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The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies
Stijn Vanderzande1, Ping Zheng2, Lichun Cai3
1Department of Horticulture, Washington State University, Pullman, WA, USA. stijn.vanderzande@wsu.edu.
Scientific Reports
|May 8, 2020
Summary
Researchers upgraded the cherry SNP array with new markers, significantly improving genome-wide genetic analysis. This enhanced assay provides better genetic resolution and coverage for cherry breeding and genetic studies.
Area of Science:
- Plant genetics and genomics
- Agricultural science
- Bioinformatics
Background:
- Genome-wide genetic marker assays are crucial for cherry breeding and genetic research.
- The existing 6K SNP array in cherry has limited informativeness and genomic coverage.
- An upgrade is needed to enhance the cost-efficiency and resolution of genetic analyses in cherry.
Purpose of the Study:
- To develop an improved genome-wide SNP assay for cherry.
- To increase the number of informative single nucleotide polymorphisms (SNPs) and enhance genomic coverage.
- To support advanced genetic studies in sweet and sour cherry.
Main Methods:
- A focal point strategy was employed to select new SNPs within specific genomic windows.
- Additional SNPs were chosen to target important genomic regions and organellar genomes.
- The new SNPs were added to the existing 6K SNP array, creating a +9K add-on assay.
Main Results:
- The +9K add-on provided a substantial number of new reliable, polymorphic SNPs for sweet cherry and sour cherry subgenomes.
- The assay increased genetic resolution and genome coverage compared to the original SNP array.
- The new SNPs established informative focal points across the cherry genome.
Conclusions:
- The upgraded SNP assay significantly enhances the utility of genome-wide scans in cherry.
- Improved genetic resolution and coverage will facilitate a deeper understanding of cherry genetics.
- This advancement will aid in identifying the genetic control of key traits and elucidating relationships within cherry populations.
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