Identification and estimation of a QTL model and its effects

A joint segregation analysis of a genetic system and the effects of QTLs ba sed on the six populations P-1, F-1, P-2, B-1, B-2 and F-2 is proposed in t his paper. The major steps were as follows. Firstly, under the supposition that the segregating population was composed of component distributions con trolled by a major gene(s) and modified by both polygenes and environments, four groups and 17 types of genetic models, including a one major-gene mod el, a two major-gene model, a polygene model, and a mixed one-major gene an d polygene model, were set up. Secondly, the joint maximum-likelihood funct ion was constructed from the six generations so as to estimate the paramete rs of component distributions through an EM algorithm. Thirdly, the best-fi tting genetic model was chosen according to Akaike's information criterion, a likelihood-ratio test, and tests for goodness of fit. Fourthly, the rela ted genetic parameters, including gene effects, as well as the genetic vari ances of major genes and polygenes, were obtained from the estimates of com ponent distributions. Finally, the individuals in segregating populations w ere classified into their major-gene genotypes according to their posterior probabilities. An example of the genetic analysis of plant height of a ric e cross between Nanjing No. 6 and Guangcong was used to illustrate the abov e procedure. The method was especially appropriate to those crops with easy to obtain hybrid seeds.