The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

Authors: HUNG, HSIAOYI - North Carolina State University; Browne, Christopher; Guill, Katherine; COLES, NATHAN - Pioneer Hi-Bred International; ELLER, MAGEN - Monsanto Corporation; Garcia, Arturo; Lepak, Nicholas; Melia-Hancock, Susan; OROPEZA-ROSAS, MARCO - Terral Seed; SALVO, STELLA - University Of Wisconsin; UPADYAYULA, NARASIMHAM - Monsanto Corporation; Buckler, Edward - Ed; Flint-Garcia, Sherry; McMullen, Michael; ROCHEFORD, TORBERT - Purdue University; Holland, Jim - Jim

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2011
Publication Date: 4/20/2012
Citation: Hung, H., Browne, C.J., Guill, K.E., Coles, N., Eller, M., Garcia, A., Lepak, N.K., Melia-Hancock, S., Oropeza-Rosas, M., Salvo, S., Upadyayula, N., Buckler IV, E.S., Flint Garcia, S.A., Mcmullen, M.D., Rocheford, T., Holland, J.B. 2012. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity. 108:490-499.

Interpretive Summary: The maize Nested Association Mapping population is an extremely powerful resource for identifying genes affecting complex traits. A practical drawback to the use of this resource is its very large genetic sample size: 5,000 unique genetic lines. Many researchers do not have resources to evaluate the entire set of lines. Therefore, we investigated if researchers would be advised to select among the 25 different families that compose the whole population for those families whose parents were most genetically distinct or had the largest trait differences as a method to reduce the sample size. We found that genetic variation within families was only loosely related to the amount of parental trait (phenotypic) differences, and not at all to genetic distance of the parents. We recommend that users sample as many families as possible, employing a weighted sampling scheme that weights families from more distinct parents more heavily.

Technical Abstract: The choice of populations for quantitative genetics experiments impacts inferences about genetic architecture and prospective selection gains. Plant breeding and quantitative genetics studies are often conducted in one or a few among many possible biparental families. Trait genotypic variation within a family is indicative of the family's breeding potential and informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide breeding programs and experimental studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of about 200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to eleven environments. Genetic distances among parents were estimated with 44 SSR and 2303 SNP markers. Regression of within-family genetic variance estimates on parental phenotypic or genotypic distances revealed that phenotypic parental distances were related to progeny genetic variances for about half of the traits measured. Genetic distances were rarely informative as to progeny variation. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.