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Evidence of Selection at the Ramosa1 Locus During Maize Domestication

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Evidence of Selection at the Ramosa1 Locus During Maize Domestication Molecular Ecology (2010) 19, 1296–1311 doi: 10.1111/j.1365-294X.2010.04562.x Evidence of selection at the ramosa1 locus during maize domestication BRANDI SIGMON and ERIK VOLLBRECHT Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA Abstract Modern maize was domesticated from Zea mays parviglumis, a teosinte, about 9000 years ago in Mexico. Genes thought to have been selected upon during the domestication of crops are commonly known as domestication loci. The ramosa1 (ra1) gene encodes a putative transcription factor that controls branching architecture in the maize tassel and ear. Previous work demonstrated reduced nucleotide diversity in a segment of the ra1 gene in a survey of modern maize inbreds, indicating that positive selection occurred at some point in time since maize diverged from its common ancestor with the sister species Tripsacum dactyloides and prompting the hypothesis that ra1 may be a domestication gene. To investigate this hypothesis, we examined ear phenotypes resulting from minor changes in ra1 activity and sampled nucleotide diversity of ra1 across the phylogenetic spectrum between tripsacum and maize, including a broad panel of teosintes and unimproved maize landraces. Weak mutant alleles of ra1 showed subtle effects in the ear, including crooked rows of kernels due to the occasional formation of extra spikelets, correlating a plausible, selected trait with subtle variations in gene activity. Nucleotide diversity was significantly reduced for maize landraces but not for teosintes, and statistical tests implied directional selection on ra1 consistent with the hypothesis that ra1 is a domestication locus. In maize landraces, a noncoding 3¢-segment contained almost no genetic diversity and 5¢-flanking diversity was greatly reduced, suggesting that a regulatory element may have been a target of selection. Keywords: maize, plant domestication, positive selection, ramosa1 Received 7 July 2009; revision received 13 November 2009; accepted 17 November 2009 2009). For example, in many modern crops, accelerated Introduction selection of preferable traits has occurred within the last Agriculture began some 10 000 years ago, when prehis- few 100 years, in a process known as crop improvement toric farmers in both the New and Old World began that is temporally well separated from domestication. domesticating plants and animals through selection on Darwin recognized the artificial selection that occurred desirable traits. In plants such characters included seed during the domestication of plants and animals as anal- or grain quality, yield and ease of harvest among ogous to the process of natural selection that drives the numerous other traits (Smith 1995). The domestication evolution of species, and studies of domesticated spe- process typically spans hundreds to thousands of years cies inform our understanding of the genetic basis of during which time preferred traits might be selected on evolutionary diversification (Doebley et al. 2006). singly or in combination with others. Due to continued In the context of either natural or artificial forces, dif- selection after or in concert with initial domestication ferent modes of selection on phenotypes lead to differ- events, cultural and ecological adaptation results in ent outcomes in allele frequencies. For instance, locally adapted, diversified crops (Purugganan & Fuller directional selection on a preferred phenotype as may occur in domestication and ⁄ or cultural adaptation leads Correspondence: Erik Vollbrecht, Fax: +1 515 294 6755; to an increase in frequency of the corresponding E-mail: [email protected] allele(s), whereas balancing selection maintains multiple Ó 2010 Blackwell Publishing Ltd SELECTION AT RAMOSA1 DURING MAIZE DOMESTICATION 1297 alleles. For genes that are associated with positively approach in which a candidate gene(s) known to func- selected traits in domestication and improvement, the tion in the morphological development of the maize ear process may leave behind so-called signatures of selec- is (are) examined for evidence of selection may prove tion in the form of distinctive patterns of reduced nucleo- more fruitful. tide diversity (Tanksley & McCouch 1997). When a wild ramosa1 is a mutant of maize that has been studied progenitor and intermediate cultivars are extant and can by geneticists for many years (Gernert 1912) but only be sampled, appropriate statistical tests (Sabeti et al. recently come to be understood at the molecular level. 2006) may identify and differentiate these signatures of The ra1 gene encodes a plant-specific C2H2, EPF-sub- selection in the genome, and pinpoint a selective event to class zinc finger transcription factor. It is expressed in a a particular phase of crop evolution. boundary domain near the base of particular meristems Molecular, archaeobotanical and palaeoecological evi- in the inflorescences (the ear and tassel), thereby regu- dence suggest a single domestication event for maize, lating fate of the adjacent meristem (Vollbrecht et al. around 9000 years ago in Mexico (Matsuoka et al. 2002; 2005). ra1 is a component of a genetic pathway, termed Piperno et al. 2009). Maize was domesticated from its the ramosa pathway, that imposes a spikelet pair or wild ancestor Zea mays ssp. parviglumis (hereafter short branch identity as branch meristems are initiated referred to as teosinte) (Doebley 2004). Maize and during tassel and ear development (Vollbrecht et al. teosinte have many similarities but exhibit striking 2005; Bortiri et al. 2006; Satoh-Nagasawa et al. 2006). differences in plant architecture and ear morphology. Morphologically, normal ra1 gene function results in Phenotype-driven approaches such as mutant and QTL the unbranched appearance of the ear and the upper studies have shown that the molecular basis for some part of the tassel, by causing both structures to produce of these major phenotypic differences may be explained short, determinate spikelet pair branches (Fig. 1a–d). In by selection on a few domestication loci of major effect. plants that contain strong mutant ra1 alleles and there- In particular, the teosinte branched1 (tb1) gene explains fore lack ra1 gene function, the ears and tassels have most of the difference in plant architecture (Doebley additional long branches, leading to a highly disorga- et al. 1995, 1997; Clark et al. 2004, 2006). Other domesti- nized ear (Fig. 1c and f). By contrast, in weak ra1 cation and diversification loci may include genes mutants the tassels contain just a few extra branches involved in biochemical traits, such as those involved in (Fig. 1b, arrowhead) and ears have crooked rows but the production of starch (Whitt et al. 2002) or those are otherwise relatively normal (Fig. 1e). Crooked rows responsible for the carotenoid-rich yellow endosperm probably affect grain yield in maize and are common to (Palaisa et al. 2004). These examples are among a few other mutants, including ramosa2 mutants where they putative domestication loci in maize for which an form as a consequence of spikelet triplets being pro- accompanying, selected trait is clearly discernible. duced in place of spikelet pairs (Bortiri et al. 2006). Candidate domestication loci may also be identified Thus, it is reasonable to hypothesize that the phenotype by genotype-driven approaches, such as strictly molecu- of weak ra1 mutants has a similar developmental basis, lar, large-scale screens for genes with signatures of arti- but this has not been examined. ficial selection (Casa et al. 2005; Chapman et al. 2008). Existing molecular data concerning ra1 function beg Such studies in maize suggest that more than 1000 the question of whether or not ra1 may have been a tar- genes may have been selected on during the derivation get of selection given the gene’s role in ear develop- of modern maize (Wright et al. 2005; Yamasaki et al. ment. Previously, nucleotide diversity in a 700-bp 2005). A disadvantage of this approach is that when segment of the ra1 gene in maize was examined in a candidate genes are defined by strictly molecular crite- panel of diverse, modern inbred lines and a signature ria, the corresponding gene functions are a priori of selection was detected relative to the neighbouring unknown. Thus, while these approaches hold great genus Tripsacum (Vollbrecht et al. 2005). These data sug- promise for identifying genes that contribute to adap- gested an event of positive selection somewhere tive traits (Ross-Ibarra et al. 2007), relating such domes- between the present and the point in time when maize tication loci to a selected trait is challenging. Notably, and tripsacum diverged from their common ancestor in maize many of these putative domestication loci several million years ago, with caveats. First, studies identified by genomics are hypothesized to be have shown that sampling a small region of a locus expressed preferentially in the ear (Hufford et al. 2007), may lead to erroneous conclusions about positive selec- and to perhaps be related to selection on ear traits, tion (Yamasaki et al. 2008). Second, previous work because among the grasses the prolific maize ear is a could not distinguish during which time period the unique and highly derived organ. Moreover, in the ear putative selection occurred: the evolution of teosinte, the basis of maize-teosinte phenotype differences is maize domestication and ⁄ or modern maize improve- poorly understood. Thus, a modified, genotype-driven ment. To find evidence of selection at ra1 during the Ó 2010 Blackwell Publishing Ltd 1298 B. SIGMON and E. VOLLBRECHT (a) (b) (c) Fig. 1 Maize ramosa1 mutant pheno- types in mature tassels and ears. Wild- type (inbred Mo17) tassel (a) and ear (d), weak mutant (ra1-63.3359 in Mo17) tassel (b) and ear (e), and strong mutant (ra1-R in a hybrid background) tassel (c) and ear (f). Weak mutant tassels have a few additional long branches (arrow- head) when compared with wild type, whereas strong mutant tassels have long branches extending up the central rachis. Wild-type ears have straight rows, whereas weak mutant ears have crooked rows. Strong mutants exhibit branched ears.
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