Development and characterization of 37 SNP markers in the ark shell Scapharca subcrenata using RAD sequencing and high resolution melting analysis

Development and characterization of 37 SNP markers in the ark shell Scapharca subcrenata using... The ark shell Scapharca subcrenata, an important fishery resource in Asian countries, has been suffering from severe population decline in recent years. To facilitate genetic conservation studies, novel single nucleotide polymorphisms (SNPs) markers were developed using next generation sequencing for this species, which yielded a total of 781,860 putative SNPs. To validate these markers, 96 SNP genotyping assays were designed to characterize polymorphisms using high resolution melting (HRM) analysis in 32 individuals from a wild population. As a result, 37 SNPs showed polymorphisms with MAF ranging from 0.0313 to 0.4844. The observed heterozygosity ranged from 0 to 0.8333, while the expected heterozygosity varied from 0.0605 to 0.4995. After the Bonferroni correction, 5 of the 37 loci showed significant departure from Hardy–Weinberg equilibrium. These novel SNP markers will be useful for future investigation of population structure and conservation genetics of the ark shell S. subcrenata. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Conservation Genetics Resources Springer Journals

Development and characterization of 37 SNP markers in the ark shell Scapharca subcrenata using RAD sequencing and high resolution melting analysis

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Publisher
Springer Netherlands
Copyright
Copyright © 2017 by Springer Science+Business Media Dordrecht
Subject
Life Sciences; Conservation Biology/Ecology; Ecology; Biodiversity; Evolutionary Biology; Plant Genetics and Genomics; Animal Genetics and Genomics
eISSN
1877-7260
D.O.I.
10.1007/s12686-016-0679-8
Publisher site
See Article on Publisher Site

Abstract

The ark shell Scapharca subcrenata, an important fishery resource in Asian countries, has been suffering from severe population decline in recent years. To facilitate genetic conservation studies, novel single nucleotide polymorphisms (SNPs) markers were developed using next generation sequencing for this species, which yielded a total of 781,860 putative SNPs. To validate these markers, 96 SNP genotyping assays were designed to characterize polymorphisms using high resolution melting (HRM) analysis in 32 individuals from a wild population. As a result, 37 SNPs showed polymorphisms with MAF ranging from 0.0313 to 0.4844. The observed heterozygosity ranged from 0 to 0.8333, while the expected heterozygosity varied from 0.0605 to 0.4995. After the Bonferroni correction, 5 of the 37 loci showed significant departure from Hardy–Weinberg equilibrium. These novel SNP markers will be useful for future investigation of population structure and conservation genetics of the ark shell S. subcrenata.

Journal

Conservation Genetics ResourcesSpringer Journals

Published: Jan 10, 2017

References

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