University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-2012 The volutE ionary Genetics of Seed Shattering and Flowering Time, Two Weed Adaptive Traits in US Weedy Rice Carrie S. Thurber University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Plant Biology Commons Recommended Citation Thurber, Carrie S., "The vE olutionary Genetics of Seed Shattering and Flowering Time, Two Weed Adaptive Traits in US Weedy Rice" (2012). Open Access Dissertations. 626. https://scholarworks.umass.edu/open_access_dissertations/626 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. THE EVOLUTIONARY GENETICS OF SEED SHATTERING AND FLOWERING TIME, TWO WEED ADAPTIVE TRAITS IN US WEEDY RICE A Dissertation Presented by CARRIE S. THURBER Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY September 2012 Plant Biology Graduate Program © Copyright by Carrie S. Thurber 2012 All Rights Reserved THE EVOLUTIONARY GENETICS OF SEED SHATTERING AND FLOWERING TIME, TWO WEED ADAPTIVE TRAITS IN US WEEDY RICE A Dissertation Presented by CARRIE S. THURBER Approved as to style and content by: _______________________________________ Ana L. Caicedo, Chair _______________________________________ Samuel P. Hazen, Member _______________________________________ Lynn S. Adler, Member _______________________________________ Jeffrey L. Blanchard, Member ____________________________________ Elsbeth L. Walker, Director, Plant Biology Graduate Program DEDICATION “Weed is not a category of nature but a human construct, a defect of our perception.” Michael Pollan, Second Nature This dissertation is dedicated to my parents who always supported me in my academic pursuits. ACKNOWLEDGMENTS I would like to thank my advisor, Ana Caicedo, for her mentoring and my fellow Plant Biology graduate program and lab members for their assistance and friendship. v ABSTRACT THE EVOLUTIONARY GENETICS OF SEED SHATTERING AND FLOWERING TIME, TWO WEED ADAPTIVE TRAITS IN US WEEDY RICE SEPTEMBER 2012 CARRIE S. THURBER, B.S., FRAMINGHAM STATE UNIVERSTIY M.S., UNIVERSITY AT BUFFALO Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Ana L. Caicedo Weedy rice is a persistent weed of cultivated rice ( Oryza sativa ) fields worldwide, which competes with the crop and drastically reduces yields. Within the US, two main populations of genetically differentiated weedy rice exist, the straw-hulled (SH) group and the black-hulled awned (BHA) group. Current research suggests that both groups are derived from Asian cultivated rice. However, the weeds differ from the cultivated groups in various morphological traits. My research focus is on the genetic basis of two such traits: seed shattering ability and differences in flowering time. The persistence of weedy rice has been partly attributed to its ability to shatter (disperse) seed prior to crop harvesting. I have investigated the shattering phenotype in a collection of US weedy rice accessions and find that all US weedy rice groups shatter seeds easily. Additionally, I characterized the morphology of the abscission layer at the site where seed release occurs and find that weeds begin to degrade their abscission layers at least five days prior to wild plants. I also assessed allelic identity and diversity at the major shattering locus, sh4 , in weedy rice and find that all cultivated and weedy rice share similar haplotypes at sh4 . These haplotypes contain a single derived mutation associated with decreased seed vi shattering during domestication. The combination of a shared cultivar sh4 allele and a highly shattering phenotype suggests that US weedy rice have re-acquired the shattering trait after divergence from their crop progenitors through alternative genetic mechanisms. Additionally, my investigation into flowering time in weedy rice shows that weed populations differ in their flowering times. I also assessed allelic identity and diversity at two genes involved in the transition to flowering, Hd1 and Hd3a , and again found haplotype sharing between weeds and cultivars with Hd1 only accounting for some of the flowering time differences between weeds. In order to locate genomic regions containing additional candidate genes I conducted a QTL mapping study on two F 2 populations derived from crosses of weedy rice with cultivated rice. My results show sharing of QTL for flowering time between populations, yet lack of sharing of QTL for shattering. vii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ...................................................................................................v ABSTRACT ....................................................................................................................... vi LIST OF TABLES ............................................................................................................ xii LIST OF FIGURES ......................................................................................................... xiii CHAPTER 1. OVERVIEW OF DISSERTATION TOPIC ....................................................................1 1.1 Parallel Evolution...............................................................................................1 1.2 Oryza as a Model System ..................................................................................3 1.3 Evolution of Weedy Rice ...................................................................................5 1.4 Definition of Weedy Traits ................................................................................6 1.5 Questions of Interest ..........................................................................................9 2. MOLECULAR EVOLUTION OF SHATTERING LOCI IN UNITED STATES WEEDY RICE ...................................................................................................................12 2.1 Introduction ......................................................................................................12 2.2 Methods............................................................................................................17 2.2.1 Plant Material ....................................................................................17 2.2.2 Measurement of the Shattering Phenotype .......................................18 2.2.3 DNA Extraction, Genotyping, and Sequencing ........………………19 2.2.4 Data Analysis ....................................................................................20 2.3 Results ..............................................................................................................21 viii 2.3.1 The Shattering Phenotype in Weedy, Wild, and Cultivated Rice ......................................................................................................21 2.3.2 Diversity at the qsh1 Locus ...............................................................22 2.3.3 The Genealogy of sh4 .......................................................................23 2.3.4 Genealogy of the sh4 Genomic Region ............................................24 2.3.5 The Impact of a Selective Sweep in the sh4 Genomic Region .........27 2.4 Discussion ........................................................................................................30 3. TIMING IS EVERYTHING: EARLY DEGRADATION OF ABSCISSION LAYER IS ASSOCIATED WITH INCREASED SEED SHATTERING IN US WEEDY RICE… ..............................................................................................................................51 3.1 Background ......................................................................................................51 3.2 Results and Discussion ....................................................................................55 3.2.1 Abscission Layer Formation Differs in Wild and Cultivated Oryza ....................................................................................................55 3.2.2 Degradation of the Abscission Layer is Accelerated in Weedy Rice ..........................................................................................57 3.2.3 Seed Shattering Time Course Profiles are Altered in Weedy Rice Compared to the Wild Relatives .................................................60 3.2.4 Novel Mutations Likely Underlie the Parallel Evolution of Shattering in Weedy and Wild Rice .....................................................63 3.3 Conclusions ......................................................................................................65 3.4 Methods............................................................................................................65 3.4.1 Plant Materials for Microscopy ........................................................65 3.4.2 Microscopy .......................................................................................66 3.4.3 Time Course Shattering Measurments ..............................................67 4. EVOLUTION OF FLOWERING TIME IN US WEEDY RICE ..................................74 ix 4.1 Introduction ......................................................................................................74 4.2 Methods............................................................................................................77