Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)

Authors: KAYA, HILAL - Cornell University; AKDEMIR, DENIZ - Cornell University; LOZANO, ROBERT - Cornell University; CETIN, OZNUR - Cornell University; KAYA, HULYA - Cornell University; SAHIN, MUSTAFA - Cornell University; Smith, Jenny; BAHATTIN, YANYOLAC - Ege University; Jannink, Jean-Luc

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2019
Publication Date: 12/10/2019
Citation: Kaya, H.B., Akdemir, D., Lozano, R., Cetin, O., Kaya, H.S., Sahin, M., Smith, J.L., Bahattin, Y., Jannink, J. 2019. Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Scientific Reports. 9:18764. https://doi.org/10.1038/s41598-019-55338-w.
DOI: https://doi.org/10.1038/s41598-019-55338-w

Interpretive Summary: Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Despite this importance, genetic progress for valuable agronomic traits has been slow. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing (GBS), enabling DNA markers to be associated with important tree characteristics. We conducted the first comprehensive association 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, association was conducted using 24,977 DNA markers in the 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. Significant markers hits were mapped to their positions in the genome 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.

Technical 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.