Isolation and characterization of 49 polymorphic microsatellite loci for Decapterus maruadsi using SLAF-seq, and cross-amplification to related species

Niu, Su‐Fang; Zhai, Yun; Wu, Renxie; Zhang, Hao-Ran; Tian, Letian; Deng, Jiaxin; Xiao, Yao

doi:10.1007/s00343-019-7299-6

Cited by 2 publications

(2 citation statements)

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“…japonicus mainly used mtDNA sequences and AFLP markers (Niu et al., 2011; Zhao et al., 2015). The maternal inheritance of mtDNA makes it a better tool for phylogenetic analysis and evolutionary biology, but its ability to reveal the fine population genetic structure of marine fish is limited (Niu et al., 2019). AFLPs show high replicability and resolution, whereas they are mainly dominant rather than co‐dominant markers (Mueller & Wolfenbarger, 1999).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, several studies have reported that the specific‐locus amplified fragment sequencing (SLAF‐seq) method based on reduced representation library (RRL) can generate a large number of SSRs with long repeat motifs (Niu et al., 2019; Sun et al., 2013). SLAF‐seq has been successfully applied for developing various SSR markers in several marine fishes such as Decapterus maruadsi (Niu et al., 2019) and Lepturacanthus savala (Zhang et al., 2018). In this study, we attempted to detect a large number of diverse potential genomic microsatellites and isolate polymorphic SSR markers with long repeat motifs for T .…”

Section: Introductionmentioning

confidence: 99%

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Development and characterization of 33 polymorphic microsatellite markers in Trachurus japonicus by SLAF‐seq technology

Niu

Zhai

et al. 2020

J Appl Ichthyol

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Trachurus japonicus is an economically important fish in the northwestern Pacific Ocean. However, its resources have declined seriously and there is an urgent need for a wide‐range of investigations of the existing genetic resources. This requires a large number of diverse molecular markers with high discriminating power. In this study, we identified 43,264 perfect SSRs in T. japonicus genome using SLAF‐seq technology. Of these, we randomly selected 106 SSRs (tri‐nucleotide to hexa‐nucleotide) to test for polymorphism. Eventually, we successfully developed a total of 33 loci including 8 tri‐nucleotide and 25 long repeat motifs (tetra‐nucleotide to hexa‐nucleotide). The number of alleles (Na) of these loci ranged from 4 to 24 (mean 12.6). The observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.258 to 0.969 (mean 0.723) and from 0.452 to 0.962 (mean 0.827), respectively. All loci except TJ6‐7 were highly informative (PIC > 0.5). These results showed that the shortlisted 33 loci exhibited moderate to relatively high genetic diversity, of which 18 were regarded as highly polymorphic and well‐resolved. In summary, these diverse and potential microsatellites detected in our study provide substantial genetic basis for the screening of polymorphic SSR markers of T. japonicus and also provide a powerful tool to perform further studies on the genetic resource assessment and conservation of T. japonicus.

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Section: Introductionmentioning

confidence: 99%