Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein–Protein Interactions

Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL homodimerization is an anomaly or indicative of broader trends, we characterized PIL dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PIL homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PIL homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PIL protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PIL dimerization activity. Furthermore, ectopic expression of a Joinvillea PIL homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner. Key words: PISTILLATA, Poales, APETALA3, convergent molecular evolution, B-class MADS box genes, evolution of flower development

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1, and to identify a new allele of defective kernel1. Our method provides a quick, simple way to clone genes in maize

Boundary domain genes were recruited to suppress bract growth and promote branching in maize

Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling and genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and promote branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in nongrasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a nonautonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses

Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits.

Shoot apical meristems are stem cell niches that balance proliferation with the incorporation of daughter cells into organ primordia. This balance is maintained by CLAVATA-WUSCHEL feedback signaling between the stem cells at the tip of the meristem and the underlying organizing center. Signals that provide feedback from organ primordia to control the stem cell niche in plants have also been hypothesized, but their identities are unknown. Here we report FASCIATED EAR3 (FEA3), a leucine-rich-repeat receptor that functions in stem cell control and responds to a CLAVATA3/ESR-related (CLE) peptide expressed in organ primordia. We modeled our results to propose a regulatory system that transmits signals from differentiating cells in organ primordia back to the stem cell niche and that appears to function broadly in the plant kingdom. Furthermore, we demonstrate an application of this new signaling feedback, by showing that weak alleles of fea3 enhance hybrid maize yield traits.The fea3-0 allele was kindly provided by Victor Shcherbak, Krasnodar Res. Inst. Agric., Russia. We acknowledge funding from a collaborative agreement with Dupont Pioneer, and from NSF Plant Genome Research Program grant # IOS-1238202 and MCB-1027445, and with the support of the Gatsby Charitable Foundation (GAT3395/PR4) and Swedish Research Council (VR2013-4632) to HJ, and "Next-Generation BioGreen 21 Program (SSAC, Project No. PJ01137901)" Rural Development Administration, Republic of Korea. We also thank Ulises Hernandez for assistance with cloning, Amandine Masson for assistance with peptide assays, and members of the Jackson lab for comments on the manuscript.This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by Nature Publishing Group

Plant Science Decadal Vision 2020–2030: Reimagining the Potential of Plants for a Healthy and Sustainable Future

Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far‐reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1–4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant‐based medicines, and green infrastructure. Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a parts store that supports tinkering and supports query, prediction, and rapid‐response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non‐invasive imaging, sensors, and plug‐and‐play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence‐assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people\u27s natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems

The evolution of floral morphology in the Zingiberales: an investigation into possible roles for the GLOBOSA-like and TEOSINTE BRANCHED 1-like genes

The rapid rise and diversification of the angiosperms has puzzled biologists for centuries; processes leading to current angiosperm diversity remain a key question in evolutionary biology, with particular focus on the morphological diversity of flowers. The Zingiberales are an order of tropical monocots that represent an ideal group of plants to study the evolution of floral morphology. The order contains approximately 2,500 species, many of which form specialized pollination relationships with bees, birds, bats, dung beetles, moths, butterflies, and primates (lemurs) via alterations in floral form. After developing a technique for visualizing and then studying gene expression in floral apices, I investigated the role of two candidate gene families, the GLOBOSA (GLO)-like genes and the CYCLOIDEA/ TEOSINTE BRANCHED 1 (CYC/TB1)-like genes, in the evolution of floral morphology in the Zingiberales. Evolutionary developmental biology often combines methods for examining morphology (e.g. Scanning Electron Microscopy) with analyses of gene expression (e.g. RNA in situ hybridization). Due to differences in tissue preparation for SEM and gene expression analyses, the same specimen cannot be used for both sets of techniques. I developed a method that couples extended-depth-of-field (EDF) epi-illumination microscopy to in situ hybridization in a sequential format, enabling both surface microscopy and gene expression analyses to be carried out on the same specimen (Chapter 1). I first created a digital image of inflorescence apices using epi-illumination microscopy and commercially available EDF software. I then performed RNA in situ hybridizations on photographed apices to assess expression of two developmental genes: Knotted1 (Kn1) in Zea mays (Poaceae) and a GLO homolog in Musa basjoo (Musaceae). I demonstrate that expression signal is neither altered nor reduced in the imaged apices as compared with unphotographed controls. The demonstrated method reduces the amount of sample material necessary for developmental research and enables individual floral development to be placed in the context of the entire inflorescence. While the technique presented is particularly relevant to floral developmental biology, it is applicable to any research where observation and description of external features can be fruitfully linked with analyses of gene expression.The MADS box transcription factor family has long been identified as an important contributor to the control of floral development. It is often hypothesized that the evolution of floral development across angiosperms and within specific lineages may occur as a result of duplication, functional diversification, and changes in regulation of MADS box genes. In Chapter 2 I examine the role of GLO-like genes, members of the B-class MADS box gene lineage, in the evolution of floral development within the monocot order Zingiberales. I assessed changes in perianth and stamen whorl morphology in a phylogenetic framework. I identified GLO homologs from 50 Zingiberales species and investigated the evolution of this gene lineage. Expression of two GLO homologs was assessed in Costus spicatus Swartz (Costaceae) and Musa basjoo Siebold (Musaceae). Based on the phylogenetic data and expression results, I propose several family-specific losses and gains of GLO homologs that appear to be associated with key morphological changes. The GLO-like gene lineage has diversified concomitant with the evolution of the dimorphic perianth and the staminodial labellum. Duplications and expression divergence within the GLO-like gene lineage may have played a role in floral diversification in the Zingiberales.In the Zingiberales, evolutionary shifts in symmetry occur in all floral whorls, making this an ideal group of plants in which to study the evolution of this important ecological and developmental trait. The CYC/TB1-like genes have been implicated in the development and evolution of floral symmetry in divergent angiosperm lineages, and I thus chose them as a candidate gene family to investigate their role in the evolution of floral symmetry within the Zingiberales (Chapter 3). I identified both Zingiberales-specific gene duplications and a duplication in the TB1-like (TBL) lineage that predates the divergence of the commelinid monocots. I examined the expression of two TBL genes in Costus spicatus (Costaceae) and Heliconia stricta (Heliconiaceae), two Zingiberales taxa with divergent floral symmetries. I found that TBL gene expression shifts concomitant with shifts in floral symmetry. Through this body of work we have gained some insight into the mechanics of angiosperm evolution. Duplications in the GLO-like gene lineage in the Zingiberales may have allowed for gene sub- or neofunctionalization and the evolution of new morphologies; in particular, the evolution of differentiated sepals and petals and of the staminodial labellum. In addition, this study adds to the growing body of evidence that CYC/TB1-like genes have been repeatedly recruited through the course of evolution to generate bilateral floral symmetry (zygomorphy). Although this work certainly doesn't preclude the involvement of as yet uncharacterized genes and gene families, it adds to the growing body of evidence that angiosperms as a group do indeed have a genetic `toolkit': a core set of genes that have been variously deployed through evolutionary time to generate both convergent and divergent floral morphologies

Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; hypomorphic and hypermorphic alleles; altered protein-protein interactions; altered domain content; altered protein stability; and altered activity as an activator or repressor. Variability was also observed in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution

SampleTable

Table with sampled species name, order, major clade, sample number (for cell images and outlines), sample ID (for cell images and outlines), and leaf sid