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Open Mao Thesis V10 5.Pdf The Pennsylvania State University The Graduate School Intercollege Graduate Program of Plant Biology THE ALLOTETRAPLOID EVOLUTIONARY ORIGIN OF ANNUAL BLUEGRASS A Dissertation in Plant Biology by Qing Mao © 2014 Qing Mao Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 The dissertation of Qing Mao was reviewed and approved* by the following: David R.Huff Professor of Turfgrass Breeding & Genetics Dissertation Advisor Chair of Committee Majid Foolad Professor of Plant Genetics John Kaminski Associate Professor of Turfgrass Management Dawn Luthe Professor of Plant Stress Biology Gabriele Monshausen Assistant Professor of Biology Teh-hui Kao Distinguished Professor of Biochemistry and Molecular Biology Chair of Intercollege Graduate Degree Program in Plant Biology *Signatures are on file in the Graduate School iii ABSTRACT Poa annua L., or annual bluegrass, is an agronomically and ecologically important grass species. It is morphologically highly variable, representing a continuum from annual to perennial types. In order to explain the wide distribution and variability in Poa annua, efforts have been made to discover its evolutionary origin ever since the 1930s; however, no definitive conclusions have been made. Our phylogenetic analysis using nuclear and chloroplast gene sequences is the first to confirm that Poa annua (2n=4x=28) is an allotetraploid between an annual grass species Poa infirma Kunth. (2n=2x=14) and a perennial grass species Poa supina Schrad. (2n=2x=14), with the former serving as the maternal parent. Our data also suggest a recent origin of Poa annua, and possibly multiple crosses between the parental species led to the present day Poa annua. Previous phylogenetic studies have suggested that the genomes of Poa infirma and Poa supina are very divergent, representing the largest genetic distance between species within the genus Poa. By analyzing meiotic chromosome pairing data in amphihaploid Poa annua published by Hovin, we were able to determine that the genomes of Poa infirma and Poa supina indeed are very distinct, and we designated them II and SS, making the genomic constitution of Poa annua IISS. Prior to the present study, the biggest controversy on the origin of Poa annua was that its karyotype did not match the combination of the two putative parents Poa infirma and Poa supina. With the two parental species confirmed with DNA sequencing data, it could now be concluded that chromosomal rearrangements must have occurred during the evolutionary origin of Poa annua. In order to explore the extent and patterns of iv chromosomal rearrangements in Poa annua, fluorescent in situ hybridization was performed to compare rDNA loci in Poa annua and its parents. Our data show variations of genomic rDNA loci between Poa annua and its parents, and among different Poa annua individuals, suggesting that not only did chromosomal rearrangements occur in Poa annua, but also genomic variation exists within this species. Small RNAs play a wide range of regulatory roles in plant development and are associated with polyploid evolution. Four small RNA profiles were generated from young seedlings of Poa infirma, Poa supina, perennial-type Poa annua and annual-type Poa annua. Analyses showed that the four profiles are highly similar in terms of small RNA length distribution, miRNA families and expression levels, indicating that the morphological and life history variation observed 1) between the two types of Poa annua, and 2) among allotetraploid Poa annua and the two diploid parental species are not attributable to the small RNAs examined. However, the profiles generated from this study could serve as a baseline for future work. In summary, the discoveries from this thesis work enhanced our understanding of the phenotypic variability and incredible adaptability of Poa annua, and provided insights into plant polyploid evolution. v TABLE OF CONTENTS LIST OF FIGURES ..................................................................................................... vii! LIST OF TABLES ....................................................................................................... x! ACKNOWLEDGEMENTS ......................................................................................... xii! Chapter 1 Introduction ................................................................................................ 1! Poa annua L. ........................................................................................................ 1! Morphology of Poa annua ............................................................................ 1! Wide distribution of Poa annua .................................................................... 3! Utility of Poa annua in turf ........................................................................... 4! Origin of Poa annua ...................................................................................... 6! Polyploid Evolution .............................................................................................. 7! Plant polyploidy ............................................................................................. 7! Genetic and epigenetic changes in polyploids ............................................... 8! Mechanism of polyploid effects .................................................................... 10! Small RNA in polyploid evolution ................................................................ 11! Objectives of research ........................................................................................... 13! References ............................................................................................................. 15! Chapter 2 The evolutionary origin of Poa annua L. ................................................... 20! Abstract ................................................................................................................. 21! Background ........................................................................................................... 22! Materials and Methods ......................................................................................... 25! Plant material ................................................................................................. 25! Flow cytometry .............................................................................................. 26! DNA extraction ............................................................................................. 27! DNA amplification, cloning and sequencing ................................................ 28! Sequence alignment and phylogenetic analyses ............................................ 29! Results ................................................................................................................... 30! Species comparisons of Poa infirma, Poa supina, and Poa annua ............... 30! Phylogenetic analyses of nuclear genes trx and CDO504 ............................. 31! Phylogenetic analyses of chloroplast genes trnTLF and ndhF ...................... 32! Genetic distances among Poa infirma, Poa supina, and Poa annua ............. 33! Statistical parsimony network analyses ......................................................... 34! Discussion ............................................................................................................. 36! The origin of Poa annua ................................................................................ 36! Genomic designation of Poa infirma and Poa supina ................................... 37! Chromosomal rearrangements in Poa annua ................................................ 39! Acknowledgements ............................................................................................... 41! References ............................................................................................................. 42! vi Chapter 3 Chromosomal rearrangements in Poa annua ............................................. 60! Background ........................................................................................................... 60! Materials and Methods ......................................................................................... 61! Plant materials ............................................................................................... 61! Chromosome preparations ............................................................................. 62! FISH experiment ........................................................................................... 62! Results ................................................................................................................... 64! FISH with 5S rDNA probes .......................................................................... 64! FISH with 45S rDNA probes ........................................................................ 64! Discussion ............................................................................................................. 65! Acknowledgement ................................................................................................ 66! References ............................................................................................................. 67! Chapter 4 Characterizing small RNA profiles of allotetraploid Poa annua L. and its diploid parents .................................................................................................. 73! Abstract ................................................................................................................
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