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Profiling Volatile Compounds in Blackcurrant Fruit using Headspace Solid-Phase Microextraction Coupled to Gas Chromatography-Mass Spectrometry
Published on: June 9, 2021
Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum)
Joanne R Russell1, Micha Bayer, Clare Booth
1Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK. joanne.russell@hutton.ac.uk
BMC Plant Biology
|November 1, 2011
Summary
Second-generation sequencing (2GS) enabled discovery of 7,000 SNPs and 3,000 SSRs in blackcurrant, significantly advancing marker development for genetic mapping and breeding applications.
Area of Science:
- Plant genetics
- Genomics
- Bioinformatics
Background:
- Second-generation sequencing (2GS) offers a viable alternative to Sanger sequencing for non-model species.
- Large-scale SNP discovery in blackcurrant (Ribes nigrum L.) was performed using transcriptome-based 2GS 454 sequencing.
- The goal was to generate novel markers for a high-density linkage map.
Purpose of the Study:
- To discover a large number of novel single nucleotide polymorphism (SNP) and expressed sequence tag-simple sequence repeat (EST-SSR) markers in blackcurrant.
- To develop a high-density genetic linkage map for blackcurrant using these novel markers.
- To validate the utility of developed markers in diverse Ribes germplasm and for downstream breeding applications.
Main Methods:
- Utilized 2GS 454 sequencing of parental genotypes from a blackcurrant reference mapping population.
- Identified SNPs and EST-SSRs from transcriptome data.
- Developed a 384-SNP OPA assay using the Illumina BeadXpress platform.
- Constructed SNP-based linkage maps from two blackcurrant mapping populations.
Main Results:
- Generated over 700,000 reads, identifying 7,000 SNPs and 3,000 novel EST-SSRs.
- Developed and validated a 384-SNP assay across diverse Ribes germplasm.
- Constructed SNP-based maps incorporating 48% and 27% of assayed SNPs, with additional SNPs placed using quantitative trait mapping.
- Discovered a high proportion of novel genes with diverse functions.
Conclusions:
- 2GS technology significantly surpasses previous methods for marker development in terms of quantity and informativeness.
- The developed markers demonstrate high potential utility in blackcurrant breeding programs.
- This study highlights the effectiveness of 2GS for genomic research in non-model plant species.
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