Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome...

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Developing microsatellite markers is crucial for genetic studies but faces challenges in identifying informative polymorphic loci.
• Next-generation sequencing has simplified marker cloning, but efficient screening for polymorphic and informative markers remains difficult.
• Current methods for differentiating polymorphic from non-polymorphic loci and selecting markers with a high effective number of alleles are laborious and manual.

Purpose of the Study:

• To develop an efficient strategy for identifying and developing highly polymorphic microsatellite markers.
• To overcome the hurdles of differentiating polymorphic loci and ensuring markers are sufficiently informative for broad deployment.
• To refine marker development by screening for length variants in next-generation sequencing data.

Main Methods:

• A strategy was developed to screen next-generation sequencing reads from multiple genotypes for repeats exhibiting the most length variants.
• These selected variants were then developed into microsatellite markers.
• The strategy was validated using Illumina paired-end transcriptome sequences from 11 tetraploid garden roses.

Main Results:

• Of 48 tested markers, 46 were polymorphic, with 10 amplifying more than one locus.
• An initial refinement step identified replicate markers, which were subsequently filtered out.
• The refined approach yielded 18 highly polymorphic markers, averaging 11.7 alleles per marker in 11 tetraploid roses, surpassing previous benchmarks.

Conclusions:

• The developed strategy significantly advances the efficient development of highly polymorphic microsatellite markers.
• This approach streamlines the selection of informative markers, reducing labor and improving marker quality for genetic research.
• The method effectively identifies markers with a high effective number of alleles, suitable for diverse applications.