The Evolution of Color and Form in the Species Hemerocallis: A Study in Controlled Gene Expression Terrence P. McGarty, Ph.D.1 Abstract This paper presents an overview of the development of color in the genus Hemerocallis from the perspective of the underlying genetic mechanisms. This genus has several well known and distributed species and has been hybridized extensively over the past one hundred years. In this paper we review the genus and the hybrids and then we provide a review of the current state of research in color expression in flowers such as this genus. The review of the current research summarizes many of the most recent efforts in gene control and expression and the resulting enzyme controls in the anthocyanin pathways. We focus on the anthocyanidin pathways but also discuss recent work in the carotenoid and flavonol pathways as well. The questions still outstanding is; how do all of these pieces come together to create the hybrids as we now know them and a corollary which is; can we use what is known to develop more sophisticated hybrids. Contents 1 Introduction..........................................................................................................................................................3 1.1 Overview ....................................................................................................................................................3 1.2 Why This Genus.........................................................................................................................................4 1.3 Prior Work..................................................................................................................................................5 1.3.1 Genetic Structure of Hemerocallis.........................................................................................................5 1.3.2 Gene Expression and Pathway Control..................................................................................................5 1.3.3 Modeling of Gene Expression: Analysis and Synthesis ........................................................................6 2 Hemerocallis Species and Color ..........................................................................................................................6 2.1 The Species.................................................................................................................................................6 2.2 The Early and Latter Hybrids ...................................................................................................................12 3 Classic Genetics .................................................................................................................................................15 3.1 Mendellian Analysis.................................................................................................................................15 3.2 Breeding and Hybridizing ........................................................................................................................18 3.3 Summary of Mendellian Approach ..........................................................................................................18 4 Flower Color Expression....................................................................................................................................19 4.1 Pathways and Enzymes ............................................................................................................................19 4.2 Anthocyanins............................................................................................................................................20 4.3 Other Color Elements ...............................................................................................................................24 4.4 Carotenoids...............................................................................................................................................24 4.5 Flavones....................................................................................................................................................25 4.6 Pathways...................................................................................................................................................26 4.6.1 Anthocyanin Pathway..........................................................................................................................27 4.6.2 Carotenoid Pathway.............................................................................................................................31 4.6.3 Flavonol Pathway ................................................................................................................................32 5 Genetic Influence ...............................................................................................................................................32 5.1 Plant Cells.................................................................................................................................................32 5.2 Plant DNA ................................................................................................................................................34 1 Copyright, © 2006, Terrence P. McGarty, all rights reserved. Dr. McGarty is Head of Plant Research at The Telmarc Gardens, a subsidiary of The Telmarc Group, LLC. McGarty: Hemerocallis Gene Expression and Control 5.3 Plant Gene Processes................................................................................................................................35 5.4 Activators .................................................................................................................................................37 5.5 Repressors ................................................................................................................................................40 5.6 Summary of Actions.................................................................................................................................40 6 Expression Analysis and Implications ...............................................................................................................41 6.1 Approach: Engineering versus Science ....................................................................................................41 6.2 A Control Paradigm..................................................................................................................................41 6.3 Cell Signalling: Intra and Inter Cell..........................................................................................................42 6.4 A Model for Secondary Production..........................................................................................................44 6.4.1 Linear Models......................................................................................................................................45 6.4.2 Second Order Models ..........................................................................................................................46 6.5 Pattern Initiation .......................................................................................................................................47 6.6 Methods for Verification and Validation..................................................................................................51 7 Conclusions........................................................................................................................................................52 8 References..........................................................................................................................................................54 9 Web Sites ...........................................................................................................................................................57 Page 2 of 57 McGarty: Hemerocallis Gene Expression and Control 1 INTRODUCTION The development of color in hybrids of plants can be viewed in many ways. One, the Mendellian approach, is that there is some element, called a gene, which is on a chromosome, and there is some mixing set of rules, dominant and recessive, which when applied allow for the control of the color development. The recent point of view is that there are genetic pathways which are controlled by enzymes, proteins, and that understanding the mechanisms of the control of these pathways is key to understanding the process. However, the questions we raise herein, and then seek answers in the current literature, and finally propose possible paths of inquiry are as follows: 1. Given a dozen or more species plants which are relatively stable and consistent in the wiled, how does the variation in color in hybrids arise. Namely, what is the cellular basis of color, and moreover what is the genetic set of mechanisms which control this. 2. Given the complexity of color, form and variegation in the hybrids, what is the genetic basis for the control mechanisms intracell and intercell. For example, how are such colorations as eyezones formed and what is the intercellular communications mechanisms which effect this. 3. Given what now appears to be a set of well understood pathways control mechanisms by enzymes produced within the cell and the gene control mechanisms for expression of these proteins, how are these combined to produce intra cellular coloration and what are the inter cellular communications which