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Sequence Diversity and Copy Number Variation of Mutator-Like Transposases in Wheat
Genetics and Molecular Biology, 31, 2, 539-546 (2008) Copyright © 2008, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Research Article Sequence diversity and copy number variation of Mutator-like transposases in wheat Nobuaki Asakura1, Shinya Yoshida2, Naoki Mori3, Ichiro Ohtsuka1 and Chiharu Nakamura3 1Laboratory of Biology, Faculty of Engineering, Kanagawa University, Yokohama, Japan. 2Hyogo Institute of Agriculture, Forestry & Fisheries, Kasai, Japan. 3Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan. Abstract Partial transposase-coding sequences of Mutator-like elements (MULEs) were isolated from a wild einkorn wheat, Triticum urartu, by degenerate PCR. The isolated sequences were classified into a MuDR or Class I clade and di- vided into two distinct subclasses (subclass I and subclass II). The average pair-wise identity between members of both subclasses was 58.8% at the nucleotide sequence level. Sequence diversity of subclass I was larger than that of subclass II. DNA gel blot analysis showed that subclass I was present as low copy number elements in the genomes of all Triticum and Aegilops accessions surveyed, while subclass II was present as high copy number ele- ments. These two subclasses seemed uncapable of recognizing each other for transposition. The number of copies of subclass II elements was much higher in Aegilops with the S, Sl and D genomes and polyploid Triticum species than in diploid Triticum with the A genome, indicating that active transposition occurred in S, Sl and D genomes be- fore polyploidization. DNA gel blot analysis of six species selected from three subfamilies of Poaceae demonstrated that only the tribe Triticeae possessed both subclasses. -
Identify New Resistant Genes for Eyespot Diseases of Wheat In
IDENTIFICATION AND MAPPING OF RESISTANCE GENES FOR EYESPOT OF WHEAT IN AEGILOPS LONGISSIMA By HONGYAN SHENG i A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy WASHINGTON STATE UNIVERSITY Department of Plant Pathology May 2011 © Copyright by HONGYAN SHENG, 2011 All Rights Reserved To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of HONGYAN SHENG find it satisfactory and recommend that it be accepted. _________________________________________ Timothy D. Murray, Ph. D., Chair _________________________________________ Xianming Chen, Ph. D. _________________________________________ Scot H. Hulbert, Ph. D. _________________________________________ Tobin L. Peever, Ph. D. _________________________________________ Stephen S. Jones, Ph. D. ii ACKNOWLEDGMENT I would like to express my sincere gratitude and appreciation to my mentor and major advisor, Dr. Timothy D. Murray, for all his guidance, support, patience, and encouragement throughout my entire Ph. D. process at Washington State University. I am grateful to Dr. Murray for sharing his knowledge of plant pathology, providing insight into this dissertation, and leading me to the complex and fascinating world of genetics. My grateful appreciation goes to my committee members, Dr. Tobin L. Peever, Dr. Xianming Chen, Dr. Scot H. Hulbert, and Dr. Stephen S. Jones for their helpful advice and guidance during my graduate work and critical review of my dissertation. I would especially like to thank Dr. Deven R. See (USDA-ARS Regional Small Grains Genotyping Laboratory at Pullman, WA) for providing techniques and equipments for marker analysis work. Most of all, I am grateful for his critical suggestion leading to successful results. -
Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits from Aegilops Species Into Bread Wheat (Triticum Aestivum)
ORIGINAL RESEARCH published: 24 January 2019 doi: 10.3389/fpls.2018.01993 Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum) Alexandra M. Przewieslik-Allen 1*, Amanda J. Burridge 1, Paul A. Wilkinson 1, Mark O. Winfield 1, Daniel S. Shaw 1, Lorna McAusland 2, Julie King 2, Ian P. King 2, Keith J. Edwards 1 and Gary L. A. Barker 1 1 Life Sciences, University of Bristol, Bristol, United Kingdom, 2 Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom The genus Aegilops contains a diverse collection of wild species exhibiting variation Edited by: in geographical distribution, ecological adaptation, ploidy and genome organization. István Molnár, Centre for Agricultural Research Aegilops is the most closely related genus to Triticum which includes cultivated wheat, (MTA), Hungary a globally important crop that has a limited gene pool for modern breeding. Aegilops Reviewed by: species are a potential future resource for wheat breeding for traits, such as adaptation Parveen Chhuneja, Punjab Agricultural University, India to different ecological conditions and pest and disease resistance. This study describes Kentaro Yoshida, the development and application of the first high-throughput genotyping platform Kobe University, Japan specifically designed for screening wheat relative species. The platform was used to Pilar Hernandez, Instituto de Agricultura Sostenible screen multiple accessions representing all species in the genus Aegilops. Firstly, the (IAS), Spain data was demonstrated to be useful for screening diversity and examining relationships *Correspondence: within and between Aegilops species. Secondly, markers able to characterize and track Alexandra M. -
Contribution of Chloroplast DNA in the Biodiversity of Some Aegilops Species
African Journal of Biotechnology Vol. 10(12), pp. 2212-2215, 21 March, 2011 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB10.2151 ISSN 1684–5315 © 2011 Academic Journals Full Length Research Paper Contribution of chloroplast DNA in the biodiversity of some Aegilops species Abdallah Mahmoud Sliai 1 and Sayed Amin Mohamed Amer 1,2* 1Faculty of Science, Taif University, Kingdom of Saudi Arabia. 2Zoology Department, Faculty of Science, Cairo University, Egypt. Accepted 21 February, 2011 Four Aegilops species ( Aegilops longissima , Aegilops speltoides , Aegilops searsii and Aegilops caudata ) belonging to the family Poaceae were used in this study. Nucleotides of 1651 bp from 5.8 S rRNA gene and the intergenic spacers trnT-trnL and trnL-trnF from the chloroplast DNA were combined together in order to investigate the genetic diversity among the earlier mentioned species. Maximum- parsimony and Neighbor-joining computational methods for tree building were applied to construct the relationship among the Aegilops species. In all trials, one parsimonious tree was obtained, in which, the A. speltoides was the oldest and was out of a cluster containing the other three Aegilops species. A. searsii and A. caudata were sisters to each other, while A. longissima was basal in this cluster. These findings did not agree with previous karyotypic studies in which A. searsii was the oldest, and A. caudata was recently originated, while both A. longissima and A. speltoides were intermediate. The present study therefore revealed the significance of molecular markers in clarifying the genetic diversity on the inter- and intra-specific levels. These markers can also be applied for taxonomic consequences and have an economic importance in the genetic amelioration programs. -
Phenotypic Diversity in the Wheat Wild Relative Aegilops Longissima
PHENOTYPIC DIVERSITY IN THE WHEAT WILD RELATIVE AEGILOPS LONGISSIMA A THESIS SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY SHUYI HUANG IN PARTIAL FULFILLMENT OF REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE Adviser: Brian J. Steffenson November 2016 © Shuyi Huang 2016 Acknowledgements I would like to express my sincere gratitude and appreciation to my mentor and major advisor, Dr. Brian Steffenson, for all his guidance, support, patience, and encouragement throughout my study at University of Minnesota. I am grateful to Dr. Steffenson for sharing his knowledge of plant pathology, providing insight into this thesis, and leading me to the fascinating and meaningful world of crop improvement and research. My grateful appreciation also goes to Dr. James Kolmer and Dr. James Anderson, who served on my thesis committee. Dr. Kolmer and Dr. Anderson provided their helpful advice and guidance during my graduate work and a critical review of my thesis. From all of these individuals, I have gained the knowledge and experience to be a good and independent scientist. I extend my gratitude to Dr. Xianming Chen (USDA-ARS) at Pullman, Washington for providing the materials and guidance for working with the stripe rust pathogen. Dr. Hanan Sela and Dr. Eitan Millet of the Institute for Cereal Crops Improvement at Tel Aviv University (ICCI-TAU) generously shared their extensive knowledge about Aegilops longissima with me. I thank the ICCI-TAU in Tel Aviv, Israel and Leibniz-Institute für Pflanzengenetik und Kulturpflanzenforschung (IPK) in Gatersleben Germany for providing the Ae. longissima germplasm that made this project possible. -
Reevaluation of Systematic Relationships in Triticum L. and Aegilops L
AN ABSTRACT OF THE THESIS OF Laura A. Morrison for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on October 21, 1994. Title: Reevaluation of Systematic Relationships in Triticum L. and Aegilops L. Based on Comparative Morphological and Anatomical Investigations of Dispersal Mechanisms Redacted for Privacy Abstract approved: Kenton L. Chambers Comparative morphological and anatomical studies of the dispersal mechanisms characterizing the wheat complex (Triticum L. and Aegilops L.) have documented patterns of adaptive radiation which may have significance for evolutionary relationships. These patterns, which form an array of diverse types of diaspores among the diploid taxa, appear conceptually to have a starting point in the dimorphic inflorescence of Ae. speltoides. Separate dispersal trends, centered primarily in features of rachis disarticulation, lead in the direction of novel diaspore types for Aegilops and in the direction of domestication for Triticum. With respect to the taxonomy, this structural evidence supports the traditional Linnaean generic circumscriptions and suggests a need for a monographic revision of Triticum. In documenting the dispersal mechanisms, these studies have clarified conventional interpretations and have offered new insights on the developmental relationships linking the wild and domesticated taxa of the wheat complex. Although genetic studies were not encompassed within this research, a consideration of the genetic explanations for rachis disarticulation and glume closure suggests that the phenotypic traits typically used in genetic studies are not well understood. Given that the reticulate nature of genomic relationships in the wheats is coupled with intergrading variation and polymorphic species, a proposal is made for a broader evolutionary view than is found in the strict cladistic concept. -
Genes Encoding Plastid Acetyl-Coa Carboxylase and 3-Phosphoglycerate Kinase of the Triticum͞aegilops Complex and the Evolutionary History of Polyploid Wheat
Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum͞Aegilops complex and the evolutionary history of polyploid wheat Shaoxing Huang*†, Anchalee Sirikhachornkit*, Xiujuan Su*, Justin Faris‡§, Bikram Gill‡, Robert Haselkorn*, and Piotr Gornicki*¶ *Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637; and ‡Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 Contributed by Robert Haselkorn, April 12, 2002 The classic wheat evolutionary history is one of adaptive radiation of at the diploid level from a common diploid ancestor and conver- the diploid Triticum͞Aegilops species (A, S, D), genome convergence gence at the polyploid level involving the diverged diploid genomes and divergence of the tetraploid (Triticum turgidum AABB, and (2). Various Aegilops species contributed significantly to the genetic Triticum timopheevii AAGG) and hexaploid (Triticum aestivum, makeup of the polyploid wheats. Extensive classical analyses and AABBDD) species. We analyzed Acc-1 (plastid acetyl-CoA carboxylase) more recent molecular studies have provided information on the and Pgk-1 (plastid 3-phosphoglycerate kinase) genes to determine identity of donors and some of the patterns of genome evolution of phylogenetic relationships among Triticum and Aegilops species of the Triticum͞Aegilops species (3). A review of Triticum and Aegilops the wheat lineage and to establish the timeline of wheat evolution taxonomy and related literature is available from the Wheat based on gene sequence comparisons. Triticum urartu was confirmed Genetic Resource Center at ksu.edu͞wgrc. as the A genome donor of tetraploid and hexaploid wheat. The A The Triticum and Aegilops genera contain 13 diploid and 18 genome of polyploid wheat diverged from T. -
THE ROLE of Aegilops SPECIES in the ORIGIN and IMPROVEMENT of COMMON WHEAT
ACTA AGROBOTANICA Vol. 66 (4), 2013: 7–14 Reviews DOI: 10.5586/aa.2013.046 THE ROLE OF Aegilops SPECIES IN THE ORIGIN AND IMPROVEMENT OF COMMON WHEAT Roman Prażak University of Life Sciences in Lublin, Subdepartment of Plant Biology, Faculty of Agricultural Sciences Szczebrzeska 102, 22-400 Zamość, Poland e-mail: [email protected] Received: 22.04.2013 Abstract rust [9,10,11,12,13,14,15,16,17,18,19,20,21,22], to Some Aegilops species participated in wheat evolu- powdery mildew (Blumeria graminis) [23,24,25], tion playing a major role in wheat domestication and therefore to eyespot (Pseudocercosporella herpotrichoides) the genus Aegilops represents a big part of the additional gene [26,27], to tan spot (Pyrenophora tritici-repentis) [28], pool determining important traits of wheat. Breeders have been to nematodes and insects [29,30,31], and to pre-harvest using these genes for many years to produce improved cultivars. sprouting [32]; and tolerance for soil salinity, drought Wide crosses between its wild relatives are sources of desira- [33,34] and soil acidification [35,10]. ble characteristics for genetic improvement of common wheat. An example of the transfer of beneficial traits Triticum aestivum evolution and methods for transfer of alien from Aegilops species to cultivated wheat is the trans- material into wheat, briefly reviewed in this article, include in- location from Ae. ventricosa introduced in France to the corporation of the whole genomes, single chromosomes, small winter variety VPM1, conferring resistance – owing to chromosomal segments, single genes and cytoplasm substitu- tion in wheat. the genes Pch1 and Pch2 – to eyespot, caused by Pseu- docercosporella herpotrichoides [26]. -
Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits from Aegilops Species Into Bread Wheat (Triticum Aestivum)
Przewieslik-Allen, A. M., Burridge, A. J., Wilkinson, P. A., Winfield, M. O., Shaw, D. S., McAusland, L., King, J., King, I. P., Edwards, K. J., & Barker, G. L. A. (2019). Developing a high-throughput SNP-based marker system to facilitate the introgression of traits from Aegilops species into bread wheat (Triticum aestivum). Frontiers in Plant Science, 9(1993), [1993]. https://doi.org/10.3389/fpls.2018.01993 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.3389/fpls.2018.01993 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Frontiers at DOI: 10.3389/fpls.2018.01993. Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ ORIGINAL RESEARCH published: 24 January 2019 doi: 10.3389/fpls.2018.01993 Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum) Alexandra M. Przewieslik-Allen 1*, Amanda J. Burridge 1, Paul A. Wilkinson 1, Mark O. Winfield 1, Daniel S. Shaw 1, Lorna McAusland 2, Julie King 2, Ian P. King 2, Keith J. Edwards 1 and Gary L. A. Barker 1 1 Life Sciences, University of Bristol, Bristol, United Kingdom, 2 Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom The genus Aegilops contains a diverse collection of wild species exhibiting variation Edited by: in geographical distribution, ecological adaptation, ploidy and genome organization. -
Dated Tribe-Wide Whole Chloroplast Genome Phylogeny Indicates
Bernhardt et al. BMC Evolutionary Biology (2017) 17:141 DOI 10.1186/s12862-017-0989-9 RESEARCHARTICLE Open Access Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae Nadine Bernhardt1* , Jonathan Brassac1, Benjamin Kilian1,2 and Frank R. Blattner1,3 Abstract Background: Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe’s evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. Results: The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationshipsandestimatedivergencetimesofthetaxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. Conclusions: The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups. Keywords: Hybridization, Whole chloroplast genome, Phylogeny, Next-generation sequencing, Divergence times, Triticeae, Wheat, Triticum, Aegilops, Psathyrostachys Background mode of evolution within Triticeae. -
A 250 Plastome Phylogeny of the Grass Family (Poaceae): Topological Support Under Different Data Partitions
A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions Jeffery M. Saarela1, Sean V. Burke2, William P. Wysocki3, Matthew D. Barrett4,5, Lynn G. Clark6, Joseph M. Craine7, Paul M. Peterson8, Robert J. Soreng8, Maria S. Vorontsova9 and Melvin R. Duvall2 1 Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, Canada 2 Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA 3 Center for Data Intensive Sciences, University of Chicago, Chicago, IL, USA 4 Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, Australia 5 School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia 6 Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA 7 Jonah Ventures, Manhattan, KS, USA 8 Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA 9 Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK ABSTRACT The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries Submitted 8 August 2017 and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal Accepted 8 January 2018 Published 2 February 2018 was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single Corresponding authors Jeffery M. -
Mapping Resistance Genes for Oculimacula Acuformis in Aegilops Longissima
Theor Appl Genet DOI 10.1007/s00122-014-2361-4 ORIGINAL PAPER Mapping resistance genes for Oculimacula acuformis in Aegilops longissima Hongyan Sheng · Deven R. See · Timothy D. Murray Received: 27 February 2014 / Accepted: 13 July 2014 © Springer-Verlag Berlin Heidelberg 2014 Abstract chromosomal locations as some for resistance to O. yallun- Key message This study identified three QTL confer- dae, except that a QTL for resistance to O. yallundae was ring resistance to Oculimacula acuformis in Aegilops found in chromosome 7Sl but not for O. acuformis. Thus, longissima and their associated markers, which can be it appears that some genes at the same locus in Ae. long- useful in marker-assisted selection breeding for eyespot issima may control resistance to both eyespot pathogens. resistance. QTL effective against both pathogens will be most useful Abstract Oculimacula acuformis is one of two species for breeding programs and have potential to improve the of soilborne fungi that cause eyespot of wheat, the other effectiveness and genetic diversity of eyespot resistance. being Oculimacula yallundae. Both pathogens can coex- ist in the same field and produce elliptical lesions on stem bases of wheat that are indistinguishable. Pch1 and Pch2 Introduction are the only two eyespot resistance genes readily avail- able to wheat breeders, but neither provides complete Eyespot, a stem base disease of wheat, is caused by Ocu- control. A new source of eyespot resistance was identified limacula acuformis Crous & W. Gams (syn: Tapesia acu- from Aegilops longissima (2n 14, SlSl), a wild relative formis, Wallwork & Spooner) and O. yallundae Crous & = of wheat. Three QTL for resistance to O.