Optimal Design for Marker-assisted Gene Pyramiding in Cross Population

Abstract

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-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 the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a 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. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies.

An Overview of Mapping Quantitative Trait Loci in Peanut (Arachis hypogaea L.)

“…Pyramiding is the simultaneous integration of several QTL from multiple parents into a single genotype to create superior lines and varieties [ 101 , 102 , 111 ]. Marker-assisted QTL pyramiding can speed up the process by lowering the number of generations that the researchers must evaluate to ensure that they have the desired QTL combination [ 112 ]. The QTL pyramiding method consists of two fundamental steps: the QTL fixation step, which aims to fix the target QTL into a homozygous state, and the pyramiding step, which aims to accumulate all the target QTL into a single genotype known as the root genotype [ 113 ].…”

Functional genes polymorphism associations with egg quality traits in the populations of dual-purpose

“…One of the most promising types of marker assisted selection (MAS) in the context of selection with local chicken breeds is the method of Marker-Assisted-Pyramiding (MAP) (Xu et al, 2012). This approach is used for genotyping of birds by the combination of markers (loci), whose allelic variants are associated with the manifestation of similar economic traits.…”