Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

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

doi:10.1007/s00343-016-5250-7

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Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

OriginalPaper | Updated：2023-05-16

- Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing
- Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing
- 海洋湖沼学报（英文） 2017年35卷第1期页码：203-214
- Affiliations：
  
  1. Key Laboratory for Sustainable Utilization of Marine Fisheries Resources Ministry of Agriculture Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences
  2. College of Ocean and Earth Sciences Xiamen University
- Author bio：
- Funds：
  
  Supported by the National High Technology Research and Development Program of China (863 Program) (No. 2012AA10A409);LU Xia and LUAN Sheng contributed equally to this work.;An erratum to this article is available at;http://dx.doi.org/10.1007/s00343-017-7466-6;.
- DOI：10.1007/s00343-016-5250-7
  中图分类号：
- 网络首发：2015-12-28，
  
  纸质出版：2017
- Accepted：
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Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing[J]. 海洋湖沼学报（英文）, 2017,35(1):203-214.

Lu, X., Luan, S., Kong, J. et al. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing., Chin. J. Ocean. Limnol. 35, 203–214 (2017). https://doi.org/10.1007/s00343-016-5250-7
Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing[J]. 海洋湖沼学报（英文）, 2017,35(1):203-214. DOI： 10.1007/s00343-016-5250-7.

Lu, X., Luan, S., Kong, J. et al. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing., Chin. J. Ocean. Limnol. 35, 203–214 (2017). https://doi.org/10.1007/s00343-016-5250-7 DOI：

摘要

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.

关键词

Keywords

references

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