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

Hilal Betul Kaya,Deniz Akdemir,Oznur Cetin,Bahattin Tanyolac,Hulya Sozer Kaya,Jean-Luc Jannink,Mustafa Sahin,Roberto Lozano,Jenny L Smith

doi:10.1038/s41598-019-55338-w

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.

Highlights

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide
The descriptive statistics of leaf length (LL), leaf width (LW), fruit weight (FW), stone weight (SW) and fruit flesh pit ratio (FFPR) showed substantial variation was observed in all traits (Supplementary Table S1)
We used a diverse panel of 183 olive accessions from two different Genbank resources (TOGR and National Clonal Germplasm Repository (NCGR)) to identify significant markers associated with LL, LW, FW, SW and FFPR

Summary

Introduction

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. There are more than 100 olive germplasm collections at international, national and regional levels in mostly Mediterranean countries for conservation and breeding purposes[8]. These collections have been extensively used in molecular studies including identification, molecular characterization and mapping studies[9,10,11]. GWAS has evolved as a powerful tool to dissect the genetic architecture of complex traits in large germplasm sets It does, require a large number of markers for whole genome scans in crops with low linkage disequilibrium (LD) and high haplotype diversity[20]

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