Development and Characterization of EST-SSR Markers from Scapharca broughtonii and Their Transferability in Scapharca subcrenata and Tegillarca granosa

Meng Li,Zhi-Meng Zhuang,Chun-Ya Zhou,Yan-Jun Fan,Lin Lin,Ling Zhu

doi:10.3390/molecules170910716

Abstract

Twenty-five novel EST-derived simple sequence repeat (EST-SSR) markers were developed in the ark shell Scapharca broughtonii. Polymorphisms of these EST-SSR markers were evaluated in 48 wild individuals collected from Shidao, Shandong Province, China. A total of 202 alleles were detected at 25 loci. The numbers of alleles per locus ranged from 4 to 14, with an average of 8.08. The observed and expected heterozygosities varied from 0.2917 to 1.000 and from 0.3570 to 0.9002, respectively. After sequential Bonferroni correction for multiple tests, only one locus was found to deviate from Hardy-Weinberg equilibrium. Twenty-five EST-SSR markers showed a high rate of across-species transferability (100%) in Scapharca subcrenata and a low rate of across-genus transferability (20%) in Tegillarca granosa. These EST-SSRs will be helpful for QTL mapping, molecular breeding and investigation of population genetic diversity in ark shell S. broughtonii and other Scapharca species.

Highlights

The ark shell Scapharca broughtonii (S. broughtonii), a member of the family Arcidae distributed along the northwestern Pacific coast, is a commercially important bivalve species in Asian countries [1].the natural resources of S. broughtonii in China have declined drastically due to the unsustainable exploitation and environmental impacts over the last decades [1]
EST-derived simple sequence repeat (EST-SSR) markers contain high transferability because EST-SSRs are derived from expressed sequences that are more conserved than the non-genic sequences and found in other relative species [11]
These EST-SSRs will be helpful for QTL mapping, molecular breeding and investigation of population genetic diversity in ark shell S. broughtonii and other Scapharca species

Summary

Introduction

The ark shell Scapharca broughtonii (S. broughtonii), a member of the family Arcidae distributed along the northwestern Pacific coast, is a commercially important bivalve species in Asian countries [1]. Characterizing the population structure of S. broughtonii would help understanding the effect of overexploitation and environmental changes and provide important information for maintenance and management of ark shell resources. EST-SSR markers have been identified and used extensively for comparative mapping [12], DNA fingerprinting [13], biodiversity [13], evolutionary studies [14] and so on. We report the development and characterization of 25 EST-SSRs, and the transferability of EST-SSRs across-species in Scapharca subcrenata and across-genus in Tegillarca granosa. These EST-SSRs will be helpful for QTL mapping, molecular breeding and investigation of population genetic diversity in ark shell S. broughtonii and other Scapharca species

Results and Discussion

Experimental

Primer Design and Validation

Conclusions