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Development and Validation of Single Nucleotide Polymorphism (SNP) Markers from an Expressed Sequence Tag (EST) Database in Olive Flounder (Paralichthys olivaceus)

김현철|박종원|이정호|이영미|노재구|박철지|김경길|김정은
한국발생생물학회 (The Korea Society Of Developmental Biology)|2014.12|발생과 생식 (DEVELOPMENT & REPRODUCTION)|제18권 제4호|pp. 275-286

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참고문헌

키워드

Single nucleotide polymorphisms (SNPs)Olive flounderParalichthys olivaceusExpressed sequence tag (EST)Heterozygosity
주제분류생물학

초록

To successful molecular breeding, identification and functional characterization of breeding related genes anddevelopment of molecular breeding techniques using DNA markers are essential. Although the development of a usefulmarker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breedingand developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely usedfor genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. Weidentified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of atotal 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region,and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was notdetected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29,respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supportsthat developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study canbe basic data for researches for immunity gene and characteristic with SNP.

Abstract

To successful molecular breeding, identification and functional characterization of breeding related genes anddevelopment of molecular breeding techniques using DNA markers are essential. Although the development of a usefulmarker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breedingand developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely usedfor genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. Weidentified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of atotal 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region,and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was notdetected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29,respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supportsthat developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study canbe basic data for researches for immunity gene and characteristic with SNP.

참고문헌 (25)

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Development of Polymorphic Microsatellite Markers Suitable for Genetic Linkage Mapping of Olive Flounder Paralichthys olivaceus공희정, 김영옥, 김우진, 남보혜, 신은하, 안철민, 정형택한국수산과학회 · Fisheries and Aquatic Sciences2013 · 제16권 제4호Expressed Sequence Tag Analysis of Olive Flounder (Paralichthys olivaceus): Genes and Expression Profile from the Liver김경길, 김규원, 김영옥, 김우진, 박두원, 박중연, 이정호한국수산과학회 · Fisheries and Aquatic Sciences2003 · 제6권 제3호An EST-based approach for identifying genes expressed in the gills of olive flounder Paralichthys olivaceus김경길, 김영옥, 김우진, 김종현, 김현철, 노재구, 명정인, 민병화, 박철지, 이정호수산생명의학회 · 한국어병학회지2009 · 제22권 제3호황금색 넙치(Paralichthys olivaceus)의 발현을 예측할 수 있는 Microsatellite Marker 개발곽주리, 김민성, 김태환, 박지빈, 서종표, 이우재, 조현경, 한재용한국수산과학회 · 한국수산과학회지2020 · 제53권 제4호EST-based Identification of Genes Expressed in the Brain of the Olive Flounder Paralichthys olivaceus김경길, 김영옥, 김우진, 김종현, 김현철, 노재구, 명정인, 민병화, 박철지, 이정호한국수산과학회 · Fisheries and Aquatic Sciences2009 · 제12권 제4호Molecular Characterization of the Ocular EST Clones from the Olive Flounder, Paralichthys olivaceus김경길, 김영옥, 김우진, 김종현, 김현철, 노재구, 명정인, 민병화, 박종원, 박철지, 이정호, 하수진한국발생생물학회 · 발생과 생식2010 · 제14권 제2호

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