Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing
The large-scale loach, Paramisgurnus dabryanus , is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using speci...
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| Veröffentlicht in: | Conservation genetics resources 2022-06, Vol.14 (2), p.137-141 |
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| creator | Fu, Jianjun Wan, Shunpeng Zhu, Wenbin Wang, Lanmei Luo, Mingkun Zheng, Xianhu Dong, Zaijie |
| description | The large-scale loach,
Paramisgurnus dabryanus
, is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using specific-locus amplified fragment sequencing with eight
P. dabryanus
specimens. Thirty-six SLAF sequences were randomly selected for the verification of SNP loci with 32 fin clips of
P. dabryanus
, and 76 SNP loci were identified from 22 SLAF sequences. The minor allele frequency, observed heterozygosity, expected heterozygosity, and polymorphic information content of these SNP loci ranged from 0.047 to 0.500, 0.094 to 0.969, 0.091 to 0.510, and 0.085 to 0.411, respectively. Ten loci deviated significantly from the Hardy–Weinberg equilibrium (
P
< 0.05). The novel SNP loci identified and validated in this study will serve as valuable genomic resources for
P. dabryanus
. |
| doi_str_mv | 10.1007/s12686-021-01251-2 |
| format | Article |
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Paramisgurnus dabryanus
, is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using specific-locus amplified fragment sequencing with eight
P. dabryanus
specimens. Thirty-six SLAF sequences were randomly selected for the verification of SNP loci with 32 fin clips of
P. dabryanus
, and 76 SNP loci were identified from 22 SLAF sequences. The minor allele frequency, observed heterozygosity, expected heterozygosity, and polymorphic information content of these SNP loci ranged from 0.047 to 0.500, 0.094 to 0.969, 0.091 to 0.510, and 0.085 to 0.411, respectively. Ten loci deviated significantly from the Hardy–Weinberg equilibrium (
P
< 0.05). The novel SNP loci identified and validated in this study will serve as valuable genomic resources for
P. dabryanus
.</description><identifier>ISSN: 1877-7260</identifier><identifier>ISSN: 1877-7252</identifier><identifier>EISSN: 1877-7260</identifier><identifier>DOI: 10.1007/s12686-021-01251-2</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Genetics and Genomics ; Biodiversity ; Biomedical and Life Sciences ; Commercial fishing ; Conservation Biology/Ecology ; Ecology ; Enzymes ; Evolutionary Biology ; Farms ; Fishery sciences ; Gene frequency ; Genetic diversity ; Genetic testing ; Heterozygosity ; Laboratories ; Life Sciences ; Paramisgurnus dabryanus ; Plant Genetics and Genomics ; Single-nucleotide polymorphism ; Technical Note ; Thermal cycling</subject><ispartof>Conservation genetics resources, 2022-06, Vol.14 (2), p.137-141</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c270t-f287985eb23c60072929269528618e1308f2eb217359ff86226dea27fdef22653</cites><orcidid>0000-0001-5428-1053</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12686-021-01251-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12686-021-01251-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids></links><search><creatorcontrib>Fu, Jianjun</creatorcontrib><creatorcontrib>Wan, Shunpeng</creatorcontrib><creatorcontrib>Zhu, Wenbin</creatorcontrib><creatorcontrib>Wang, Lanmei</creatorcontrib><creatorcontrib>Luo, Mingkun</creatorcontrib><creatorcontrib>Zheng, Xianhu</creatorcontrib><creatorcontrib>Dong, Zaijie</creatorcontrib><title>Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing</title><title>Conservation genetics resources</title><addtitle>Conservation Genet Resour</addtitle><description>The large-scale loach,
Paramisgurnus dabryanus
, is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using specific-locus amplified fragment sequencing with eight
P. dabryanus
specimens. Thirty-six SLAF sequences were randomly selected for the verification of SNP loci with 32 fin clips of
P. dabryanus
, and 76 SNP loci were identified from 22 SLAF sequences. The minor allele frequency, observed heterozygosity, expected heterozygosity, and polymorphic information content of these SNP loci ranged from 0.047 to 0.500, 0.094 to 0.969, 0.091 to 0.510, and 0.085 to 0.411, respectively. Ten loci deviated significantly from the Hardy–Weinberg equilibrium (
P
< 0.05). The novel SNP loci identified and validated in this study will serve as valuable genomic resources for
P. dabryanus
.</description><subject>Animal Genetics and Genomics</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Commercial fishing</subject><subject>Conservation Biology/Ecology</subject><subject>Ecology</subject><subject>Enzymes</subject><subject>Evolutionary Biology</subject><subject>Farms</subject><subject>Fishery sciences</subject><subject>Gene frequency</subject><subject>Genetic diversity</subject><subject>Genetic testing</subject><subject>Heterozygosity</subject><subject>Laboratories</subject><subject>Life Sciences</subject><subject>Paramisgurnus dabryanus</subject><subject>Plant Genetics and Genomics</subject><subject>Single-nucleotide polymorphism</subject><subject>Technical Note</subject><subject>Thermal cycling</subject><issn>1877-7260</issn><issn>1877-7252</issn><issn>1877-7260</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9UMFOAyEUJEYTa_UHPJF40QMKb11gj01jtUmjTapnQlnYbm3ZCruHevPPRddET4YD82Bm3nuD0Dmj14xScRMZcMkJBUYog5wROEADJoUgAjg9_IOP0UmMa0q5zAAG6GNaWt_Wrja6rRuPtS-xWemgTWtD_d4_Ng4LjhePc7zV4dWGiGuP25XFGx0qS6LRm4QbbVb4cp602zpWXfBdxKVehr1O6Aov97iLta_wYjaa4GjfOutNqk_RkdObaM9-7iF6mdw9jx_I7Ol-Oh7NiAFBW-JAikLmdgmZ4WllKNLhRQ6SM2lZRqWD9MlElhfOSQ7AS6tBuNK6hPNsiC56311oUu_YqnWThkwtFXABtwXLeJFY0LNMaGIM1qldqNPWe8Wo-opa9VGrFLX6jlpBEmW9KCayr2z4tf5H9QmKboDc</recordid><startdate>20220601</startdate><enddate>20220601</enddate><creator>Fu, Jianjun</creator><creator>Wan, Shunpeng</creator><creator>Zhu, Wenbin</creator><creator>Wang, Lanmei</creator><creator>Luo, Mingkun</creator><creator>Zheng, Xianhu</creator><creator>Dong, Zaijie</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FE</scope><scope>8FH</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><orcidid>https://orcid.org/0000-0001-5428-1053</orcidid></search><sort><creationdate>20220601</creationdate><title>Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing</title><author>Fu, Jianjun ; Wan, Shunpeng ; Zhu, Wenbin ; Wang, Lanmei ; Luo, Mingkun ; Zheng, Xianhu ; Dong, Zaijie</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c270t-f287985eb23c60072929269528618e1308f2eb217359ff86226dea27fdef22653</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biodiversity</topic><topic>Biomedical and Life Sciences</topic><topic>Commercial fishing</topic><topic>Conservation Biology/Ecology</topic><topic>Ecology</topic><topic>Enzymes</topic><topic>Evolutionary Biology</topic><topic>Farms</topic><topic>Fishery sciences</topic><topic>Gene frequency</topic><topic>Genetic diversity</topic><topic>Genetic testing</topic><topic>Heterozygosity</topic><topic>Laboratories</topic><topic>Life Sciences</topic><topic>Paramisgurnus dabryanus</topic><topic>Plant Genetics and Genomics</topic><topic>Single-nucleotide polymorphism</topic><topic>Technical Note</topic><topic>Thermal cycling</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fu, Jianjun</creatorcontrib><creatorcontrib>Wan, Shunpeng</creatorcontrib><creatorcontrib>Zhu, Wenbin</creatorcontrib><creatorcontrib>Wang, Lanmei</creatorcontrib><creatorcontrib>Luo, Mingkun</creatorcontrib><creatorcontrib>Zheng, Xianhu</creatorcontrib><creatorcontrib>Dong, Zaijie</creatorcontrib><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><jtitle>Conservation genetics resources</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fu, Jianjun</au><au>Wan, Shunpeng</au><au>Zhu, Wenbin</au><au>Wang, Lanmei</au><au>Luo, Mingkun</au><au>Zheng, Xianhu</au><au>Dong, Zaijie</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing</atitle><jtitle>Conservation genetics resources</jtitle><stitle>Conservation Genet Resour</stitle><date>2022-06-01</date><risdate>2022</risdate><volume>14</volume><issue>2</issue><spage>137</spage><epage>141</epage><pages>137-141</pages><issn>1877-7260</issn><issn>1877-7252</issn><eissn>1877-7260</eissn><abstract>The large-scale loach,
Paramisgurnus dabryanus
, is a commercially important fish species in East Asia. However, little is known about the genetics of this species. In this study, a total of 715,539 putative single nucleotide polymorphism (SNP) loci from 157,274 sequences were identified using specific-locus amplified fragment sequencing with eight
P. dabryanus
specimens. Thirty-six SLAF sequences were randomly selected for the verification of SNP loci with 32 fin clips of
P. dabryanus
, and 76 SNP loci were identified from 22 SLAF sequences. The minor allele frequency, observed heterozygosity, expected heterozygosity, and polymorphic information content of these SNP loci ranged from 0.047 to 0.500, 0.094 to 0.969, 0.091 to 0.510, and 0.085 to 0.411, respectively. Ten loci deviated significantly from the Hardy–Weinberg equilibrium (
P
< 0.05). The novel SNP loci identified and validated in this study will serve as valuable genomic resources for
P. dabryanus
.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s12686-021-01251-2</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0001-5428-1053</orcidid></addata></record> |
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| subjects | Animal Genetics and Genomics Biodiversity Biomedical and Life Sciences Commercial fishing Conservation Biology/Ecology Ecology Enzymes Evolutionary Biology Farms Fishery sciences Gene frequency Genetic diversity Genetic testing Heterozygosity Laboratories Life Sciences Paramisgurnus dabryanus Plant Genetics and Genomics Single-nucleotide polymorphism Technical Note Thermal cycling |
| title | Identification and characterization of 76 SNP markers in the large-scale loach (Paramisgurnus dabryanus) by using SLAF sequencing |
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