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| Content Provider | Springer Nature Link |
|---|---|
| Author | Lu, Xia Luan, Sheng Kong, Jie Hu, Longyang Mao, Yong Zhong, Shengping |
| Copyright Year | 2017 |
| 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 marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide 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 (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). 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 (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing 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, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution. |
| Starting Page | 203 |
| Ending Page | 214 |
| Page Count | 12 |
| File Format | |
| ISSN | 02544059 |
| Journal | Chinese Journal of Oceanology and Limnology |
| Volume Number | 35 |
| Issue Number | 1 |
| e-ISSN | 19935005 |
| Language | English |
| Publisher | Science Press |
| Publisher Date | 2015-12-28 |
| Publisher Place | Heidelberg |
| Access Restriction | Subscribed |
| Subject Keyword | Marsupenaeus japonicus genome-wide SSR markers genome survey sequencing functional annotation Oceanography |
| Content Type | Text |
| Resource Type | Article |
| Subject | Water Science and Technology Oceanography |
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