Molecular evolution of a reproductive barrier in maize and related species

Abstract

Three cross-incompatibility loci each control a distinct reproductive barrier in domesticated maize (Zea mays ssp. mays) and its wild teosinte relatives. These three loci, Teosinte crossing barrier 1 (Tcb1), Gametophytic factor 1 (Ga1), andGa2, each play a key role in preventing hybridization between populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes a matching pair of silk- and pollen-active pectin methylesterases (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly which contains active versions of all three loci. We then examined fifty-two assembled genomes from seventeen species to classify haplotype diversity and identify sites under diversifying selection during the evolution of the causal genes. We show thatGa2, the oldest of these three loci, was duplicated to formGa1at least 12 million years ago.Tcb1, the youngest locus, arose as a duplicate ofGa1before or around the time of diversification of theZeagenus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at theGa1locus is a conservedga1allele (ga1-O), which is non-coding due to conserved stop codons in full-length gene copies that are between 610 thousand and 1.5 million years old. We show that thega1-Oallele is associated with and likely generates 24-nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functionalGa1alleles. In previously-published crosses, thega1-Oallele associates with reduced function of the typically dominant functional alleles for theGa1andTcb1barriers. Taken together, this seems to be an example of a type of epigenetic trans-homolog silencing known as paramutation functioning at a locus controlling a reproductive barrier.