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Almost 30 years have passed since the first publication reporting regeneration of transformed peach plants. Nevertheless, the general applicability of genetic transformation of this species has not yet been established. Many strategies have been tested in order to obtain an efficient peach transformation system. Despite the amount of time and the efforts invested, the lack of success has significantly limited the utility of peach as a model genetic system for trees, despite its relatively short generation time; small, high-quality genome; and well-studied genetic resources. Additionally, the absence of efficient genetic transformation protocols precludes the application of many biotechnological tools in peach breeding programs. In this review, we provide an overview of research on regeneration and genetic transformation in this species and summarize novel strategies and procedures aimed at producing transgenic peaches. Promising future approaches to develop a robust peach transformation system are discussed, focusing on the main bottlenecks to success including the low efficiency of A. tumefaciens-mediated transformation, the low level of correspondence between cells competent for transformation and those that have regenerative competence, and the high rate of chimerism in the few shoots that are produced following transformation.

First-Generation Sequencing (FGS) revolutionized molecular biology in general, and bioarchaeology in particular. That allowed to study ancient DNA (aDNA) remains for the first time. Second-Generation Sequencing (SGS) further improved throughput, reducing time and cost per sequenced nucleotide base. Most importantly, it allowed to sequence full ancient-genomes, like the ones of Neanderthals. Third-Generation Sequencing (TGS) improved even more SGS throughput, also allowing to sequence single molecules, without requiring previous amplification or modification steps. That is revolutionary, overcoming putative biases associated to such steps. This opens the door for true-direct RNA sequencing [without retrotranscription into complementary DNA (cDNA)], including ancient RNA (aRNA). Different TGS platforms are arising, promising exciting new discoveries on bioarchaeology for both aDNA and aRNA, La secuenciación de primera generación (FGS; del inglés, “First-Generation Sequencing”) revolucionó la biología molecular en general, y la bioarqueología en particular. Ello permitió estudiar restos de ADN antiguo (ADNa) por primera vez. La secuenciación de segunda generation (SGS; del inglés, “Second-Generation Sequencing”) mejoró aún más el rendimiento, reduciendo el tiempo y coste por base nucleotídica secuenciada. Además, permitió secuenciar genomas antiguos completos, como los de neandertales. La secuenciación de tercera generación (TGS; del inglés, “Third-Generation Sequencing”) mejoró aún más el rendimiento de SGS, permitiendo además secuenciar moléculas individuales, sin requerir pasos previos de amplificación o modificación. Ello es revolucionario, evitando posibles sesgos asociados a tales pasos previos. Esto abre la puerta para la secuenciación directa verdadera del ARN [sin retrotranscripción en ADN complementario (ADNc)], incluyendo ARN antiguo (ARNa). Diferentes plataformas de TGS están surgiendo, prometiendo nuevos y emocionante descubrimientos en bioarqueología, tanto para ADNa como ARNa

The nucleic-acid revolution started 31 years ago. The development of the second-generation sequencing (SGS) has allowed a higher throughput and lower price per sequenced base, opening the possibility to sequence ancient genomes, including epigenetics. The main SGS platforms are described in this review: i) Roche 454 Life Sciences, based on emulsion PCR (emPCR) and further pyrosequencing; ii) Illumina (bridge-amplification and subsequent reversible-terminator sequencing); iii) Life Technologies SOLiD (emPCR coupled with oligonucleotide ligation to interrogate DNA); and iv) Life Technologies Ion-Torrent-chip (emPCR, further using microchip pH-meters). Different ancient genomes (including viruses, microorganisms, plants and animals) have been sequenced. This has allowed to study the evolution of pathogens, domestication of microorganisms, plants and animals, paleodiets and paleoenvironments, including climate changes. Some hurdles and challenges must yet be overcome, but the steady technological advances in nucleic-acid isolation, sequencing and bioinformatics (together with higher computing power) promise a bright future for bioarchaeology in general, and paleogenomics in particular, allowing to analyze not just single genomes, but also to address ancient population genomics and evolution.

Glucose is preferentially stored as starch in plants. Thus, the remains of such polysaccharide may represent an invaluable source of archaeological evidence. The genomics, proteomics and metabolomics pathways can be also exploited to ascertain key events in phylogenetic processes. This includes the reconstruction of polyploidization events in plants and the identification of taxonomic positions. These developments are particularly relevant for the study of selection, evolution and domestication events of microorganisms, plants and animals. They include the adaptation to such food resource and the study of paleodiets and their implications for ancient and modern animals, including humans, La glucosa se almacena preferentemente como almidón en plantas. Por tanto, los restos de tal polisacárido pueden representar una fuente inestimable de información arqueológica. La genómica, proteómica y rutas metabolómicas pueden ser también explotadas para determinar eventos cruciales en procesos filogenéticos. Estos incluyen la reconstrucción de eventos de poliploidización en plantas y la identificación de posiciones taxonómicas. Estos desarrollos son particularmente relevantes para el estudio de procesos de selección, evolución y domesticación de microorganismos, plantas y animales. Incluyen la adaptación a tal recurso alimentario y el estudio de las paleodietas y sus implicaciones para animales ancestrales y modernos, incluyendo los humanos

Glucose is preferentially stored as starch in plants. Thus, the remains of such polysaccharide may represent an invaluable source of archaeological evidence. The genomics, proteomics and metabolomics pathways can be also exploited to ascertain key events in phylogenetic processes. This includes the reconstruction of polyploidization events in plants and the identification of taxonomic positions. These developments are particularly relevant for the study of selection, evolution and domestication events of microorganisms, plants and animals. They include the adaptation to such food resource and the study of paleodiets and their implications for ancient and modern animals, including humans, La glucosa se almacena preferentemente como almidón en las plantas. Por tanto, los restos de tal polisacárido pueden representar una fuente inestimable de información arqueológica. La genómica, proteómica y rutas metabolómicas pueden ser también explotadas para determinar eventos cruciales en procesos filogenéticos. Estos incluyen la reconstrucción de eventos de poliploidización en plantas y la identificación de posiciones taxonómicas. Estos desarrollos son particularmente relevantes para el estudio de procesos de selección, evolución y domesticación de microorganismos, plantas y animales. Incluyen la adaptación a tal recurso alimentario y el estudio de las paleodietas y sus implicaciones para animales ancestrales y modernos, incluyendo los humanos.

[ES] Los microsatélites son marcadores moleculares ampliamente utilizados en estudios de biodiversidad, siendo particularmente útiles en la identificación varietal. Otra de las aplicaciones más recientes de los microsatélites se halla en el campo de la agroalimentación, siendo una herramienta útil en el desarrollo de sistemas de trazabilidad y autentificación. La comparación de secuencias y genomas (genómica comparativa) ha permitido recientemente desarrollar nuevas herramientas como los polimorfismos de un solo nucleótido (SNP; del inglés, “Single Nucleotide Polymorphisms”) e inserciones/deleciones (del inglés, “indels”), que completan la cobertura genómica de los microsatélites. Los principales objetivos de esta tesis son el uso y evaluación de: i) marcadores microsatélite basados en secuencias nucleares, como herramientas en el estudio y caracterización de la agrodiversidad, en especies olvidadas e infrautilizadas (cultivos prometedores), como la higuera; y ii) marcadores microsatélite e inserciones/deleciones basados en la comparación de genomas de cloroplastos de olivo, para la identificación varietal y la aplicabilidad de ellos a la trazabilidad de los aceites de oliva de distintas variedades. Los resultados han demostrado que se trata de herramientas eficaces en la caracterización de este germoplasma local, poniendo de manifiesto la gran variabilidad que éste alberga. Todo ello ha permitido identificar variedades de olivo, tanto a partir de hoja como de aceite. Algunos de los haplotipos identificados pueden ser empleados en la trazabilidad del aceite de oliva., Microsatellites are molecular markers widely used for biodiversity studies, being particularly useful in varietal identification. A more recent application of these markers is in the agrifood field, being a suitable tool for the development of authentication and traceability systems. Comparisons of sequences and genomes (comparative genomics) have recently allowed the development of new tools, such as single nucleotide polymorphisms (SNP) and insertions/deletions (indels), which complete the genomic coverage of microsatellites. The main goals of the present thesis are the use and evaluation of: i) nuclear sequence-based microsatellite markers, as a tool for the study and characterization of the agrodiversity in neglected and underutilized species (promising crops), such as the fig tree; and ii) microsatellite and indel markers, based on comparisons of genome chloroplast of the olive tree, for varietal identification and their application to the traceability of olive oils from different varieties. Nuclear sequence-based microsatellite markers have been selected to evaluate the germplasm agrodiversity in fig tree. The presence of unique alleles has allowed the discrimination amongst local populations. The results have demonstrated that these markers are effective tools in the characterization of this local germplasm, revealing a high level of variability. All this has allowed the identification of olive tree varieties, both from the leaves and from the olive oils. Some haplotypes could be used for olive-oil traceability purposes., [EN] Microsatellites are molecular markers widely used for biodiversity studies, being particularly useful in varietal identification. A more recent application of these markers is in the agrifood field, being a suitable tool for the development of authentication and traceability systems. Comparisons of sequences and genomes (comparative genomics) have recently allowed the development of new tools, such as single nucleotide polymorphisms (SNP) and insertions/deletions (indels), which complete the genomic coverage of microsatellites. The main goals of the present thesis are the use and evaluation of: i) nuclear sequence-based microsatellite markers, as a tool for the study and characterization of the agrodiversity in neglected and underutilized species(promising crops), such as the fig tree; and ii) microsatellite and indel markers, based on comparisons of genome chloroplast of the olive tree, for varietal identification and their application to the traceability of olive oils from different varieties. Nuclear sequence-based microsatellite markers have been selected to evaluate the germplasm agrodiversity in fig tree. The presence of unique alleles has allowed the discrimination amongst local populations. The results have demonstrated that these markers are effective tools in the characterization of this local germplasm, revealing a high level of variability. All this has allowed the identification of olive tree varieties, both from the leaves and from the olive oils. Some haplotypes could be used for olive-oil traceability purposes.

The routine use of molecular makers in wheat breeding programmes has long benn hampered by the difficulties in achieving cheap, polymorphic and locus-specific makers. Recently, insertion site-based polymorphism (ISBP) makers have been evidencied as very specific and polymorphic tools for genomics and genetic studies in hexaploid wheat, capable of homogeneously saturating the wheat genome.

Olive oil traceability remains a challenge nowadays. DNA analysis is the preferred approach to an effective varietal identification, without any environmental influence. Specifically, olive organelle genomics is the most promising approach for setting up a suitable set of markers as they would not interfere with the pollinator variety DNA traces. Unfortunately, plastid DNA (cpDNA) variation of the cultivated olive has been reported to be low. This feature could be a limitation for the use of cpDNA polymorphisms in forensic analyses or oil traceability, but rare cpDNA haplotypes may be useful as they can help to efficiently discriminate some varieties. Recently, the sequencing of olive plastid genomes has allowed the generation of novel markers. In this study, the performance of cpDNA markers on olive oil matrices, and their applicability on commercial Protected Designation of Origin (PDO) oils were assessed. By using a combination of nine plastid loci (including multi-state microsatellites and short indels), it is possible to fingerprint six haplotypes (in 17 Spanish olive varieties), which can discriminate high-value commercialized cultivars with PDO. In particular, a rare haplotype was detected in genotypes used to produce a regional high-value commercial oil. We conclude that plastid haplotypes can help oil traceability in commercial PDO oils and set up an experimental methodology suitable for organelle polymorphism detection in the complex olive oil matrices. © 2013 Pérez-Jiménez et al.

The common fig tree (Ficus carica L.) is a Mediterranean crop with problematic cultivar identification. The recovery and conservation of possible local varieties for ecological production requires the previous genetic characterization of the available germplasm. In this context, 42 lines corresponding to 12 local varieties and two caprifigs, in addition to 15 reference samples have been fingerprinted using 21 SSR markers. A total of 77 alleles were revealed, detecting a useful level of genetic variability within the local germplasm pools. UPGMA clustering analysis has revealed the genetic structure and relationships among the local and reference germplasm. Eleven of the local varieties could be identified and defined as obtained clusters, showing that SSR analysis is an efficient method to evaluate the Andalusian fig tree diversity for on-farm conservation. © 2012 The Authors.