Power of the joint segregation analysis method for testing mixed major-gene and polygene inheritance models of quantitative traits

Understanding the genetic architecture of quantitative traits can greatly a ssist the design of strategies for their manipulation in plant-breeding pro grams. For a number of traits, genetic variation can be the result of segre gation of a few major genes and many polygenes (minor genes). The joint seg regation analysis (JSA) is a maximum-likelihood approach for fitting segreg ation models through the simultaneous use of phenotypic information from mu ltiple generations. Our objective in this paper was to use computer simulat ion to quantify the power of the JSA method for testing the mixed-inheritan ce model for quantitative traits when it was applied to the six basic gener ations: both parents (P-1 and P-2), F-1, F-2, and both backcross generation s (B-1 and B-2) derived from crossing the F-1 to each parent. A total of 19 68 genetic model-experiment scenarios were considered in the simulation stu dy to quantify the power of the method. Factors that interacted to influenc e the power of the JSA method to correctly detect genetic models were: (1) whether there were one or two major genes in combination with polygenes, (2 ) the heritability of the major genes and polygenes, (3) the level of dispe rsion of the major genes and polygenes between the two parents, and (4) the number of individuals examined in each generation (population size). The g reatest levels of power were observed for the genetic models defined with s imple inheritance; e.g., the power was greater than 90% for the one major g ene model, regardless of the population size and major-gene heritability. L ower levels of power were observed for the genetic models with complex inhe ritance (major genes and polygenes), low heritability, small population siz es and a large dispersion of favourable genes among the two parents; e.g., the power was less than 5% for the two major-gene model with a heritability value of 0.3 and population sizes of 100 individuals. The JSA methodology was then applied to a previously studied sorghum data-set to investigate th e genetic control of the putative drought resistance-trait osmotic adjustme nt in three crosses. The previous study concluded that there were two major genes segregating for osmotic adjustment in the three crosses. Application of the JSA method resulted in a change in the proposed genetic model. The presence of the two major genes was confirmed with the addition of an unspe cified number of polygenes.