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Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish
Yellow 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 catf...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6271634/ https://www.ncbi.nlm.nih.gov/pubmed/25314602 http://dx.doi.org/10.3390/molecules191016402 |
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author | Zhang, Jin Ma, Wenge Song, Xiaomin Lin, Qiaohong Gui, Jian-Fang Mei, Jie |
author_facet | Zhang, Jin Ma, Wenge Song, Xiaomin Lin, Qiaohong Gui, Jian-Fang Mei, Jie |
author_sort | Zhang, Jin |
collection | PubMed |
description | Yellow 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 (H(O)), expected heterozygosity (H(E)), 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. |
format | Online Article Text |
id | pubmed-6271634 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-62716342018-12-27 Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish Zhang, Jin Ma, Wenge Song, Xiaomin Lin, Qiaohong Gui, Jian-Fang Mei, Jie Molecules Article Yellow 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 (H(O)), expected heterozygosity (H(E)), 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. MDPI 2014-10-13 /pmc/articles/PMC6271634/ /pubmed/25314602 http://dx.doi.org/10.3390/molecules191016402 Text en © 2014 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zhang, Jin Ma, Wenge Song, Xiaomin Lin, Qiaohong Gui, Jian-Fang Mei, Jie Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish |
title | Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish |
title_full | Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish |
title_fullStr | Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish |
title_full_unstemmed | Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish |
title_short | Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish |
title_sort | characterization and development of est-ssr markers derived from transcriptome of yellow catfish |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6271634/ https://www.ncbi.nlm.nih.gov/pubmed/25314602 http://dx.doi.org/10.3390/molecules191016402 |
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