Genomewide mining characterization and developm

Authors: Xia Lu Sheng Luan Jie Kong Longyang Hu Yong Mao Shengping Zhong

Publish Date: 2015/12/28

Volume: 35, Issue: 1, Pages: 203-214

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Abstract

The kuruma prawn Marsupenaeus japonicus is one of the most cultivated and consumed species of shrimp However very few molecular genetic/genomic resources are publically available for it Thus the characterization and distribution of simple sequence repeats SSRs remains ambiguous and the use of SSR markers in genomic studies and markerassisted selection is limited The goal of this study is to characterize and develop genomewide SSR markers in M japonicus by genome survey sequencing for application in comparative genomics and breeding A total of 326 945 perfect SSRs were identified among which dinucleotide repeats were the most frequent class 4408 followed by mononucleotides 2967 trinucleotides 1896 tetranucleotides 566 hexanucleotides 107 and pentanucleotides 056 In total 151 541 SSR loci primers were successfully designed A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population of which 27 loci 900 were successfully amplified with specific products and 24 800 were polymorphic For the amplified polymorphic loci the alleles ranged from 5 to 17 with an average of 963 and the average PIC value was 0796 A total of 58 256 SSRcontaining sequences had significant Gene Ontology annotation these are good functional molecular marker candidates for association studies and comparative genomic analysis The newly identified SSRs significantly contribute to the M japonicus genomic resources and will facilitate a number of genetic and genomic studies including high density linkage mapping genomewide association analysis markeraided selection comparative genomics analysis population genetics and evolution

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