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EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives.
Genes (Basel). 2020 08 10; 11(8)G

Abstract

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.

Authors+Show Affiliations

CNR-Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy.IFAPA-Centro Alameda del Obispo, Avda Menendez Pidal, s/n, E-14004 Cordoba, Spain.IFAPA-Centro Alameda del Obispo, Avda Menendez Pidal, s/n, E-14004 Cordoba, Spain.IFAPA-Centro Alameda del Obispo, Avda Menendez Pidal, s/n, E-14004 Cordoba, Spain.CNR-Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy.CNR-Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy.CNR-Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32785094

Citation

Mariotti, Roberto, et al. "EST-SNP Study of Olea Europaea L. Uncovers Functional Polymorphisms Between Cultivated and Wild Olives." Genes, vol. 11, no. 8, 2020.
Mariotti R, Belaj A, De La Rosa R, et al. EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives. Genes (Basel). 2020;11(8).
Mariotti, R., Belaj, A., De La Rosa, R., Leòn, L., Brizioli, F., Baldoni, L., & Mousavi, S. (2020). EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives. Genes, 11(8). https://doi.org/10.3390/genes11080916
Mariotti R, et al. EST-SNP Study of Olea Europaea L. Uncovers Functional Polymorphisms Between Cultivated and Wild Olives. Genes (Basel). 2020 08 10;11(8) PubMed PMID: 32785094.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives. AU - Mariotti,Roberto, AU - Belaj,Angjelina, AU - De La Rosa,Raul, AU - Leòn,Lorenzo, AU - Brizioli,Federico, AU - Baldoni,Luciana, AU - Mousavi,Soraya, Y1 - 2020/08/10/ PY - 2020/07/14/received PY - 2020/08/04/revised PY - 2020/08/07/accepted PY - 2020/8/14/entrez PY - 2020/8/14/pubmed PY - 2021/3/24/medline KW - EST–SNPs KW - Olea europaea subsp. europaea KW - candidate genes KW - conservation KW - cultivars KW - functional markers KW - genomics-assisted breeding KW - oleasters KW - subsp. guanchica JF - Genes JO - Genes (Basel) VL - 11 IS - 8 N2 - 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. SN - 2073-4425 UR - https://www.unboundmedicine.com/medline/citation/32785094/EST_SNP_Study_of_Olea_europaea_L__Uncovers_Functional_Polymorphisms_between_Cultivated_and_Wild_Olives_ DB - PRIME DP - Unbound Medicine ER -