Linkage analysis is now being widely used to map markers on each chromosome in the human genome, to map genetic diseases, and to identify genetic forms of common diseases. Two-locus linkage analysis and multi-locus analysis have been investigated comprehensively, and many computer programs have been developed to perform linkage analysis. Yet there exists a shortcoming in traditional methods, i.e., the parameter space of two-locus recombination fractions has not been emphasized sufficiently in the usual analyses. In this paper, we propose a new strategy for estimating the two-locus recombination fractions based on data of backcross family in the framework of some natural and necessary parameter restrictions. The new strategy is based on a restricted projection algorithm, which can provide fast reasonable estimates of recombination fraction, and can therefore serve as a superior alternative algorithm. Results obtained from both real and simulated data indicate that the new algorithm performs well in the estimation of recombination fractions and outperforms current methods.

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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.

Abstract. This paper studies the main effects and interactive effects between genes on immunosuppression susceptibility caused by ultraviolet radiation in population of mice. We present a two-step strategy, i.e., we first establish one full linear model based on all main effects and interactive effects, and use the Dantzig selector method to screen the genotype effects preliminary; then via the idea of stepwise regression, under the other model we further detect the significant main effects and interactive effects for the UV-induced immunosuppression susceptibility. The most significant main effect site that we identified is D10Mit170, and the most significant interactive sites are D6Mit389 and D16Mit131.

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