Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Abstract

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

“…and facilitate the accurate mating designs with parental analysis to accelerate the breeding progress [8]. The accessible molecular marker includes: (1) hybridization-based type such as restriction fragment length polymorphism (RFLP) and its modified forms, (2) PCR and electrophoresis-based type including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), inter simple sequence repeat (ISSR), and simple sequence repeat (SSR) etc., and (3) sequencing-based type dominated by single nucleotide polymorphism (SNP) [9][10][11]. Of these, SNPs have proved to be the most abundant form of variation within a species at genome level that provides more detailed insights into the genetic base of a population [10].…”

Doubled haploid based parental lines are most suitable in predicting heterosis using microsatellites and in development of highly heterotic F1hybrids inBrassica oleracea

“…Of 350 microsatellites, > 50% was EST-SSRs primers, and EST-SSRs are derived from transcribed regions of genome and are having highly conserved sequences among homologous genes. They depicts the allelic diversity within or adjacent to genes and that might be more informative functionally and have higher transferability rate to related taxa in contrast to genomic SSRs [75, 80]. Then, we obtained high value of mean expected heterozygosity ( H e ), which is 0.68 indicating high genetic diversity in the studied genotypes as H e corresponds to genetic diversity.…”

Development of simple sequence repeat markers in Pyropia yezoensis (Bangiales, Rhodophyta) by high‐throughput sequencing technology

“…SSRs were detected based on the following criteria: (a) SSR repeat motifs ranging 2–6 bp in size; (b) minimal length of the SSR was 12 bp; (c) upstream and downstream of SSR were longer than 100 bp for primer design respectively; (d) minimal distance of two SSRs was 12 bp. Mono‐nucleotide repeats were excluded in the present study since they could result from sequencing errors or mismatches (Taheri et al, ).…”

“…Genic SSRs are derived from coding regions which are usually conserved, leading to lower polymorphisms in comparison with genomic SSRs (Varshney, Graner, & Sorrells, ; Zhou et al, ). Currently, next‐generation sequencing (NGS) technologies are considered as cheaper and more powerful tools than traditional sequencing methods for molecular marker development in model and non‐model organisms (Taheri et al, ; Yu et al, ). For species without a reference genome sequence, the sequencing of a combination of small‐insert library and assembly of DNA sequences may represent an effective approach to develop genomic SSR markers (Zhou et al, ).…”