The genetic architecture of teosinte catalyzed and constrained maize domestication

Abstract

The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.

Genetic analysis of prolificacy in “Sikkim Primitive”—A prolific maize (Zea mays) landrace of North‐Eastern Himalaya

“…While in cultivated maize, generally one ear per plant is observed, teosinte possesses multiple ears per plant (Doebley & Stec, ). Domesticated maize thus said to be “not prolific”, while its progenitor teosinte is regarded as “prolific” (Doebley, Stec, & Gustus, ; Yang et al, ). Among cultivated maize, “Sikkim Primitive” locally popular as “Murali Makai” is a unique landrace found in North‐Eastern Himalayan region of India, as it possesses 7–9 ears per plant compared to one ear observed in other maize genotypes (Sharma, Prasanna, & Ramesh, ).…”

Adaptive phenotypic divergence in an annual grass differs across biotic contexts*

“…; Yang et al. ). For example, differences between the direction of selection and the major axis of trait variation may cause trait divergence among populations to reflect the major axis of the G matrix in individual populations (Schluter ; Chenoweth et al.…”

“…The course of adaptation to divergent environments can be strongly affected by trait variance and covariance (Schluter 1996;Etterson and Shaw 2001;Chenoweth et al 2010;Yang et al 2019). For example, differences between the direction of selection and the major axis of trait variation may cause trait divergence among populations to reflect the major axis of the G matrix in individual populations (Schluter 1996;Chenoweth et al 2010;McGlothlin et al 2018).…”

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

“…The teosinte (Zea mays ssp. parviglumis; N = 20) were collected near Palmar Chico, Mexico [28]. We harvested the third leaf of the teosintes and Mexican landraces for DNA extraction using a modified CTAB procedure [62].…”

“…Here, we sequenced genomes from a set of geographically widespread Mexican landraces and a natural population of teosinte collected near Palmar Chico, Mexico [28], from which we generated genomic sequences and methylomes in base-pair resolution. Additionally, we profiled the teosinte (accession no.…”