From Many, One: Genetic Control of Prolificacy during Maize Domestication

TL;DR

This study identifies a key genetic locus, prol1.1, that controls prolificacy in maize domestication by regulating gt1 gene expression, leading to architectural changes that improved harvestability.

Contribution

It uncovers a specific cis-regulatory change upstream of gt1 that influenced maize architecture during domestication, linking genetic variation to phenotypic evolution.

Findings

Identification of prol1.1 as a major QTL for prolificacy

Fine-mapping of prol1.1 to a 2.7 kb regulatory region

Evidence of positive selection on the maize allele of prol1.1

Abstract

A reduction in number and an increase in size of inflorescences is a common aspect of plant domestication. When maize was domesticated from teosinte, the number and arrangement of ears changed dramatically. Teosinte has long lateral branches that bear multiple small ears at their nodes and tassels at their tips. Maize has much shorter lateral branches that are tipped by a single large ear with no additional ears at the branch nodes. To investigate the genetic basis of this difference in prolificacy (the number of ears on a plant), we performed a genome-wide QTL scan. A large effect QTL for prolificacy (prol1.1) was detected on the short arm of chromosome one in a location that has previously been shown to influence multiple domestication traits. We fine-mapped prol1.1 to a 2.7 kb interval or causative region upstream of the grassy tillers1 gene, which encodes a homeodomain leucine zipper transcription factor. Tissue in situ hybridizations reveal that the maize allele of prol1.1 is associated with up-regulation of gt1 expression in the nodal plexus. Given that maize does not initiate secondary ear buds, the expression of gt1 in the nodal plexus in maize may suppress their initiation. Population genetic analyses indicate positive selection on the maize allele of prol1.1, causing a partial sweep that fixed the maize allele throughout most of domesticated maize. This work shows how a subtle cis-regulatory change in tissue specific gene expression altered plant architecture in a way that improved the harvestability of maize.