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  • 1
    Online Resource
    Online Resource
    Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.
    MDPI AG ; 2021
    In:  Plants Vol. 10, No. 11 ( 2021-11-19), p. 2514-
    Details
    In: Plants, MDPI AG, Vol. 10, No. 11 ( 2021-11-19), p. 2514-
    Abstract: Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data.
    Type of Medium: Online Resource
    ISSN: 2223-7747
    URL: Article
    DOI: 10.3390/plants10112514
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2704341-1
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  • 2
    Online Resource
    Online Resource
    Transposon activation is a major driver in the genome evolution of cultivated olive trees ( Olea europaea L.)
    Wiley ; 2020
    In:  The Plant Genome Vol. 13, No. 1 ( 2020-03)
    Details
    In: The Plant Genome, Wiley, Vol. 13, No. 1 ( 2020-03)
    Abstract: The primary domestication of olive ( Olea europaea L.) in the Levant dates back to the Neolithic period, around 6,000–5,500 BC, as some archeological remains attest. Cultivated olive trees are reproduced clonally, with sexual crosses being the sporadic events that drive the development of new varieties. In order to determine the genomic changes which have occurred in a modern olive cultivar, the genome of the Picual cultivar, one of the most popular olive varieties, was sequenced. Additional 40 cultivated and 10 wild accessions were re‐sequenced to elucidate the evolution of the olive genome during the domestication process. It was found that the genome of the ‘Picual’ cultivar contains 79,667 gene models, of which 78,079 were protein‐coding genes and 1,588 were tRNA. Population analyses support two independent events in olive domestication, including an early possible genetic bottleneck. Despite genetic bottlenecks, cultivated accessions showed a high genetic diversity driven by the activation of transposable elements (TE). A high TE gene expression was observed in presently cultivated olives, which suggests a current activity of TEs in domesticated olives. Several TEs families were expanded in the last 5,000 or 6,000 years and produced insertions near genes that may have been involved in selected traits during domestication as reproduction, photosynthesis, seed development, and oil production. Therefore, a great genetic variability has been found in cultivated olive as a result of a significant activation of TEs during the domestication process.
    Type of Medium: Online Resource
    ISSN: 1940-3372 , 1940-3372
    URL: Issue
    URL: Article
    DOI: 10.1002/tpg2.v13.1
    DOI: 10.1002/tpg2.20010
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2440458-5
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  • 3
    Online Resource
    Online Resource
    Transcriptomic Analysis of Olea europaea L. Roots during the Verticillium dahliae Early Infection Process
    Wiley ; 2017
    In:  The Plant Genome Vol. 10, No. 1 ( 2017-03)
    Details
    In: The Plant Genome, Wiley, Vol. 10, No. 1 ( 2017-03)
    Abstract: Olive cultivation is affected by a wide range of biotic constraints. Verticillium wilt of olive is one of the most devastating diseases affecting this woody crop, inflicting major economic losses in many areas, particularly within the Mediterranean Basin. Little is known about gene‐expression changes during plant infection by Verticillium dahliae of woody plants such as olive. A complete RNA‐seq transcriptomic analysis of olive tree roots was made. Trinity assembler proved to be the best option to assemble the olive and V. dahliae transcriptomes. The olive transcriptome (Oleup) consisted of 68,259 unigenes (254,252 isoforms/transcripts), and the V. dahliae transcriptome (Vedah) consisted of 37,425 unigenes (52,119 isoforms/transcripts). Most unigenes of the Oleup transcriptome corresponded to cellular processes (12,339), metabolic processes (10,974), single‐organism processes (7263), and responses to stimuli (5114). As for the Vedah transcriptome, most unigenes correspond to metabolic processes (25,372), cellular processes (23,718), localization (6385), and biological regulation (4801). Differential gene‐expression analysis of both transcriptomes was made at 2 and 7 d post‐infection. The induced genes of both organisms during the plant‐pathogen interaction were clustered in six subclusters, depending on the expression patterns during the infection. Subclusters A to C correspond to plant genes, and subcluster D to F correspond to V. dahliae genes. A relevant finding was that the differentially expressed gene (DEGs) included in subclusters B and C were highly enriched in proteolysis as well as protein‐folding and biosynthesis genes. In addition, a reactive oxygen species (ROS) defense was induced first in the pathogen and later in the plant roots.
    Type of Medium: Online Resource
    ISSN: 1940-3372 , 1940-3372
    URL: Article
    DOI: 10.3835/plantgenome2016.07.0060
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2440458-5
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  • 4
    Online Resource
    Online Resource
    Identification of Genetic Markers and Genes Putatively Involved in Determining Olive Fruit Weight
    MDPI AG ; 2022
    In:  Plants Vol. 12, No. 1 ( 2022-12-29), p. 155-
    Details
    In: Plants, MDPI AG, Vol. 12, No. 1 ( 2022-12-29), p. 155-
    Abstract: The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p 〈 10−10. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination.
    Type of Medium: Online Resource
    ISSN: 2223-7747
    URL: Article
    DOI: 10.3390/plants12010155
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2704341-1
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