Genetic diversity analysis of olive germplasm (Olea europaea L.) with genotyping-by-sequencing technology

Authors: ZHU, SHENLONG - Zhejiang Academy Of Agricultural Sciences; NIU, ERLI - Zhejiang Academy Of Agricultural Sciences; SHI, AINONG - University Of Arkansas; Mou, Beiquan

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2019
Publication Date: 8/21/2019
Citation: Zhu, S., Niu, E., Shi, A., Mou, B. 2019. Genetic diversity analysis of olive germplasm (Olea europaea L.) with genotyping-by-sequencing technology. Frontiers in Genetics. 10:755. https://doi.org/10.3389/fgene.2019.00755.
DOI: https://doi.org/10.3389/fgene.2019.00755

Interpretive Summary: Olive (Olea europaea L.) is one of the valuable fruit trees and the second largest woody oil plant in the world. Olive is a very important edible oil crop and has been cultivated about 4,000 years in the Mediterranean area. In this study, using the genotyping-by-sequencing (GBS) technology, we carried out genetic diversity analysis on 57 olive accessions with different geographical origins. A total of 383.85 million data points was obtained and 250,178 high-quality molecular markers were generated, indicating that these markers are very abundant in the olive genome. Genetic structure and genetic analyses showed that the 57 olive accessions could be classified into two groups (Group I and Group II). Generally, no clear geographical distributions of cultivars were observed between the two groups. In the Group II, cultivars could be further divided into two subgroups (Group IIa and Group IIb) which seem to be associated with their fruit sizes. The five Chinese-bred varieties were all clustered in Group II, showing a closer genetic relationship with those from the central Mediterranean region and a narrow genetic background. It is therefore necessary for Chinese olive breeding programs to incorporate other genetic basis by utilizing germplasm from other regions, particularly from east Mediterranean region as breeding parents. The results showed that GBS is an effective marker choice for cultivar characterization and genetic diversity analysis in olive, and will help us better understand the genetic backgrounds of the crop. This information is important for both utilizing the existing olive varieties and developing new cultivars.

Technical Abstract: Olive (Olea europaea L.) is a very important edible oil crop that has been cultivated about 4,000 years in the Mediterranean area. We carried out genetic diversity analysis using the genotyping-by-sequencing (GBS) technology on 57 olive accessions of different geographic origin. A total of 383.85 million clean reads were obtained and 250,178 high-quality SNPs (single nucleotide polymorphism) were generated, indicating that GBS-SNPs are very abundant in olive genome. Genetic structure and phylogenetic analysis separated the 57 olive accessions into two groups (Group I and Group II). Generally, no clear geographical distributions of cultivars were observed between the two groups. The average nucleotide diversity (p) specific for Group I and Group II were 0.317 and 0.305. The fixation index (Fst) between Group I and Group II was 0.033. Cultivars in Group II were further divided into two subgroups (Group IIa and Group IIb) based on fruit size. The five Chinese varieties clustered in Group II, showing a closer genetic relationship with those from the central Mediterranean region, and had a narrow genetic background. It is, therefore, necessary for Chinese olive breeding programs to broaden their genetic base by utilizing germplasm from other regions, particularly from the eastern Mediterranean. The results showed that GBS is an effective marker choice for cultivar characterization and genetic diversity analysis in olive, and will help to better understand the genetic background of the crop.