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Diversity
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Plant Genetics and Biotechnology in Biodiversity
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Plant Genetics and Biotechnology in Biodiversity

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Plant Diversity".

Deadline for manuscript submissions: closed (30 September 2017) | Viewed by 83421

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. Rosa Rao

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Guest Editor
Department of Agriculture, University of Naples "Federico II", Via Università 100, 80055 Portici, Italy
Interests: plant biotechnology; genetic and genomic characterization of plant germplasm; molecular markers; ‘omics’ in plant defense studies
Dr. Giandomenico Corrado

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Guest Editor
Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Via Università 100, 80055 Portici, Italy
Interests: crop biodiversity; landraces; genetic modification; DNA polymorphism; genetic fingerprinting
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant biodiversity is central to the implementation of sustainable production systems, ensuring global food security, and increasing crop resistance and resiliance to climate change and invasive and native biotic stresses. Plant genetic resources (PGR) have been collected and exchanged for centuries, but the rapid development of novel tools for genetic analysis is changing the way we can uncover diversity and exploit its value in agriculture. The integration of novel analytical tools is currently crucial for translating research into a much-needed, more efficient management and use of PGR.

The forthcoming Special Issue aims to provide an overview of recent topics on plant genetics and biotechnology in biodiversity, with enphasis on agricultural genetic diversity. Papers will present current trends on genetic resources description, conservation, management and research, and will highlight how new approaches and methodogies can boost both our understanding and exploitation of PGR.

This Special Issue is launched to honor the memory of Prof. Gian Tommaso Scarascia Mugnozza, and in recognition of his many contributions to plant breeding and genetic resources.

Prof. Rosa Rao
Dr. Giandomenico Corrado
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant conservation genetics
  • plant biodiversity
  • plant biotechnology in conservation and bioprospecting
  • DNA markers
  • plant genomics
  • biodiversity in bio-based economy

Published Papers (14 papers)

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Editorial

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3 pages, 181 KiB  
Editorial
Special Issue: Plant Genetics and Biotechnology in Biodiversity
by Giandomenico Corrado and Rosa Rao
Diversity 2018, 10(2), 19; https://doi.org/10.3390/d10020019 - 27 Mar 2018
Cited by 2 | Viewed by 3316
Abstract
The rapid progress and increasing affordability of novel investigation tools in plant genetics and biotechnology offer previously inaccessible opportunities for the exploitation of plant genetic diversity in agriculture. The Special Issue was lunched to highlight how new technologies are improving both genotyping and [...] Read more.
The rapid progress and increasing affordability of novel investigation tools in plant genetics and biotechnology offer previously inaccessible opportunities for the exploitation of plant genetic diversity in agriculture. The Special Issue was lunched to highlight how new technologies are improving both genotyping and phenotyping methods, thus allowing us to uncover crop diversity and use genetic variability for plant breeding with remarkable precision and speed. Three thematic reviews report on scientific, technological, and legal advances in plant diversity and agriculture. Three contributions provide specific examples of the exploitation of different kinds of genetic resources, ranging from landraces to mutant populations. Six research articles are illustrative examples of the study of molecular and/or phenotypic diversity to address basic or applied questions in different plant species. Finally, this SI was also launched to honor the memory of Prof. Gian Tommaso Scarascia Mugnozza and a dedicated Editorial acknowledges his work in plant breeding and biodiversity protection. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
10 pages, 3936 KiB  
Editorial
The Contribution of Professor Gian Tommasso Scarascia Mugnozza to the Conservation and Sustainable Use of Biodiversity
by Mario Augusto Pagnotta and Arshiya Noorani
Diversity 2018, 10(1), 4; https://doi.org/10.3390/d10010004 - 16 Jan 2018
Cited by 2 | Viewed by 4016
Abstract
During his lifetime, Professor Scarascia Mugnozza contributed significantly to the field of population genetics, his research ranging from wheat breeding in arid and semi-arid regions, to the conservation of forest ecosystems. He promoted regional networks across the Mediterranean, linking science and policy at [...] Read more.
During his lifetime, Professor Scarascia Mugnozza contributed significantly to the field of population genetics, his research ranging from wheat breeding in arid and semi-arid regions, to the conservation of forest ecosystems. He promoted regional networks across the Mediterranean, linking science and policy at national and international levels, focusing on the conservation and sustainable use of genetic diversity. In addition, he worked intensely on improvement of knowledge bases, raising awareness on how research could inform international agreements, and thus lead to evidence-based policies. The loss of biodiversity and the resulting implications for environmental, socio-economic, political, and ethical management of plant genetic resources were of major concern, and he highlighted the absolute necessity for conservation of genetic diversity, stressing the importance of building positive feedback linkages among ex situ, in situ, on-farm conservation strategies, and participatory approaches at the community level. His work emphasized the importance of access to diverse plant genetic resources by researchers and farmers, and promoted equitable access to genetic resources through international frameworks. Farmers’ rights, especially those in centres of origin and diversity of cultivated plants, were a key concern for Professor Scarascia Mugnozza, as their access to germplasm needed to be secured as custodians of diversity and the knowledge of how to use these vital resources. Consequently, he promoted the development of North-South cooperation mechanisms and platforms, including technology transfer and the sharing of information of how to maintain and use genetic resources sustainably. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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Research

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13 pages, 9248 KiB  
Article
Olive Tree (Olea europaea L.) Diversity in Traditional Small Farms of Ficalho, Portugal
by Maria Manuela Veloso, Maria Cristina Simões-Costa, Luís C. Carneiro, Joana B. Guimarães, Célia Mateus, Pedro Fevereiro and Cândido Pinto-Ricardo
Diversity 2018, 10(1), 5; https://doi.org/10.3390/d10010005 - 18 Jan 2018
Cited by 11 | Viewed by 5064
Abstract
The genetic diversity of “Gama” and “Bico de Corvo”, local cultivars of olive tree (Olea europaea) from seven traditional orchards of Ficalho (Alentejo region, Portugal), was studied to characterize the local diversity and assess the level of on farm diversity. Two [...] Read more.
The genetic diversity of “Gama” and “Bico de Corvo”, local cultivars of olive tree (Olea europaea) from seven traditional orchards of Ficalho (Alentejo region, Portugal), was studied to characterize the local diversity and assess the level of on farm diversity. Two different analytical systems were used: endocarp morphological characteristics and genetic analysis by microsatellite markers (Simple Sequence Repeats or SSR). The seven screened loci were polymorphic and allowed the identification of 23 distinct SSR profiles within the 27 trees analyzed. A total of 52 different alleles were scored, with an average of 7.43 alleles/SSR locus, and considerable genetic diversity was found. Neighbor-Joining algorithm cluster analysis and principal co-ordinate analysis (PCoA) allowed for the identification of the genetic relationships between several accessions. The 27 Olea accessions were clearly separated into three different groups. SSR analysis was more precise than endocarp characterization in the classification of genetic diversity among the olive tree cultivars. The study shows reasonable olive tree diversity in Ficalho, indicating that these traditional orchards are important reservoirs of old minor cultivars and incubators of new genotypes. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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393 KiB  
Article
Allelic Variants of Glutamine Synthetase and Glutamate Synthase Genes in a Collection of Durum Wheat and Association with Grain Protein Content
by Domenica Nigro, Stefania Fortunato, Stefania Lucia Giove, Giacomo Mangini, Ines Yacoubi, Rosanna Simeone, Antonio Blanco and Agata Gadaleta
Diversity 2017, 9(4), 52; https://doi.org/10.3390/d9040052 - 16 Nov 2017
Cited by 20 | Viewed by 3882
Abstract
Wheat is one of the most important crops grown worldwide. Despite the fact that it accounts for only 5% of the global wheat production, durum wheat (Triticum turgidum L. subsp. durum) is a commercially important tetraploid wheat species, which originated and [...] Read more.
Wheat is one of the most important crops grown worldwide. Despite the fact that it accounts for only 5% of the global wheat production, durum wheat (Triticum turgidum L. subsp. durum) is a commercially important tetraploid wheat species, which originated and diversified in the Mediterranean basin. In this work, the candidate gene approach has been applied in a collection of durum wheat genotypes; allelic variants of genes glutamine synthetase (GS2) and glutamate synthase (GOGAT) were screened and correlated with grain protein content (GPC). Natural populations and collections of germplasms are quite suitable for this approach, as molecular polymorphisms close to a locus with evident phenotypic effects may be closely associated with their character, providing a better physical resolution than genetic mapping using ad hoc constituted populations. A number of allelic variants were detected both for GS2 and GOGAT genes, and regression analysis demonstrated that some variations are positively and significantly related to the GPC effect. Additionally, these genes map into homoeologous chromosome groups 2 and 3, where several authors have localized important quantitative trait loci (QTLs) for GPC. The information outlined in this work could be useful in breeding and marker-assisted selection programs. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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1853 KiB  
Article
Patterns of Spontaneous Nucleotide Substitutions in Grape Processed Pseudogenes
by Andrea Porceddu and Salvatore Camiolo
Diversity 2017, 9(4), 45; https://doi.org/10.3390/d9040045 - 13 Oct 2017
Cited by 2 | Viewed by 3926
Abstract
Pseudogenes are dead copies of genes. Owing to the absence of functional constraint, all nucleotide substitutions that occur in these sequences are selectively neutral, and thus represent the spontaneous pattern of substitution within a genome. Here, we analysed the patterns of nucleotide substitutions [...] Read more.
Pseudogenes are dead copies of genes. Owing to the absence of functional constraint, all nucleotide substitutions that occur in these sequences are selectively neutral, and thus represent the spontaneous pattern of substitution within a genome. Here, we analysed the patterns of nucleotide substitutions in Vitis vinifera processed pseudogenes. In total, 259 processed pseudogenes were used to compile two datasets of nucleotide substitutions. The ancestral states of polymorphic sites were determined based on either parsimony or site functional constraints. An overall tendency towards an increase in the pseudogene A:T content was suggested by all of the datasets analysed. Low association was seen between the patterns and rates of substitutions, and the compositional background of the region where the pseudogene was inserted. The flanking nucleotide significantly influenced the substitution rates. In particular, we noted that the transition of G→A was influenced by the presence of C at the contiguous 5′ end base. This finding is in agreement with the targeting of cytosine to methylation, and the consequent methyl-cytosine deamination. These data will be useful to interpret the roles of selection in shaping the genetic diversity of grape cultivars. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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6822 KiB  
Article
Venetian Local Corn (Zea mays L.) Germplasm: Disclosing the Genetic Anatomy of Old Landraces Suited for Typical Cornmeal Mush Production
by Fabio Palumbo, Giulio Galla, Liliam Martínez-Bello and Gianni Barcaccia
Diversity 2017, 9(3), 32; https://doi.org/10.3390/d9030032 - 16 Aug 2017
Cited by 17 | Viewed by 4993
Abstract
Due to growing concern for the genetic erosion of local varieties, four of the main corn landraces historically grown in Veneto (Italy)—Sponcio, Marano, Biancoperla and Rosso Piave—were characterized in this work. A total of 197 phenotypically representative plants collected from field populations were [...] Read more.
Due to growing concern for the genetic erosion of local varieties, four of the main corn landraces historically grown in Veneto (Italy)—Sponcio, Marano, Biancoperla and Rosso Piave—were characterized in this work. A total of 197 phenotypically representative plants collected from field populations were genotyped at 10 SSR marker loci, which were regularly distributed across the 10 genetic linkage groups and were previously characterized for high polymorphism information content (PIC), on average equal to 0.5. The population structure analysis based on this marker set revealed that 144 individuals could be assigned with strong ancestry association (>90%) to four distinct clusters, corresponding to the landraces used in this study. The remaining 53 individuals, mainly from Sponcio and Marano, showed admixed ancestry. Among all possible pairwise comparisons of individual plants, these two landraces exhibited the highest mean genetic similarity (approximately 67%), as graphically confirmed through ordination analyses based on PCoA centroids and UPGMA trees. Our findings support the hypothesis of direct gene flow between Sponcio and Marano, likely promoted by the geographical proximity of these two landraces and their overlapping cultivation areas. Conversely, consistent with its production mainly confined to the eastern area of the region, Rosso Piave scored the lowest genetic similarity (<59%) to the other three landraces and firmly grouped (with average membership of 89%) in a separate cluster, forming a molecularly distinguishable gene pool. The elite inbred B73 used as tester line scored very low estimates of genetic similarity (on average <45%) with all the landraces. Finally, although Biancoperla was represented at K = 4 by a single subgroup with individual memberships higher than 80% in almost all cases (57 of 62), when analyzed with an additional level of population structure for K = 6, it appeared to be entirely (100%) constituted by individuals with admixed ancestry. This suggests that the current population could be the result of repeated hybridization events between the two accessions currently bred in Veneto. The genetic characterization of these heritage landraces should prove very useful for monitoring and preventing further genetic erosion and genetic introgression, thus preserving their gene pools, phenotypic identities and qualitative traits for the future. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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229 KiB  
Article
Putting Plant Genetic Diversity and Variability at Work for Breeding: Hybrid Rice Suitability in West Africa
by Raafat El-Namaky, Mamadou M. Bare Coulibaly, Maji Alhassan, Karim Traore, Francis Nwilene, Ibnou Dieng, Rodomiro Ortiz and Baboucarr Manneh
Diversity 2017, 9(3), 27; https://doi.org/10.3390/d9030027 - 10 Jul 2017
Cited by 5 | Viewed by 4939
Abstract
Rice is a staple food in West Africa, where its demand keeps increasing due to population growth. Hence, there is an urgent need to identify high yielding rice cultivars that fulfill this demand locally. Rice hybrids are already known to significantly increase productivity. [...] Read more.
Rice is a staple food in West Africa, where its demand keeps increasing due to population growth. Hence, there is an urgent need to identify high yielding rice cultivars that fulfill this demand locally. Rice hybrids are already known to significantly increase productivity. This study evaluated the potential of Asian hybrids with good adaptability to irrigated and rainfed lowland rice areas in Mali, Nigeria, and Senegal. There were 169 hybrids from China included in trials at target sites during 2009 and 2010. The genotype × environment interaction was highly significant (p < 0.0001) for grain yield indicating that the hybrids’ and their respective cultivar checks’ performance differed across locations. Two hybrids had the highest grain yield during 2010 in Mali, while in Nigeria, four hybrids in 2009 and one hybrid in 2010 had higher grain yield and matured earlier than the best local cultivar. The milling recovery, grain shape and cooking features of most hybrids had the quality preferred by West African consumers. Most of the hybrids were, however, susceptible to African rice gall midge (AfRGM) and Rice Yellow Mottle Virus (RMYV) isolate Ng40. About 60% of these hybrids were resistant to blast. Hybrids need to incorporate host plant resistant for AfRGM and RYMV to be grown in West Africa. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
2714 KiB  
Article
The Phylogeny and Biogeography of Phyla nodiflora (Verbenaceae) Reveals Native and Invasive Lineages throughout the World
by Caroline L. Gross, Mohammad Fatemi, Mic Julien, Hannah McPherson and Rieks Van Klinken
Diversity 2017, 9(2), 20; https://doi.org/10.3390/d9020020 - 10 May 2017
Cited by 8 | Viewed by 6725
Abstract
Phyla nodiflora is an herbaceous perennial and an enigmatic species. It is indigenous to the Americas but is considered a natural component of the flora in many areas and a weed in others. Our aim was to circumscribe the native range of P. [...] Read more.
Phyla nodiflora is an herbaceous perennial and an enigmatic species. It is indigenous to the Americas but is considered a natural component of the flora in many areas and a weed in others. Our aim was to circumscribe the native range of P. nodiflora, to explore dispersal mechanisms and routes and to test the hypothesis that P. nodiflora is native outside of the Americas. Determining whether distributions are natural or human-induced has implications for decisions regarding weed control or conservation. We undertook phylogenetic analyses using sequence variation in nuclear DNA marker ITS (Internal Transcribed Spacer) for a global sample of 160 populations of P. nodiflora sourced from Asia, Australia, central America, the Mediterranean, southern North America, South America and Africa. Analyses included maximum likelihood, maximum parsimony, a Bayesian estimation of phylogeny and a parsimony network analysis which provided a genealogical reconstruction of ribotypes. We evaluated phylogenies against extensive historical and biogeographical data. Based on the sequences, 64 ribotypes were identified worldwide within P. nodiflora and considerable geographic structure was evident with five clades: one unsupported and the remaining weakly supported (bootstrap support ranging from 52% to 71%). Populations from central and southern North America formed the core area in the indigenous range and we have detected at least three native lineages outside of this range. Within Australia P. nodiflora is represented by at least one native lineage and several post-European introductions. Phyla nodiflora is one of the few species in the family Verbenaceae to have a pan-tropical native distribution, probably resulting from natural dispersal from America to Africa then to Australasia. However, it has also undergone human-mediated dispersal, which has obscured the native-origin of some ribotypes. These introductions present a risk of diluting the pan-tropical structure evident in this species and therefore they have important conservation implications. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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Review

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11 pages, 234 KiB  
Review
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)
by Pedro Carbonell, Aranzazu Alonso, Adrián Grau, Juan Francisco Salinas, Santiago García-Martínez and Juan José Ruiz
Diversity 2018, 10(1), 12; https://doi.org/10.3390/d10010012 - 27 Feb 2018
Cited by 15 | Viewed by 4661
Abstract
In 1998, the plant breeding team at the School of Engineering of Orihuela (EPSO), part of the Miguel Hernández University (UMH) in Elche, commenced a tomato breeding program. Marker-assisted selection and backcrossing were used to simultaneously introduce three genes (Tm-2a, Ty-1 [...] Read more.
In 1998, the plant breeding team at the School of Engineering of Orihuela (EPSO), part of the Miguel Hernández University (UMH) in Elche, commenced a tomato breeding program. Marker-assisted selection and backcrossing were used to simultaneously introduce three genes (Tm-2a, Ty-1, and Sw-5) that confer resistance to relevant viruses, such as tomato mosaic virus (ToMV), tomato yellow curl virus (TYLCV), and tomato spotted wilt virus (TSWV), to traditional varieties of local tomatoes, specifically the “Muchamiel” and the “De la pera” types. After each backcross, cleaved amplified polymorphic sequence (CAPS) molecular markers were used to select the plants with the resistance genes of interest. A previously described marker was used for TSWV, and new markers were designed for ToMV, and TYLCV using available sequences in the National Center for Biotechnology Information (NCBI) database. In parallel to the breeding program, several molecular markers—Sequence Related Amplified Polymorphism (SRAP), Simple Sequence Repeats (SSRs), Amplified Fragment Length Polymorphisms (AFLPs), Single Nucleotide Polymorphisms (SNPs), and (GATA)4 probes—were used to study genetic variability, and to identify a collection of Spanish and Italian traditional tomato varieties. The results showed a limited genetic variability among cultivated tomato varieties. The breeding lines Muchamiel UMH 1200, and De la pera 1203 (both with homozygous resistance to the three viruses) were the first new varieties that were obtained. They were included in the Register of Protected Plant Varieties in 2013. Lines without a resistance to TYLCV were also developed, and protected in 2017. We have begun to use SNP massive genotyping for studies of genetic association, and for selecting plants with the Ty-1 gene with less linkage drag. Molecular markers have been extremely useful in identifying the different steps of the tomato breeding program at EPSO-UMH. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
3437 KiB  
Review
Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities
by Carla Ceoloni, Ljiljana Kuzmanović, Roberto Ruggeri, Francesco Rossini, Paola Forte, Alessia Cuccurullo and Alessandra Bitti
Diversity 2017, 9(4), 55; https://doi.org/10.3390/d9040055 - 01 Dec 2017
Cited by 27 | Viewed by 6958
Abstract
Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat ( [...] Read more.
Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat (T. durum, 4x), widening the genetic base is a priority and primary target to cope with the many challenges that the crop has to face. These include recent climate changes, as well as actual and projected demographic growth, contrasting with reduction of arable land and water reserves. All of these environmental and societal modifications pose major constraints to the required production increase in the wheat crop. A sustainable approach to address this task implies resorting to non-conventional breeding strategies, such as “chromosome engineering”. This is based on cytogenetic methodologies, which ultimately allow for the incorporation into wheat chromosomes of targeted, and ideally small, chromosomal segments from the genome of wild relatives, containing the gene(s) of interest. Chromosome engineering has been successfully applied to introduce into wheat genes/QTL for resistance to biotic and abiotic stresses, quality attributes, and even yield-related traits. In recent years, a substantial upsurge in effective alien gene exploitation for wheat improvement has come from modern technologies, including use of molecular markers, molecular cytogenetic techniques, and sequencing, which have greatly expanded our knowledge and ability to finely manipulate wheat and alien genomes. Examples will be provided of various types of stable introgressions, including pyramiding of different alien genes/QTL, into the background of bread and durum wheat genotypes, representing valuable materials for both species to respond to the needed novelty in current and future breeding programs. Challenging contexts, such as that inherent to the 4x nature of durum wheat when compared to 6x bread wheat, or created by presence of alien genes affecting segregation of wheat-alien recombinant chromosomes, will also be illustrated. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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233 KiB  
Review
Towards the Genomic Basis of Local Adaptation in Landraces
by Giandomenico Corrado and Rosa Rao
Diversity 2017, 9(4), 51; https://doi.org/10.3390/d9040051 - 04 Nov 2017
Cited by 24 | Viewed by 5375
Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions [...] Read more.
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
226 KiB  
Review
International Instruments for Conservation and Sustainable Use of Plant Genetic Resources for Food and Agriculture: An Historical Appraisal
by Andrea Sonnino
Diversity 2017, 9(4), 50; https://doi.org/10.3390/d9040050 - 01 Nov 2017
Cited by 16 | Viewed by 5600
Abstract
This paper critically reviews the evolution of concepts and principles that inspired the adoption and enforcement of international instruments related to the conservation, exchange and sustainable use of plant genetic resources for food and agriculture, including agreements, governance and programs. The review spans [...] Read more.
This paper critically reviews the evolution of concepts and principles that inspired the adoption and enforcement of international instruments related to the conservation, exchange and sustainable use of plant genetic resources for food and agriculture, including agreements, governance and programs. The review spans from the pioneering attempts to regulate this matter, to the negotiations that led to the current regulatory framework, covering the creation of the Panel of Experts on Plant Exploration and Introduction of Food and Agriculture Organization (FAO) in 1965, the establishment of the International Board for Plant Genetic Resources (IBPGR) in 1974 and the FAO Commission on Plant Genetic Resources for Food and Agriculture in 1983, the adoption of the International Undertaking in 1983 and, more recently (2001), the International Treaty for Plant Genetic Resources for Food and Agriculture. The conceptual contribution, offered by Prof. Scarascia Mugnozza and other visionary scholars, to the establishment of these international instruments, is highlighted. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
1310 KiB  
Review
NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops
by Nunzio D’Agostino and Pasquale Tripodi
Diversity 2017, 9(3), 38; https://doi.org/10.3390/d9030038 - 15 Sep 2017
Cited by 30 | Viewed by 10707
Abstract
Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses [...] Read more.
Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore “gene space” and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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84957 KiB  
Review
Barley Developmental Mutants: The High Road to Understand the Cereal Spike Morphology
by Valeria Terzi, Giorgio Tumino, Donata Pagani, Fulvia Rizza, Roberta Ghizzoni, Caterina Morcia and Antonio Michele Stanca
Diversity 2017, 9(2), 21; https://doi.org/10.3390/d9020021 - 11 May 2017
Cited by 8 | Viewed by 11903
Abstract
A better understanding of the developmental plan of a cereal spike is of relevance when designing the plant for the future, in which innovative traits can be implemented through pre-breeding strategies. Barley developmental mutants can be a Mendelian solution for identifying genes controlling [...] Read more.
A better understanding of the developmental plan of a cereal spike is of relevance when designing the plant for the future, in which innovative traits can be implemented through pre-breeding strategies. Barley developmental mutants can be a Mendelian solution for identifying genes controlling key steps in the establishment of the spike morphology. Among cereals, barley (Hordeum vulgare L.) is one of the best investigated crop plants and is a model species for the Triticeae tribe, thanks to several characteristics, including, among others, its adaptability to a wide range of environments, its diploid genome, and its self-pollinating mating system, as well as the availability of its genome sequence and a wide array of genomic resources. Among them, large collections of natural and induced mutants have been developed since the 1920s, with the aim of understanding developmental and physiological processes and exploiting mutation breeding in crop improvement. The collections are not only comprehensive in terms of single Mendelian spike mutants, but with regards to double and triple mutants derived from crosses between simple mutants, as well as near isogenic lines (NILs) that are useful for genetic studies. In recent years the integration of the most advanced omic technologies with historical mutation-genetics research has helped in the isolation and validation of some of the genes involved in spike development. New interrogatives have raised the question about how the behavior of a single developmental gene in different genetic backgrounds can help in understanding phenomena like expressivity, penetrance, phenotypic plasticity, and instability. In this paper, some genetic and epigenetic studies on this topic are reviewed. Full article
(This article belongs to the Special Issue Plant Genetics and Biotechnology in Biodiversity)
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