A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data

Abstract

Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.

Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources

“…This method enables the accurate genotyping of thousands of SSRs with over 94% accuracy [26]. Additionally, Tian et al developed software based on RNA-seq data to identify polymorphic SSRs, and more than 92% of the identified SSRs exhibited polymorphisms [31]. Current methods for optimizing SSR markers primarily focus on the integration of sequencing and genotyping technologies.…”

“…Additionally, gel electrophoresis, which is the conventional method to identify SSR typing results, has limitations such as poor resolution and limited capacity for high-throughput screening [30]. Several optimizations have been performed on the SSR assay [31]. For example, the amplification efficiency is improved by optimizing the PCR system [32]; combining multiple SSR markers into one PCR reaction system for multiple PCR can significantly reduce the time and cost of genotyping [33].…”

De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer

“…As very little information on the population genetic structure of M. vitrata, particularly from the Indian subcontinent, is available, the development of microsatellites was urgent for genetic diversity analyses. The traditional methods of microsatellite development are expensive, time-consuming, and labor-intensive [17]. In silico SSR mining from the public domain is an efficient and cost-effective approach for the identification of microsatellite loci with the availability of next-generation sequencing databases and bioinformatics tools [18,19].…”