Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

Abstract

Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time-and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop (Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time-and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.

Fine-scale population genetics analysis ofPlatynereis dumerilii(Polychaeta, Nereididae) in the Black Sea: How Do Local Marine Currents Drive Geographical Differentiation?

“…With database mining, we ended up with 3 polymorphic markers out of 21 repetitive motif containing EST sequences (an efficiency of 14%). When considering the efficiency reported to the initial number of EST sequences screened, the efficiency drops to 0.16%, which is comparable with what other authors have found (Zhan et al, ). With the next generation sequencing of enriched libraries, we ended up with 10 markers out of 151 tested sequences (7% efficiency).…”

Development of SSR markers from transcriptome data for the pear rust pathogenGymnosporangium asiaticum

“…They can detect a large number of alleles, with high repeatability and inter‐species transferability, and have mainly been used in the study of bio‐effective populations, genome identification, kinship and other issues, and have even been applied in medical research (Clauss et al, 2002; Turpeinen et al, 2001; Koch et al, 2009; Hiroshi et al, 2007; Zauber et al, 2003). Despite their global applicability, the development of microsatellites requires considerable technical effort to construct the rich microsatellite libraries, which can be expensive or time‐consuming, or the number of different types of useful microsatellite loci that are successfully obtained can be limited (Peakall et al, 1998; Castoe et al, 2010; Zhan et al, 2009). Recent advances in large‐scale RNA‐seq have provided a fast, cost‐effective and reliable way to generate large expression data sets in non‐model species (Lei et al, 2017; Bhandawat et al, 2016; Zhang et al, 2012).…”

Single nucleotide polymorphism of FSHβ gene associated with reproductive traits in Japanese flounder (Paralichthys olivaceus)

“…Molecular marker-assisted selection (MAS) is being widely employed in traditional selective breeding (Zhan et al, 2009;Sun et al, 2006). Polymorphism in human FSHβ associated with fertility suggests the possible effect of balancing selection (Grigorova et al, 2007).…”