Study On Optimal System Of Marker Assisted Gene Pyramiding In Animals

Marker-assisted gene pyramiding aims to produce individuals with a superior economic trait according to the optimal breeding scheme, which involves selecting a series of target genes with favorite alleles after cross of base populations and pyramiding them into an ideal genotype. In this research, we use simulation to conduct gene pyramiding in the mixed population and cross population. In addition, we develop the software of AGPBSim based on MATLAB GUI. Main studies are as followed:1. Gene pyramiding in admixed population.Gene pyramiding was advocated for designing breeding strategies and selecting and pyramiding optimal combinations of alleles. We focused on gene agents (major genes), the admixed population was used as the base population, and individuals were coded by binary strings that represented combinations of alleles. Marker assisted selected the mating parents, and offspring were produced by the discrete recombination of two selected parents. The phenotypic value was predicted by the genotype-phenotype model. In each generation, we calculated population hamming distance, average superior genotype frequency and average phenotypic value to comprehensively measure the progress of gene pyramiding breeding. Three selection strategies—genotypic selection, simple phenotypic selection, and molecular information integration selection—were developed for nine generations. We used the three selection strategies to compare the progress of gene pyramiding. In genotypic selection, we only considered the favorite allele frequencies and base population sizes in admixed population, but in phenotypic selection, trait heritability, gene effects and gene-gene interaction effects were included in genotype-phenotype model. Examples are given for four target genes in order to compare the gene pyramiding progress. The results indicated that gene pyramiding breeding process was greatly affected by the selection model.2. Gene pyramiding in cross population.In consideration of animals traditional cross program along with the features of animal segregating population, four types of cross programs and two types of selection strategies for gene pyramiding are performed from practice perspective, two population cross for pyramiding two genes (denotedⅡ), three population cascading cross for pyramiding three genes (denotedⅢ), four population symmetry (denotedⅣ-S) and cascading cross for pyramiding four genes (denotedⅣ-C), and various schemes (denoted cross program-A-E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher initial favorite allele frequency result in higher efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding.3. AGPBSim design.AGPBSim is a genetically information integration stochastic simulation program. It was developed to investigate the effect of base population size, initial allele frequency and selection on trait by the mark-assisted gene pyramiding breeding. The process of gene pyramiding breeding was measured using population hamming distance, superior genotype frequency and average phenotypic values. AGPBSim is high flexible at various levels: hybrid scheme, population size, selection strategy, trait architecture using various genotype-phenotype models can be integrated in gene pyramiding breeding simulation. The GUI design of AGPBsim can facilitate design precise gene pyramiding breeding strategy by performing virtual breeding simulation on this platform.AGPBSim is a simulation platform for the gene pyramiding breeding, and different level of population size, initial gene frequency and flexible selection strategies can be designed on this platform, the gene pyramiding breeding progress would be predicted for us as valuable references for decision-making of breeders.Further development of accurate and practical models is necessary to link the genotype and phenotype in order to increase the accuracy of model prediction. Evolutionary computation technology will help exploit useful information and guide the precise optimal design of breeding by gene pyramiding. We hope to develop a more optimized model in future studies with the development of system biology and high-throughout array technology. More over, different cross programs and selection strategies can be designed and compared based on this gene pyramiding simulation platform.