Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen

Authors: Cai, Guohong; Fleury, Tomara; ZHANG, NING - Rutgers University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2019
Publication Date: 5/28/2019
Citation: Cai, G., Fleury, T.J., Zhang, N. 2019. Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen. Scientific Reports. 9:7969. https://doi.org/10.1038/s41598-019-44411-z.
DOI: https://doi.org/10.1038/s41598-019-44411-z

Interpretive Summary: Microsatellite DNA sequences are a tract of repetitive, short DNA motifs. They have been used as robust molecular markers in many areas of study. Development of these markers for an organism requires considerable time and resource. In this study, we described a method to simplify and speed up the marker development process. Our approach took advantage of the availability of genomic sequences from multiple individuals in many species. We applied our method on Phytophthora sojae, a soybean pathogen, and identified 157 such markers. In addition to providing a wealth of valuable molecular markers for P. sojae, our method can be used by other scientist to develop microsatellite markers for organisms under their study.

Technical Abstract: Microsatellites are a tract of repetitive, short DNA motifs (usually 1-6 bp) abundant in various genomes. They are robust molecular markers in many areas of studies. Development of microsatellite markers usually involves three steps: 1) obtaining microsatellite-containing sequences, 2) primer design, and 3) screening microsatellite loci for polymorphism. The first and third steps require considerable resources. Next generation sequencing technologies have greatly alleviated the constraint of the first step. In this study, we leveraged the availability of genome assemblies of multiple individuals in many species and designed a comparative genomics approach to bioinformatically identify polymorphic loci. Our approach can eliminate or greatly reduce the need of experimental screening for polymorphism and ensure that the flanking regions do not have length difference that would confound interpretation of genotyping results using microsatellite markers. We applied this approach on Phytophthora sojae, a soybean pathogen, and identified 157 high-quality, informative microsatellite markers in this oomycete. Our approach can be readily applied to other organisms.