The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions

Danyang Li; Cui Long; Xiaoming Pang; Delu Ning; Tao Wu; Mingliang Dong; Xiaoning Han; Huihong Guo

doi:10.7717/peerj.8573

The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions

PeerJ. 2020 Feb 13:8:e8573. doi: 10.7717/peerj.8573. eCollection 2020.

Authors

Danyang Li^#¹, Cui Long^#¹, Xiaoming Pang¹, Delu Ning², Tao Wu², Mingliang Dong¹, Xiaoning Han¹, Huihong Guo¹

Affiliations

¹ National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
² Yunnan Academy of Forestry and Grassland, Kunming, Yunnan, China.

^# Contributed equally.

Abstract

Background: Olive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars.

Method: SSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers.

Results: Twenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive.

Keywords: Genetic characteristics; Genetic relationships; Olive; Trinucleotide genomic-SSR.

Grants and funding

This research was funded by the Fundamental Research Funds for the Central Universities (No. 2017ZY24) and the National Natural Science Foundation of China (No. 31870650). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.