THE MOLECULAR BASIS OF PLANT GENETIC DIVERSITY Edited by Mahmut Çalışkan           The Molecular Basis of Plant Genetic Diversity Edited by Mahmut Çalışkan Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Marina Jozipovic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published March, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com The Molecular Basis of Plant Genetic Diversity, Edited by Mahmut Çalışkan p. cm. ISBN 978-953-51-0157-4   Contents  Preface IX Part 1 Genetic Diversity in Plant Populations 1 Chapter 1 Genomics Meets Biodiversity: Advances in Molecular Marker Development and Their Applications in Plant Genetic Diversity Assessment 3 Péter Poczai, Ildikó Varga, Neil E. Bell and Jaakko Hyvönen Chapter 2 Species Occurrence, Hybridization and Speciation in Postglacial East and South Asia 33 Liao Pei-Chun, Yi-Shan Chao and Yu-Chung Chiang Chapter 3 Genetic Diversity, Habitat Fragmentation and Epigenetic Variations 61 Josphert N. Kimatu, Geoffrey M. Muluvi and Bao Liu Chapter 4 Plant Self-Incompatibility: Or, Self-Induction of Population Genetic Diversity 73 Łukasz Wolko and Ryszard Słomski Chapter 5 Genetic Diversity of Maize Landraces as Sources of Favorable Traits 89 Snezana Mladenovic Drinic, Violeta Andjelkovic and Dragana Ignjatovic Micic Chapter 6 Genetic Biodiversity and Phylogenetic Studies in Poplar by Means of the Metallothionein Multigene Family 113 Angela Cicatelli, Renato Lupi, Francesco Sala, Han Yfan and Stefano Castiglione Chapter 7 Analysis of Genetic Diversity and SSR Allelic Variation in Rubber Tree (Hevea brasilensis) 135 Suping Feng, Yaoting Wu, Weiguo Li, Fei Yu and Jingyi Wang VI Contents Chapter 8 Genetic Diversity and Transferability of Rubus Microsatellite Markers to South American Rubus Species 151 Marta L. Marulanda, Ana M. López and Marcela Uribe Chapter 9 Genetic Diversity of Seed Orchard Crops 165 Murat Ertekin Chapter 10 Genetic Diversity of Bulgarian Phaseolus vulgaris L. Germplasm Collection Through Phaseolin and Isozyme Markers 181 N. B. Tomlekova Part 2 Diversity of Microorganisms Involved in Plant Life 231 Chapter 11 Use of Soil Microorganisms to Improve Plant Growth and Ecosystem Sustainability 233 Inés E. García de Salamone Chapter 12 Molecular Characterization of a Potyvirus Associated with a Fig Mosaic Disease in Egypt 259 Elsayed E. Hafez, A. A. Abdelkhalek and A. A. El-Morsi Chapter 13 Case Study: Sclerotinia sclerotiorum: Genetic Diversity and Disease Control 275 Silvana Petrofeza and Luiz Carlos Bhering Nasser Chapter 14 Pyrenophora tritici-repentis, Causal Agent of Tan Spot: A Review of Intraspecific Genetic Diversity 297 M. V. Moreno, S. A. Stenglein and A. E. Perelló Chapter 15 Magnaporthe oryzae Genetic Diversity and Its Outcomes on the Search for Durable Resistance 331 Klaus Konrad Scheuermann, Juliana Vieira Raimondi, Rubens Marschalek, Alexander de Andrade and Ester Wickert Chapter 16 The Nutrigenome and Gut Microbiome: Chronic Disease Prevention with Crop Phytochemical Diversity 357 Erica Daniell and Elizabeth P. Ryan   Preface  Ever since human beings adopted an agricultural way of life, they have attempted continuously to improve on what they found in nature. Once they came to understand that plant characteristics are inherited and genetic richness is an advantage against changing environmental conditions, they have developed new strategies to reveal and conserve the genetic diversity in plant populations. Plants are a distinct kingdom of organisms that possess unique properties of reproduction, development, physiology, and adaptation. Plant diversity refers to the variety of plants that exist on the Earth. Plants, in order to survive, have to compete with other plants and organisms in an ecosystem. Over time, they have developed various characteristics to help them survive, which leads to plant diversity. It is essential to have regular assessments of the conservation status of all plant species, in order to prioritize those in need of conservation action and to provide a measure of the success of actions being taken. The improvement of cultivated plants considerably depends on the extent of genetic variability available within the species. Evaluation of different genotypes, varieties, population, etc., for genetic diversity and genetic relatedness, is extremely important before taking up actions for breeding or conservation projects. Over the last few years there have been dramatic advances in plant molecular genetics and these developments have provided scientists involved in the conservation of plant genetic resources with a range of new techniques for their research. Nowadays techniques are available to analyze variations in the DNA level of plants and animals or other organisms. Differences in gene sequence can be directly observed and described - a degree of precision previously impossible to achieve. Many of the techniques that have been developed have already been used to study the extent and distribution of variation in species gene-pools and to investigate evolutionary and taxonomic relationships among plant populations. With the development of the polymerase chain reaction (PCR) based techniques, in particular, numerous molecular technologies have been, and still are being, developed, which can be used for the detection, characterization, and evaluation of genetic diversity in plant populations. These techniques can be chosen on the basis of how they display genetic differences, the type of data which they produce, the taxonomic levels at which they can be most appropriately applied, and their technical and financial requirements. X Preface The purpose of The Molecular Basis of Plant Genetic Diversity is to provide a glimpse into the dynamic process of genetic variation by presenting the thoughts of some of the scientists who are engaged in the development of new tools and ideas used to reveal genetic variation, often from very different perspectives. I would like to express my deepest gratitude to all theauthors who contributed to this book by sharing their valuable works with us. This book should prove useful to students, researchers, and experts in the area of conservation biology, genetic diversity, and molecular biology. The year 2010 was celebrated as the international year of biodiversity by the United Nations and it has been a unique opportunity to realize the vital role that biodiversity plays in sustaining the life on Earth. Let us all wish much success to all projects and initiatives dealing with the conservation of diversity of life because rich genetic resources are a prerequisite for future generations to be able to breed crop varieties and face new challenges. Prof. Dr. Mahmut Çalışkan Mustafa Kemal University, Department of Biology, Hatay Turkey . THE MOLECULAR BASIS OF PLANT GENETIC DIVERSITY Edited by Mahmut Çalışkan           The Molecular Basis of Plant Genetic Diversity Edited by Mahmut. for the detection, characterization, and evaluation of genetic diversity in plant populations. These techniques can be chosen on the basis of how they display genetic differences, the type of. on the genetic composition of the population (Avise, 2004). Detection and analysis of genetic diversity can help us to understand the molecular basis of various biological phenomena in these