Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize

Patrick J Brown,Sean Myles,Narasimham Upadyayula,Peter J Bradbury,Michael D Mcmullen,Feng Tian,Sherry Flint-Garcia,James B Holland,Torbert R Rocheford,Gregory S Mahone,Edward S Buckler,Jonathan Flint

doi:10.1371/journal.pgen.1002383

Abstract

We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects.

Highlights

The genetic architecture of a complex trait is defined by the number, effect size, frequency, and gene action of the quantitative trait loci (QTL) that affect it
We compare maize inflorescence, flowering, and leaf traits and show that inflorescence traits have distinct genetic architectures characterized by larger effects
We suggest that maize inflorescence traits, and ear traits in particular, have larger effects than flowering or leaf traits as a result of strong directional selection during maize domestication

Summary

Introduction

The genetic architecture of a complex trait is defined by the number, effect size, frequency, and gene action of the quantitative trait loci (QTL) that affect it. A comparison of studies from flies, mice, and humans shows that genetic architecture is remarkably consistent among these species, with many loci of small additive effect [1]. Distributions of QTL effect sizes are strikingly similar among different classes of mouse traits including behavior, biochemistry, immunology, and metabolism [2]. Orr [11] showed that regardless of the distance from the fitness optimum, the expected distribution of effect sizes progressively fixed during adaptation is exponential, with a small number of large-effect loci fixed first, followed by progressively larger numbers of loci with smaller effects becoming fixed. The genetic architecture of intraspecific variation consists of many loci with small effects because loci with larger effects tend to be only briefly polymorphic

Methods

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Discussion

Conclusion