Development and characterization of EST-cSNP markers in Miichthys miiuy
To promote molecular-assisted breeding in Miichthys miiuy, a normalized full-length cDNA library was established to develop the EST-cSNP markers using the double-specific nuclease normalization method combined with switching mechanism at 5 end of RNA transcript technique. The results showed that a t...
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| Format: | Article |
| Language: | English |
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Zhejiang University Press
2011-05-01
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| Series: | 浙江大学学报. 农业与生命科学版 |
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| Online Access: | https://www.academax.com/doi/10.3785/j.issn.1008-9209.2011.03.007 |
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| author | XU Tian-jun SUN Yue-na SHI Ge WANG Ri-xin |
| author_facet | XU Tian-jun SUN Yue-na SHI Ge WANG Ri-xin |
| author_sort | XU Tian-jun |
| collection | DOAJ |
| description | To promote molecular-assisted breeding in Miichthys miiuy, a normalized full-length cDNA library was established to develop the EST-cSNP markers using the double-specific nuclease normalization method combined with switching mechanism at 5 end of RNA transcript technique. The results showed that a total of 5 053 expressed sequence tags (EST) were obtained, 4 609 high quality EST sequences in which were generated. For mining single nucleotide polymorphism (SNP) from EST sequences, 707 contig sequences were assembled by Vector NTI 11.0 software. A total of 209 putative and reliable SNPs were detected in all contigs. The appearance frequency of SNPs was 0.743 SNP per 100 bp in the obtained SNP sequences. Among these SNPs, 114 of which were transition, 74 were transversion and the other 21 were indels. The overall ratio of transition to transversion was 1.54. Gene annotation indicated that some SNP-containing genes belonged to immune-related genes that encoded major histocompatibility complex, immunoglobulin, T-cell receptor and other protease, respectively, showing that the identified SNPs were useful for studying molecular genetics and molecular-assisted breeding in M. miiuy. |
| format | Article |
| id | doaj-art-3e9cc77af0e841088394ce4afd14b8d4 |
| institution | Kabale University |
| issn | 1008-9209 2097-5155 |
| language | English |
| publishDate | 2011-05-01 |
| publisher | Zhejiang University Press |
| record_format | Article |
| series | 浙江大学学报. 农业与生命科学版 |
| spelling | doaj-art-3e9cc77af0e841088394ce4afd14b8d42025-08-20T03:58:14ZengZhejiang University Press浙江大学学报. 农业与生命科学版1008-92092097-51552011-05-013728028810.3785/j.issn.1008-9209.2011.03.00710089209Development and characterization of EST-cSNP markers in Miichthys miiuyXU Tian-junSUN Yue-naSHI GeWANG Ri-xinTo promote molecular-assisted breeding in Miichthys miiuy, a normalized full-length cDNA library was established to develop the EST-cSNP markers using the double-specific nuclease normalization method combined with switching mechanism at 5 end of RNA transcript technique. The results showed that a total of 5 053 expressed sequence tags (EST) were obtained, 4 609 high quality EST sequences in which were generated. For mining single nucleotide polymorphism (SNP) from EST sequences, 707 contig sequences were assembled by Vector NTI 11.0 software. A total of 209 putative and reliable SNPs were detected in all contigs. The appearance frequency of SNPs was 0.743 SNP per 100 bp in the obtained SNP sequences. Among these SNPs, 114 of which were transition, 74 were transversion and the other 21 were indels. The overall ratio of transition to transversion was 1.54. Gene annotation indicated that some SNP-containing genes belonged to immune-related genes that encoded major histocompatibility complex, immunoglobulin, T-cell receptor and other protease, respectively, showing that the identified SNPs were useful for studying molecular genetics and molecular-assisted breeding in M. miiuy.https://www.academax.com/doi/10.3785/j.issn.1008-9209.2011.03.007<italic>Miichthys miiuy</italic>expressed sequence tags (EST)single nucleotide polymorphism (SNP) |
| spellingShingle | XU Tian-jun SUN Yue-na SHI Ge WANG Ri-xin Development and characterization of EST-cSNP markers in Miichthys miiuy 浙江大学学报. 农业与生命科学版 <italic>Miichthys miiuy</italic> expressed sequence tags (EST) single nucleotide polymorphism (SNP) |
| title | Development and characterization of EST-cSNP markers in Miichthys miiuy |
| title_full | Development and characterization of EST-cSNP markers in Miichthys miiuy |
| title_fullStr | Development and characterization of EST-cSNP markers in Miichthys miiuy |
| title_full_unstemmed | Development and characterization of EST-cSNP markers in Miichthys miiuy |
| title_short | Development and characterization of EST-cSNP markers in Miichthys miiuy |
| title_sort | development and characterization of est csnp markers in miichthys miiuy |
| topic | <italic>Miichthys miiuy</italic> expressed sequence tags (EST) single nucleotide polymorphism (SNP) |
| url | https://www.academax.com/doi/10.3785/j.issn.1008-9209.2011.03.007 |
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