scholarly journals EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 916
Author(s):  
Roberto Mariotti ◽  
Angjelina Belaj ◽  
Raul De La Rosa ◽  
Lorenzo Leòn ◽  
Federico Brizioli ◽  
...  
Keyword(s):  
Olea Europaea ◽  
Expressed Sequence Tag ◽  
Germplasm Conservation ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Wild Plants ◽  
Species Differentiation ◽  
Snp Analysis ◽  
Functional Polymorphisms ◽  
Olea Europaéa

Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. Methods: In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. Results: Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. Conclusion: This deep EST–SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

scholarly journals All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 139
Author(s):  
Marlien M. van der Merwe ◽  
Jia-Yee S. Yap ◽  
Peter D. Wilson ◽  
Helen T. Murphy ◽  
Andrew Ford
Keyword(s):  
Genetic Diversity ◽  
Allelic Variation ◽  
Germplasm Conservation ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Ex Situ ◽  
Spatial Distance ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 948-956 ◽  
Author(s):  
G. Durstewitz ◽  
A. Polley ◽  
J. Plieske ◽  
H. Luerssen ◽  
E. M. Graner ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Oilseed Rape ◽  
Expressed Sequence Tag ◽  
Diploid Species ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Snp Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

scholarly journals Olea Europaea Geminivirus: A Novel Bipartite Geminivirid Infecting Olive Trees

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 481
Author(s):  
Michela Chiumenti ◽  
Claudia Greco ◽  
Angelo De Stradis ◽  
Giuliana Loconsole ◽  
Vincenzo Cavalieri ◽  
...  
Keyword(s):  
Olea Europaea ◽  
High Throughput Sequencing ◽  
Snp Analysis ◽  
A Genome ◽  
Virion Sense ◽  
Genomic Dnas ◽  
Olive Trees ◽  
Specific Symptoms ◽  
Full Length Genome ◽  
Olea Europaéa

In 2014, high-throughput sequencing of libraries of total DNA from olive trees allowed the identification of two geminivirus-like contigs. After conventional resequencing of the two genomic DNAs, their analysis revealed they belonged to the same viral entity, for which the provisional name of Olea europaea geminivirus (OEGV) was proposed. Although DNA-A showed a genome organization similar to that of New World begomoviruses, DNA-B had a peculiar ORF arrangement, consisting of a movement protein (MP) in the virion sense and a protein with unknown function on the complementary sense. Phylogenetic analysis performed either on full-length genome or on coat protein, replication associated protein (Rep), and MP sequences did not endorse the inclusion of this virus in any of the established genera in the family Geminiviridae. A survey of 55 plants revealed that the virus is widespread in Apulia (Italy) with 91% of the samples testing positive, although no correlation of OEGV with a disease or specific symptoms was encountered. Southern blot assay suggested that the virus is not integrated in the olive genome. The study of OEGV-derived siRNA obtained from small RNA libraries of leaves and fruits of three different cultivars, showed that the accumulation of the two genomic components is influenced by the plant genotype while virus-derived-siRNA profile is in line with other geminivirids reported in literature. Single-nucleotide polymorphism (SNP) analysis unveiled a low intra-specific variability.

Adaptability, agronomic and yield performance of exotic olive (Olea europaea) cultivars in Pothwar region of Pakistan

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Muhammad Azhar Iqbal ◽  
Ishfaq Ahmad Hafiz ◽  
Nadeem Akhtar Abbasi ◽  
Muhammad Kausar Nawaz Shah
Keyword(s):  
Olea Europaea ◽  
Yield Performance ◽  
Olea Europaéa

Le climat de l’Olivier (Olea europaea L.)

1990 ◽  
Vol 16 (1) ◽  
pp. 113-121 ◽  
Author(s):  
Charles Baldy
Keyword(s):  
Olea Europaea ◽  
Olea Europaea L ◽  
Olea Europaéa

Antibacterial Activity and Phytochemical Screening of Olea Europaea Leaves from Algeria

2012 ◽  
Vol 3 (1) ◽  
pp. 66-69 ◽  
Author(s):  
Nahal Bouderba Nora ◽  
Kadi Hamid ◽  
Moghtet Snouci ◽  
Meddah Boumedien ◽  
Moussaoui Abdellah
Keyword(s):  
Antibacterial Activity ◽  
Olea Europaea ◽  
Phytochemical Screening ◽  
Olea Europaéa

Morphology and discrimination features of pollen from Italian olive cultivars (Olea europaea L.)

Grana ◽  
2016 ◽  
Vol 56 (3) ◽  
pp. 204-214 ◽  
Author(s):  
Rita Messora ◽  
Assunta Florenzano ◽  
Paola Torri ◽  
Anna Maria Mercuri ◽  
Innocenzo Muzzalupo ◽  
...  
Keyword(s):  
Olea Europaea ◽  
Olea Europaea L ◽  
Olive Cultivars ◽  
Olea Europaéa

Phenolic and lipophilic metabolite adjustments in Olea europaea (olive) trees during drought stress and recovery

2021 ◽  
Vol 185 ◽  
pp. 112695
Author(s):  
Maria Celeste Dias ◽  
Diana C.G.A. Pinto ◽  
Catarina Figueiredo ◽  
Conceição Santos ◽  
Artur M.S. Silva
Keyword(s):  
Drought Stress ◽  
Olea Europaea ◽  
Olive Trees ◽  
Olea Europaéa
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