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Genome wide association study of 5 agronomic traits in olive (Olea europaea L.).
Sci Rep. 2019 12 10; 9(1):18764.SR

Abstract

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.

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Authors+Show Affiliations

Kaya HB
Department of Bioengineering, Faculty of Engineering, Manisa Celal Bayar University, Manisa, Turkey. hilalbetul.kaya@cbu.edu.tr. School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA. hilalbetul.kaya@cbu.edu.tr.
Akdemir D
Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY, USA.
Lozano R
School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
Cetin O
Olive Research Institute, Izmir, Turkey.
Sozer Kaya H
Olive Research Institute, Izmir, Turkey.
Sahin M
Olive Research Institute, Izmir, Turkey.
Smith JL
National Clonal Germplasm Repository, USDA-ARS, One Shields Avenue, Davis, CA, USA.
Tanyolac B
Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey.
Jannink JL
School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA. USDA ARS, Robert W. Holley Center for Agriculture & Health, Ithaca, NY, USA.

MeSH

Chromosome MappingCrops, AgriculturalGenetic MarkersGenome, PlantGenome-Wide Association StudyMicrosatellite RepeatsOleaPlant BreedingPolymorphism, Single NucleotideQuantitative Trait LociSeed BankTurkeyUnited States

Pub Type(s)

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

Language

eng

PubMed ID

31822760

Citation

Kaya, Hilal Betul, et al. "Genome Wide Association Study of 5 Agronomic Traits in Olive (Olea Europaea L.)." Scientific Reports, vol. 9, no. 1, 2019, p. 18764.
Kaya HB, Akdemir D, Lozano R, et al. Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Sci Rep. 2019;9(1):18764.
Kaya, H. B., Akdemir, D., Lozano, R., Cetin, O., Sozer Kaya, H., Sahin, M., Smith, J. L., Tanyolac, B., & Jannink, J. L. (2019). Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Scientific Reports, 9(1), 18764. https://doi.org/10.1038/s41598-019-55338-w
Kaya HB, et al. Genome Wide Association Study of 5 Agronomic Traits in Olive (Olea Europaea L.). Sci Rep. 2019 12 10;9(1):18764. PubMed PMID: 31822760.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). AU - Kaya,Hilal Betul, AU - Akdemir,Deniz, AU - Lozano,Roberto, AU - Cetin,Oznur, AU - Sozer Kaya,Hulya, AU - Sahin,Mustafa, AU - Smith,Jenny L, AU - Tanyolac,Bahattin, AU - Jannink,Jean-Luc, Y1 - 2019/12/10/ PY - 2019/01/04/received PY - 2019/11/05/accepted PY - 2019/12/12/entrez PY - 2019/12/12/pubmed PY - 2020/11/12/medline SP - 18764 EP - 18764 JF - Scientific reports JO - Sci Rep VL - 9 IS - 1 N2 - Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/31822760/Genome_wide_association_study_of_5_agronomic_traits_in_olive__Olea_europaea_L___ DB - PRIME DP - Unbound Medicine ER -