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Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive
Ahmet İpek1, Meryem İpek2, Sezai Ercişli3
1Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey. maipek@uludag.edu.tr.
Functional & Integrative Genomics
|February 19, 2017
Summary
Researchers developed new SNP markers for olive trees using genotyping-by-sequencing. This advanced genetic map aids in identifying genes for important traits and supports marker-assisted selection in olive breeding.
Area of Science:
- Plant genetics
- Genomics
- Molecular biology
Background:
- Molecular markers are crucial for identifying genes related to economically important plant traits.
- Traditional methods for developing markers like SSRs and SNPs from ESTs are labor-intensive.
Purpose of the Study:
- To develop single-nucleotide polymorphism (SNP) markers within the olive transcriptome using genotyping-by-sequencing (GBS).
- To construct a high-density genetic linkage map for the olive genome.
Main Methods:
- Genotyping-by-sequencing (GBS) was applied to 125 olive DNA samples.
- Illumina sequencing reads were aligned to the olive transcriptome to identify SNPs.
- A genetic linkage map was constructed using identified SNPs, SSRs, and CAPS markers.
Main Results:
- 22,033 transcriptome-based SNP markers were identified.
- 3,384 SNP markers were successfully mapped to the olive genome.
- A saturated genetic linkage map covering 3340.8 cM across 23 linkage groups was generated.
Conclusions:
- The developed genetic map is a valuable resource for localizing quantitative trait loci (QTLs) and candidate genes in olives.
- This map will facilitate marker-assisted selection for improving economically important traits in olive breeding programs.
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