Estimating effects of a single gene and polygenes on quantitative traits from a diallel design

Abstract

A genetic model is developed with additive and dominance effects of a single gene and polygenes as well as general and specific reciprocal effects for the progeny from a diallel mating design. The methods of ANOVA, minimum norm quadratic unbiased estimation (MINQUE), restricted maximum likelihood estimation (REML), and maximum likelihood estimation (ML) are suggested for estimating variance components, and the methods of generalized least squares (GLS) and ordinary least squares (OLS) for fixed effects, while best linear unbiased prediction, linear unbiased prediction (LUP), and adjusted unbiased prediction are suggested for analyzing random effects. Monte Carlo simulations were conducted to evaluate the unbiasedness and efficiency of statistical methods involving two diallel designs with commonly used sample sizes, 6 and 8 parents, with no and missing crosses, respectively. Simulation results show that GLS and OLS are almost equally efficient for estimation of fixed effects, while MINQUE (1) and REML are better estimators of the variance components and LUP is most practical method for prediction of random effects. Data from a Drosophila melanogaster experiment (Gilbert 1985a, Theor appl Genet 69:625-629) were used as a working example to demonstrate the statistical analysis. The new methodology is also applicable to screening candidate gene(s) and to other mating designs with multiple parents, such as nested (NC Design I) and factorial (NC Design II) designs. Moreover, this methodology can serve as a guide to develop new methods for detecting indiscernible major genes and mapping quantitative trait loci based on mixture distribution theory. The computer program for the methods suggested in this article is freely available from the authors.

Quantitative genetic analysis station for the genetic analysis of complex traits

“…The ADMP model [21] can be used to estimate the maternal and paternal effect (M, P) contribution to the phenotypic outcomes [22,23]. The AMC model, which can be applied to haploid-based experiments, such as anther culture studies [24] should also be mentioned.…”

Resistance to Xanthomonas spp. in Tomato: Diallel Analysis and Gene Effects Estimative in a Breeding Programme Carried out in Brazil

“…Several major genes that have a large effect together with polygenes that have a small effect are responsible for the quantitative trait differences and it includes some pest and disease resistance. Diallel analysis can provide much useful genetic information on polygenes contributing to the trait differences among parents (Lou and Yang, 2006). The use of this genetic–statistical methodology can also provide reliable information on the potential of parents and their hybrid combinations, besides conclusions on the genetic control, to determine the most adequate breeding method to obtain superior recombined inbred lines (Cruz et al., 2004).…”

Breeding bambara groundnut (vigna subterranea (L.) verdc) for enhanced yield and nutritional quality in South Africa.

“…Also, the yield of the newly-developed crosses is higher than the yield of the popular variety MPB 51 (Brianbeck), which is widely cultivated in South Africa (Mabhaudhi et al 2014). Also, the yield attained for most crosses is comparable to MPB39 landrace, which is popularly grown in KwaZulu-Natal (Musango et al 2022).…”