Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)
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 t...
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MDPI AG
2021-12-01
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| author | A. S. M. Faridul Islam Dean Sanders Amit Kumar Mishra Vijay Joshi |
| author_facet | A. S. M. Faridul Islam Dean Sanders Amit Kumar Mishra Vijay Joshi |
| author_sort | A. S. M. Faridul Islam |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T04:02:19Z |
| format | Article |
| id | doaj.art-57865bbd124548caa763ee4b7380847b |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T04:02:19Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
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| series | Genes |
| spelling | doaj.art-57865bbd124548caa763ee4b7380847b2023-11-23T08:31:39ZengMDPI AGGenes2073-44252021-12-011212200710.3390/genes12122007Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)A. S. M. Faridul Islam0Dean Sanders1Amit Kumar Mishra2Vijay Joshi3Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USABioinformatics Resource Center, University of Wisconsin–Madison, Madison, WI 53706, USADepartment of Botany, School of Life Sciences, Mizoram University, Aizawl 796004, Mizoram, IndiaTexas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USAOlives 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.https://www.mdpi.com/2073-4425/12/12/2007genotyping-by-sequencing (GBS)SNPpopulation structureAMOVA |
| spellingShingle | A. S. M. Faridul Islam Dean Sanders Amit Kumar Mishra Vijay Joshi Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS) Genes genotyping-by-sequencing (GBS) SNP population structure AMOVA |
| title | Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS) |
| title_full | Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS) |
| title_fullStr | Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS) |
| title_full_unstemmed | Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS) |
| title_short | Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS) |
| title_sort | genetic diversity and population structure analysis of the usda olive germplasm using genotyping by sequencing gbs |
| topic | genotyping-by-sequencing (GBS) SNP population structure AMOVA |
| url | https://www.mdpi.com/2073-4425/12/12/2007 |
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