                              

Conclusion

The results of current study showed that the scenario of no generation interference leads to an increase in genetic gain, evaluation accuracy, desired allele the frequency of  major gene, and inbreeding in the EBV, PHEN and RND selection designs compared to the generation interference scenario. Hence, when aiming to stabilize the desired allele of the major gene influencing the multiple births trait in native breeds, it is recommended to use the scenario without generational interference, employing selection scheme based on EBV.