diversity Plant Genetics and Biotechnology in Biodiversity Edited by Rosa Rao and Giandomenico Corrado Printed Edition of the Special Issue Published in Diversity www.mdpi.com/journal/diversity Plant Genetics and Biotechnology in Biodiversity Plant Genetics and Biotechnology in Biodiversity Special Issue Editors Rosa Rao Giandomenico Corrado MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editors Rosa Rao Giandomenico Corrado Universita` degli Studi di Napoli Universita` degli Studi di Napoli “Federico II” “Federico II” Italy Italy Editorial Office MDPI St. Alban-Anlage 66 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Diversity (ISSN 1424-2818) from 2017 to 2018 (available at: http://www.mdpi.com/journal/diversity/special issues/plant genetics biotechnology) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. 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Contents About the Special Issue Editors ..................................... vii Preface to ”Plant Genetics and Biotechnology in Biodiversity” ................... ix Giandomenico Corrado and Rosa Rao Special Issue: Plant Genetics and Biotechnology in Biodiversity Reprinted from: Diversity 2018, 10, 19, doi: 10.3390/d10020019 .................... 1 Giandomenico Corrado and Rosa Rao Towards the Genomic Basis of Local Adaptation in Landraces Reprinted from: Diversity 2017, 9, 51, doi: 10.3390/d9040051 ..................... 4 Nunzio D’Agostino and Pasquale Tripodi NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops Reprinted from: Diversity 2017, 9, 38, doi: 10.3390/d9030038 ..................... 16 Andrea Sonnino International Instruments for Conservation and Sustainable Use of Plant Genetic Resources for Food and Agriculture: An Historical Appraisal Reprinted from: Diversity 2017, 9, 50, doi: 10.3390/d9040050 ..................... 36 Pedro Carbonell, Aranzazu Alonso, Adri´an Grau, Juan Francisco Salinas, Santiago Garc´ıa-Mart´ınez and Juan Jos´e Ruiz Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS) Reprinted from: Diversity 2018, 10, 12, doi: 10.3390/d10010012 .................... 55 Carla Ceoloni, Ljiljana Kuzmanovi´c, Roberto Ruggeri, Francesco Rossini, Paola Forte, Alessia Cuccurullo and Alessandra Bitti Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities Reprinted from: Diversity 2017, 9, 55, doi: 10.3390/d9040055 ..................... 66 Valeria Terzi, Giorgio Tumino, Donata Pagani, Fulvia Rizza, Roberta Ghizzoni, Caterina Morcia and Antonio Michele Stanca Barley Developmental Mutants: The High Road to Understand the Cereal Spike Morphology Reprinted from: Diversity 2017, 9, 21, doi: 10.3390/d9020021 ..................... 87 Maria Manuela Veloso, Maria Cristina Sim˜oes-Costa, Lu´ıs C. Carneiro, Joana B. Guimar˜aes, C´elia Mateus, Pedro Fevereiro and Cˆandido Pinto-Ricardo Olive Tree (Olea europaea L.) Diversity in Traditional Small Farms of Ficalho, Portugal Reprinted from: Diversity 2018, 10, 5, doi: 10.3390/d10010005 .....................103 Andrea Porceddu and Salvatore Camiolo Patterns of Spontaneous Nucleotide Substitutions in Grape Processed Pseudogenes Reprinted from: Diversity 2017, 9, 45, doi: 10.3390/d9040045 .....................116 Fabio Palumbo, Giulio Galla, Liliam Mart´ınez-Bello and Gianni Barcaccia Venetian Local Corn (Zea mays L.) Germplasm: Disclosing the Genetic Anatomy of Old Landraces Suited for Typical Cornmeal Mush Production Reprinted from: Diversity 2017, 9, 32, doi: 10.3390/d9030032 .....................130 v Raafat El-Namaky, Mamadou M. Bare Coulibaly, Maji Alhassan, Karim Traore, Francis Nwilene, Ibnou Dieng, Rodomiro Ortiz and Baboucarr Manneh Putting Plant Genetic Diversity and Variability at Work for Breeding: Hybrid Rice Suitability in West Africa Reprinted from: Diversity 2017, 9, 27, doi: 10.3390/d9030027 .....................145 Domenica Nigro, Stefania Fortunato, Stefania Lucia Giove, Giacomo Mangini, Ines Yacoubi, Rosanna Simeone, Antonio Blanco and Agata Gadaleta Allelic Variants of Glutamine Synthetase and Glutamate Synthase Genes in a Collection of Durum Wheat and Association with Grain Protein Content Reprinted from: Diversity 2017, 9, 52, doi: 10.3390/d9040052 .....................157 Caroline L. Gross, Mohammad Fatemi, Mic Julien, Hannah McPherson and Rieks Van Klinken The Phylogeny and Biogeography of Phyla nodiflora (Verbenaceae) Reveals Native and Invasive Lineages throughout the World Reprinted from: Diversity 2017, 9, 20, doi: 10.3390/d9020020 .....................167 Mario Augusto Pagnotta and Arshiya Noorani The Contribution of Professor Gian Tommasso Scarascia Mugnozza to the Conservation and Sustainable Use of Biodiversity Reprinted from: Diversity 2018, 10, 4, doi: 10.3390/d10010004 .....................190 vi About the Special Issue Editors Rosa Rao is Full Professor of Plant Genetics at the University of Naples “Federico II” (Italy). Her research interests include the molecular characterization of crop biodiversity, along with food authentication and multidimensional approaches for studying defences against plant enemies. Giandomenico Corrado (MSc, PhD) is currently Researcher at the University of Naples “Federico II” (Italy). He got his PhD at the University of Leeds (UK). His research activities include the molecular characterization of genetic diversity in landraces, with emphasis on the elucidation of defence mechanisms against biotic stress. vii Preface to ”Plant Genetics and Biotechnology in Biodiversity” To increase both sustainability and productivity in agriculture, crop science, from pre-breeding to production management, needs to make better use of genetic diversity. For instance, adapted and exotic genetic resources can greatly contribute to generate varieties with enhanced adaptation to different climatic conditions and with improved plasticity in response to stressful factors. These features are central to reducing vulnerability to stress and supporting more diversified and sustainable agro-ecological systems. Scientific and technical advances allow the generation of large quantities of genotypic and phenotypic data at a fraction of the cost required decades ago. Similarly, novel biotechnological approaches are revolutionizing the way we can edit or delete specific sequences of the plant genome. The impact of these innovations is wide-ranging and includes the possibility to improve our understanding and exploitation of plant genetic resources for food and agriculture (PGRFA). These new technologies are expected to transform the study of PGRFA into a more technologically intensive, information-rich science, in which the integration and interpretation of different kinds of data will be central to fully unlock the potential of genetic diversity for agriculture. Considering that the number of research articles on these topics is rapidly increasing, this Special Issue (SI) was designed to collect perspectives and experimental studies that cover contemporary advances in plant genetics and biotechnology for plant diversity in agriculture. While the usefulness of molecular tools to describe genetic polymorphisms and the importance of generic resources in agriculture has been largely covered in the literature, we felt the need to highlight how the management, description, and use of agricultural diversity is changing in the backdrop of molecular genetics and biotechnology. To this aim, we included both reviews, which summarize the current state of understanding, and experimental articles, which provide empirical cases on the description and exploitation of different kinds of plant genetic diversity. The SI was then organized into three parts. The first includes three thematic reviews on the scientific, technological, and legal advances in plant diversity and agriculture. The second part consists of three contributions on specific examples of the exploitation of different sources of genetic diversity (i.e., landraces, mutant populations, and wild-gene pools) in crops (i.e., tomato, barley, and wheat, respectively). The third part is made of six research articles on the study of molecular and/or phenotypic diversity to address basic or applied questions in trees (olive and grape), as well as herbaceous crops (maize, rice, and wheat) and wild species. In collecting the contributions, we were pleased to note that the variety of topics reflects well the wide-ranging changes made possible by recent progress in plant molecular genetics and biotechnology. This SI was also launched to honour the memory of Prof.