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Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish
Zhang, Jin1; Ma, Wenge1; Song, Xiaomin1; Lin, Qiaohong1; Gui, Jian-Fang1,2; Mei, Jie1
2014-10-01
Source PublicationMOLECULES
ISSN1420-3049
Volume19Issue:10Pages:16402-16415
AbstractYellow catfish (Pelteobagrus fulvidraco) is one of the most important freshwater fish due to its delicious flesh and high nutritional value. However, lack of sufficient simple sequence repeat (SSR) markers has hampered the progress of genetic selection breeding and molecular research for yellow catfish. To this end, we aimed to develop and characterize polymorphic expressed sequence tag (EST)-SSRs from the 454 pyrosequencing transcriptome of yellow catfish. Totally, 82,794 potential EST-SSR markers were identified and distributed in the coding and non-coding regions. Di-nucleotide (53,933) is the most abundant motif type, and AC/GT, AAT/ATT, AAAT/ATTT are respective the most frequent di-, tri-, tetra-nucleotide repeats. We designed primer pairs for all of the identified EST-SSRs and randomly selected 300 of these pairs for further validation. Finally, 263 primer pairs were successfully amplified and 57 primer pairs were found to be consistently polymorphic when four populations of 48 individuals were tested. The number of alleles for the 57 loci ranged from 2 to 17, with an average of 8.23. The observed heterozygosity (HO), expected heterozygosity (HE), polymorphism information content (PIC) and fixation index (FIS) values ranged from 0.04 to 1.00, 0.12 to 0.92, 0.12 to 0.91 and -0.83 to 0.93, respectively. These EST-SSR markers generated in this study could greatly facilitate future studies of genetic diversity and molecular breeding in yellow catfish.
SubtypeArticle
KeywordEst-ssrs Yellow Catfish 454 Pyrosequencing Genetic Diversity
DOI10.3390/molecules191016402
WOS HeadingsScience & Technology ; Physical Sciences
Indexed BySCI
Language英语
WOS Research AreaChemistry
WOS SubjectChemistry, Organic
WOS IDWOS:000344456100058
WOS KeywordLINKAGE MAP ; IDENTIFICATION ; LENGTH ; ISSR
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/20331
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Affiliation1.Huazhong Agr Univ, Freshwater Aquaculture Collaborat Innovat Ctr Hub, Coll Fisheries, Key Lab Freshwater Anim Breeding,Minist Agr, Wuhan 430070, Peoples R China
2.Univ Chinese Acad Sci, Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China
Recommended Citation
GB/T 7714
Zhang, Jin,Ma, Wenge,Song, Xiaomin,et al. Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish[J]. MOLECULES,2014,19(10):16402-16415.
APA Zhang, Jin,Ma, Wenge,Song, Xiaomin,Lin, Qiaohong,Gui, Jian-Fang,&Mei, Jie.(2014).Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish.MOLECULES,19(10),16402-16415.
MLA Zhang, Jin,et al."Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish".MOLECULES 19.10(2014):16402-16415.
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