Study On Methods For Marker-Assisted Selection Based On QTLs With Complicated Epistasis And Their Environmental Interactions

Many QTL mapping experiments are conducted for the propose of locating genes, which account for genetic variation in agriculturally important phenotypes, as a starting point for use of marker-assisted selection (MAS) in plant or animal improvement. The present study has focused in the use of QTL via MAS in breeding programs. Employing Bayesian theorem, a method for MAS based on QTLs with complicated epistasis as well as their environmental interactions is proposed. This method has been applied to population improvement of cross-fertilizing crops and selection in segregating generations of self-fertilizing crops. Computer simulations are used to investigate the efficiency and reliability of such method under a wide range of situations. This method promises to shed light on the utilization of QTL information regarding epistasis and QTL x environment (QE) interaction in breeding programs, as well as provides an increased understanding of genetic base underlying improvement of the quantitative trait. The main results and issues are summarized as follows:1. A genetic model for selection is developed, which includes effects of additive, dominance and digenic epistasis of additive x additive, additive * dominance, dominance x additive, dominance x dominance. In this paper, formulae are also derived for estimating variance and covariance components of additive, dominance and epistasis, as well as the probability of QTL genotype conditioned its phenotype and marker genotype for each individual over generations. In random mating system, breeding value, extending its original connotation with inclusion of additive x additive epistasis, is proposed as a measure used in selection. While in selfing system, a potential index that measures the probability of an individual showing superior genotype is also proposed.2. Monte Carlo simulations are conducted to study the presented MAS methods. The results indicate that such MAS can be more effective than selection based solely on phenotype in a large of situations. These results have provided strong evidences suggesting both breeding value and potential index as a more appropriate measure used in selection under their respective mating systems.3. The present study has shown that utilization of epistasis is of great importance in breeding programs, especially for optimizing the long-term selection efficiency. In presence of epistasis, MAS generally yields longer persistence response than that basedexclusively on additive or additive and dominance. Ignoring epistasis underlying selection, however, results in considerable loss in selection response, more at later generations. In addition to population size and trait heritability, genetic variance configuration plays an important role in determining in both the short- and long-term of efficiencies of MAS.4. The present study has shown that attempt for the utilization of QTL in breeding programs has to take into account of such QE interactions. When MAS is based on those QTLs evaluated in a single environment, the causal QE interactions usually reduce general response across environments, and the reduction in the cumulative general response is a function of the proportion of QE interaction involved in the improved trait. However, MAS on genetic main effects of those QTLs evaluated in multiple environments not only yields higher general response but, most importantly, the general response obtained is reasonably robust to QE interactions involved in improved trait. But the total response achieved by MAS in a specific environment is largely dependent on the total heritability of the improved trait and is little subject to relative changes between general heritability and GE interaction heritability. Therefore, plant breeders should be cautious to utilize such QTL information from one environment in the design and execution of breeding studies in another.5. The present study has shown that MAS in segregating generation of self-fertilizing crops helps increasing the probability of selectin...