Genome-wide mining, characterization, and development of microsatellite markers in <i>Marsupenaeus japonicus</i> by genome survey sequencing -- Journal of Oceanology and Limnology,2017,35(1):203-214

	Cite this paper:
	LU Xia, LUAN Sheng, KONG Jie, HU Longyang, MAO Yong, ZHONG Shengping. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing[J]. Journal of Oceanology and Limnology, 2017, 35(1): 203-214

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

LU Xia¹, LUAN Sheng¹, KONG Jie¹, HU Longyang¹, MAO Yong², ZHONG Shengping²

1 Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
2 College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China

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.

Key words: Marsupenaeus japonicus|genome-wide SSR markers|genome survey sequencing|functional annotation

Received: 2015-10-08 Revised: 2015-11-04

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Articles by LUAN Sheng

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