Evidence That the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution intga1

Abstract

teosinte glume architecture1 (tga1), a member of the SBP-box gene family of transcriptional regulators, has been identified as the gene conferring naked kernels in maize vs. encased kernels in its wild progenitor, teosinte. However, the identity of the causative polymorphism within tga1 that produces these different phenotypes has remained unknown. Using nucleotide diversity data, we show that there is a single fixed nucleotide difference between maize and teosinte in tga1, and this difference confers a Lys (teosinte allele) to Asn (maize allele) substitution. This substitution transforms TGA1 into a transcriptional repressor. While both alleles of TGA1 can bind a GTAC motif, maize-TGA1 forms more stable dimers than teosinte-TGA1. Since it is the only fixed difference between maize and teosinte, this alteration in protein function likely underlies the differences in maize and teosinte glume architecture. We previously reported a difference in TGA1 protein abundance between maize and teosinte based on relative signal intensity of a Western blot. Here, we show that this signal difference is not due to tga1 but to a second gene, neighbor of tga1 (not1). Not1 encodes a protein that has 92% amino acid similarity to TGA1 and that is recognized by the TGA1 antibody. Genetic mapping and phenotypic data show that tga1, without a contribution from not1, controls the difference in covered vs. naked kernels. No trait differences could be associated with the maize vs. teosinte alleles of not1. Our results document how morphological evolution can be driven by a simple nucleotide change that alters protein function. KEYWORDS tga1; glume architecture; teosinte; maize; domestication A LTHOUGH the study of adaptive evolution through natural or artificial selection dates back to Darwin, the genetic mechanisms that drive changes in morphology remain strongly debated (Stern and Orgogozo 2008). Questions surrounding the number of genes (few or many) and types of mutations (regulatory or coding) in these genes have been a focus in this debate (Carroll 2005(Carroll , 2008Hoekstra and Coyne 2007). These questions can only be answered through the genetic and molecular dissection of genes that have undergone selective pressure between lineages or within populations. Crop species offer a powerful system for investigating these questions since crops are the products of continuous directional selection to adapt them to the human controlled environment and human needs (Meyer and Purugganan 2013). Research on crop models is further facilitated by the extensive genetic and genomic resources available for them. Moreover, because of the recent divergence of crop species from their wild progenitors, crop-progenitor pairs remain cross-compatible and amenable to genetic analysis.Maize was domesticated in the central Balsas valley of Mexico 9000 years ago from a wild relative called teosinte (Piperno et al. 2001;Matsuoka et al. 2002). Because the morphology of modern maize is drastically different from teosinte species, the progenitor of mai...

Maize domestication and gene interaction

“…That the allele was present before domestication, and does not always generate a maize-like phenotype when present in teosinte (Vann et al, 2015) shows that the presence of the maize allele at tb1 is not enough to generate a maize-like phenotype. In contrast, the maize allele at tga1 that restructures glumes and cupules of the ear was fixed within the last 10,000 years (Wang et al, 2005), likely a result of selection on a new non-synonymous mutation (Wang et al, 2015). Of the two oldest cob samples sequenced, Ramos-Madrigal et al (2016) find the maize allele at tga1, while Vallebueno-Estrada et al (2016) do not recover the causal polymorphism, but find elevated diversity in the region, which they suggest reflects incomplete selection on the maize allele.…”

“…The maize allele of tga1 inhibits secondary sexual traits in the female flower, preventing glumes from hardening (Preston et al, 2012). A nonsynonymous mutation in exon 1 of tga1 alters dimerization of the protein, affecting its stability and preventing activation of downstream targets (Wang et al, 2015). The chromosome 4 QTL that contains tga1 explains between 27-62.4% of phenotypic variation for glume hardness (Doebley and Stec, 1991, 1993;Briggs et al, 2007).…”

“…While the tga1 ortholog in rice has pleiotropic effects on inflorescences and vegetative structures (Preston et al, 2012;Wang et al, 2015), tga1 is expressed only in the maize ear, likely a result of gene duplication of an ancestral single locus, with subsequent subfunctionalization restricting expression to the ear (Preston et al, 2012;Wang et al, 2015). The paralogous locus, not tga1(not1), retains expression profiles as found in other grasses (Wang et al, 2011, suggesting that in maize, the effects of the maize allele of tga1 are limited to the fruitcase itself, freeing it from constraints on selection imposed by pleiotropic effects elsewhere in the plant.…”

“…This phenotype of the maize allele in a teosinte background could allow visual identification of heterozygotes (Wang et al, 2005), yet none were identified in a screen of more than 2 million teosinte seeds (Beadle, 1980;Wilkes, 2004;Berg and Singer, 2005). Consistent with this, the maize allele appears to have arisen de novo during domestication (Wang et al, 2015), suggesting the necessity of human cultivation to select for this dramatic phenotype. Beyond single loci, the phenotypic means in F2's of maize × teosinte crosses and backcrosses of teosinte to maize deviate towards the teosinte parent (Lambert and Leng, 1965;Doebley et al, 1990;Doebley and Stec, 1993;Doebley et al, 1995a).…”

“…The chromosome 4 QTL that contains tga1 explains between 27-62.4% of phenotypic variation for glume hardness (Doebley and Stec, 1991, 1993;Briggs et al, 2007). Additionally, this gene appears to have pleiotropic impacts on ear disarticulation, lateral branch length, and ear phyllotaxy (Wang et al, 2015). …”