Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS).

A. S. M. Faridul Islam,Vijay Joshi,Dean Sanders,Amit Kumar Mishra

doi:10.3390/genes12122007

A. S. M. Faridul Islam, Vijay Joshi + Show 2 more

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https://doi.org/10.3390/genes12122007

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Abstract

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

Highlights

Olives (Olea europaea L.) are one of the economically important fruit and oil trees contributing to the Mediterranean food diet
The lowest and highest tering out the raw reads, the total demultiplexed reads for all the genotypes were 418.78 number reads was
A total of 33% of the total single-nucleotide polymorphism (SNP) used in the study showed half of their maximum polymorphic information content (PIC) value (0.5), indicating their suitability for future marker-assisted breeding

Summary

Introduction

Olives (Olea europaea L.) are one of the economically important fruit and oil trees contributing to the Mediterranean food diet. Several therapeutic studies have confirmed the utility of olive oil in alleviating the impacts of cardiovascular disease, obesity, metabolic syndrome, type 2 diabetes, and hypertension [3,4,5]. Most commercial olive production is confined to Mediterranean countries, more than 40 countries grow olives including Argentina, the United States (USA), Australia, Chile, and China [3,6]. California is the central oil-producing state in the USA, yielding 67,000 tons of olives at a value of USD 57,909 million [7]. Even though the US produces less than 1% of the world’s olives, it represents the third largest national market for olive oil globally, the most significant market outside the European community. Olives were believed to have been first introduced into the US by Spanish Franciscan missionaries in the late 18th century [8]

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