Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers
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摘要
Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye(Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed( H o) and expected( H e) heterozygosity ranged from 0.152 to 0.839(mean=0.464) and from 0.235 to 0.821(mean=0.618), respectively. The polymorphism information content(PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.
Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye(Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed( H o) and expected( H e) heterozygosity ranged from 0.152 to 0.839(mean=0.464) and from 0.235 to 0.821(mean=0.618), respectively. The polymorphism information content(PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.
Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye(Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed( H o) and expected( H e) heterozygosity ranged from 0.152 to 0.839(mean=0.464) and from 0.235 to 0.821(mean=0.618), respectively. The polymorphism information content(PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.
引文
Aglieri G,Papetti C,Zane L,Milisenda G,Boero F,Piraino S.2014.First evidence of inbreeding,relatedness and chaotic genetic patchiness in the holoplanktonic jellyfi sh Pelagia noctiluca(Scyphozoa,Cnidaria).PLo S One,9(6):e99647,http://dx.doi.org/10.1371/journal.pone.0099647.
Borrell Y J,Alvarez J,Blanco G et al.2011.A parentage study using microsatellite loci in a pilot project for aquaculture of the European anchovy Engraulis encrasicolus L.Aquaculture,310(3-4):305-311,http://dx.doi.org/10.1016/j.aquaculture.2010.10.025.
Botstein D,White R L,Skolnick M,Davis R W.1980.Construction of a genetic linkage map in man using restriction fragment length polymorphisms.American Journal of Human Genetics,32(3):314-331.
Callen D F,Thompson A D,Shen Y,Phillips H A,Richards RI,Mulley J C,Sutherland G R.1993.Incidence and origin of“null”alleles in the(AC)n microsatellite markers.American Journal of Human Genetics,52(5):922-927.
Dawson M N,Jacobs D K.2001.Molecular evidence for cryptic species of Aurelia aurita(Cnidaria,Scyphozoa).Biological Bulletin,200(1):92-96.
Ding G W,Chen J K.1981.The life history of Rhopilema esculenta Kishinouye.Journal of Fisheries of China,5(2):93-102.(in Chinese with English abstract)
Eichmann C,Berger B,Steinlechner M,Parson W.2005.Estimating the probability of identity in a random dog population using 15 highly polymorphic canine STRmarkers.Forensic Science International,151(1):37-44,http://dx.doi.org/10.1016/j.forsciint.2004.07.002.
Hong H X.2002.Medusa and jellyfi sh.Bulletin of Biology,37(2):13-16.(in Chinese with English abstract)
Hulak M,Kaspar V,Kohlmann K,Coward K,Te?itel J,Rodina M,Gela D,Kocour M,Linhart O.2010.Microsatellitebased genetic diversity and diff erentiation of foreign common carp(Cyprinus carpio)strains farmed in the Czech Republic.Aquaculture,298(3-4):194-201,http://dx.doi.org/10.1016/j.aquaculture.2009.10.021.
Kalinowski S T,Taper M L,Marshall T C.2007.Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.Molecular Ecology,16(5):1 099-1 106,http://dx.doi.org/10.1111/j.1365-294X.2007.03089.x.
Liang W B,Jiang L X,Yu S L.2007.The review and developmental strategies on the enhancement and releasement of jellyfi sh in off shore fi shing areas in Liaoning province.Fisheries Science,26(7):423-424.(in Chinese with English abstract)
Lu N,Jiang S,Chen J K.1997.Eff ect of temperature,salinity and light on the podocyst generation of Rhopilema esculenta Kishinouye.Fisheries Science,16(1):3-8.(in Chinese with English abstract)
Ma D Y,Hu H L,Kong J.2005.Inbreeding and its impact on aquaculture.Journal of Fisheries of China,29(6):849-856.(in Chinese with English abstract)
Moss D R,Arce S M,Otoshi C A,Doyle R W,Moss S M.2007.Eff ects of inbreeding on survival and growth of Pacifi c white shrimp Penaeus(Litopenaeus)vannamei.Aquaculture,272(S1):S30-S37,http://dx.doi.org/10.1016/j.aquaculture.2007.08.014.
Omori M,Nakano E.2001.Jellyfi sh fi sheries in southeast Asia.Hydrobiologia,451(1-3):19-26,http://dx.doi.org/10.1023/A:1011879821323.
Qiao H J,Liu X Q,Zhang X J,Jiang H B,Wang J Y,Zhang LM.2013.Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis.Chinese Journal of Oceanology and Limnology,31(2):391-397,http://dx.doi.org/http://dx.doi.org/10.1007/s00343-013-2158-3.
Rousset F.2008.GENEPOP’007:a complete reimplementation of the GENEPOP software for Windows and Linux.Molecular Ecology Resources,8(1):103-106,http://dx.doi.org/10.1111/j.1471-8286.2007.01931.x.
Ruan X H,Wang W J,Kong J,Yu F,Huang X Q.2010.Genetic linkage mapping of turbot(Scophthalmus maximus L.)using microsatellite markers and its application in QTLanalysis.Aquaculture,308(3-4):89-100,http://dx.doi.org/10.1016/j.aquaculture.2010.08.010.
Sekino M,Saitoh K,Yamada T,Kumagai A,Hara M,Yamashita Y.2003.Microsatellite-based pedigree tracing in a Japanese fl ounder Paralichthys olivaceus hatchery strain:implications for hatchery management related to stock enhancement program.Aquaculture,221(1-4):255-263,http://dx.doi.org/10.1016/S0044-8486(02)00667-1.
Sun G H,Liu X Q,Yang J M,Zhang X J,Liu A Y,Tan F Y.2010.Genetic diversity of ITS sequences in farmed and natural Rhopilema esculentum populations.Marine Sciences,34(10):90-95.(in Chinese with English abstract)
Waits L P,Luikart G,Taberlet P.2001.Estimating the probability of identity among genotypes in natural populations:cautions and guidelines.Molecular Ecology,10(1):249-256,http://dx.doi.org/10.1046/j.1365-294X.2001.01185.x.
Wang G S,Yu Z G,Mi T Z,Yao Q Z,Zhen Y,Chen S Q,Wang J Y.2014b.The research progress of environmental factors on the growth and development in Rhopilema esculenta.Marine Sciences,38(1):85-90.(in Chinese with English abstract)
Wang W J,Zhang K,Luo K,Xiao G X,Song W P,Kong J,Jin X S.2014a.Assessment of recapture rates after hatchery release of Chinese shrimp Fenneropenaeus chinensis in Jiaozhou Bay and Bohai Bay in 2012 using pedigree tracing based on SSR markers.Fisheries Science,80(4):749-755,http://dx.doi.org/10.1007/s12562-014-0743-9.
You K,Chi X P,Ma C H,Liu X T,Mu Y C,Han Z Q,Gao Z X,Ding M L,Luo C Y.2012.The analysis of jellyfi sh industry development in China.Chinese Fisheries Economics,30(5):108-112.(in Chinese with English abstract)
You K,Ma C H,Wang S J,Gao T X,Li J X,Wang X W.2010.Eff ects of aeration and feeding on podocyst germination of jellyfi sh,Rhopolema esculentum Kishinouye.Journal of Fishery Sciences of China,17(6):1 352-1 357.(in Chinese with English abstract)
Yu D H,Chu K H.2006.Genetic variation in wild and cultured populations of the pearl oyster Pinctada fucata from southern China.Aquaculture,258(1-4):220-227,http://dx.doi.org/10.1016/j.aquaculture.2006.03.024.
Zhang J H.2013.The enhancement eff ect evaluation of jellyfi sh in southern Shandong peninsula.Yantai University,Yantai.63p.(in Chinese with English abstract)
Zhao B,Zhang X M,Chen S Q,Cheng Y X,Zhang Y.2006.Eff ect of diff erent environmental factors on early development of jellyfi sh,Rhopilema esculenta.Marine Fisheries Research,27(1):87-92.(in Chinese with English abstract)
Zhu L,Yang A A,Zhou C Y,Yang H,Luo X R,Chen S Q,Zhuang Z M.2015.Characterization of 15 polymorphic microsatellite loci for the jellyfi sh Rhopilema esculentum.Conservation Genetics Resources,7(2):551-556,http://dx.doi.org/10.1007/s12686-015-0422-x.
Borrell Y J,Alvarez J,Blanco G et al.2011.A parentage study using microsatellite loci in a pilot project for aquaculture of the European anchovy Engraulis encrasicolus L.Aquaculture,310(3-4):305-311,http://dx.doi.org/10.1016/j.aquaculture.2010.10.025.
Botstein D,White R L,Skolnick M,Davis R W.1980.Construction of a genetic linkage map in man using restriction fragment length polymorphisms.American Journal of Human Genetics,32(3):314-331.
Callen D F,Thompson A D,Shen Y,Phillips H A,Richards RI,Mulley J C,Sutherland G R.1993.Incidence and origin of“null”alleles in the(AC)n microsatellite markers.American Journal of Human Genetics,52(5):922-927.
Dawson M N,Jacobs D K.2001.Molecular evidence for cryptic species of Aurelia aurita(Cnidaria,Scyphozoa).Biological Bulletin,200(1):92-96.
Ding G W,Chen J K.1981.The life history of Rhopilema esculenta Kishinouye.Journal of Fisheries of China,5(2):93-102.(in Chinese with English abstract)
Eichmann C,Berger B,Steinlechner M,Parson W.2005.Estimating the probability of identity in a random dog population using 15 highly polymorphic canine STRmarkers.Forensic Science International,151(1):37-44,http://dx.doi.org/10.1016/j.forsciint.2004.07.002.
Hong H X.2002.Medusa and jellyfi sh.Bulletin of Biology,37(2):13-16.(in Chinese with English abstract)
Hulak M,Kaspar V,Kohlmann K,Coward K,Te?itel J,Rodina M,Gela D,Kocour M,Linhart O.2010.Microsatellitebased genetic diversity and diff erentiation of foreign common carp(Cyprinus carpio)strains farmed in the Czech Republic.Aquaculture,298(3-4):194-201,http://dx.doi.org/10.1016/j.aquaculture.2009.10.021.
Kalinowski S T,Taper M L,Marshall T C.2007.Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.Molecular Ecology,16(5):1 099-1 106,http://dx.doi.org/10.1111/j.1365-294X.2007.03089.x.
Liang W B,Jiang L X,Yu S L.2007.The review and developmental strategies on the enhancement and releasement of jellyfi sh in off shore fi shing areas in Liaoning province.Fisheries Science,26(7):423-424.(in Chinese with English abstract)
Lu N,Jiang S,Chen J K.1997.Eff ect of temperature,salinity and light on the podocyst generation of Rhopilema esculenta Kishinouye.Fisheries Science,16(1):3-8.(in Chinese with English abstract)
Ma D Y,Hu H L,Kong J.2005.Inbreeding and its impact on aquaculture.Journal of Fisheries of China,29(6):849-856.(in Chinese with English abstract)
Moss D R,Arce S M,Otoshi C A,Doyle R W,Moss S M.2007.Eff ects of inbreeding on survival and growth of Pacifi c white shrimp Penaeus(Litopenaeus)vannamei.Aquaculture,272(S1):S30-S37,http://dx.doi.org/10.1016/j.aquaculture.2007.08.014.
Omori M,Nakano E.2001.Jellyfi sh fi sheries in southeast Asia.Hydrobiologia,451(1-3):19-26,http://dx.doi.org/10.1023/A:1011879821323.
Qiao H J,Liu X Q,Zhang X J,Jiang H B,Wang J Y,Zhang LM.2013.Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis.Chinese Journal of Oceanology and Limnology,31(2):391-397,http://dx.doi.org/http://dx.doi.org/10.1007/s00343-013-2158-3.
Rousset F.2008.GENEPOP’007:a complete reimplementation of the GENEPOP software for Windows and Linux.Molecular Ecology Resources,8(1):103-106,http://dx.doi.org/10.1111/j.1471-8286.2007.01931.x.
Ruan X H,Wang W J,Kong J,Yu F,Huang X Q.2010.Genetic linkage mapping of turbot(Scophthalmus maximus L.)using microsatellite markers and its application in QTLanalysis.Aquaculture,308(3-4):89-100,http://dx.doi.org/10.1016/j.aquaculture.2010.08.010.
Sekino M,Saitoh K,Yamada T,Kumagai A,Hara M,Yamashita Y.2003.Microsatellite-based pedigree tracing in a Japanese fl ounder Paralichthys olivaceus hatchery strain:implications for hatchery management related to stock enhancement program.Aquaculture,221(1-4):255-263,http://dx.doi.org/10.1016/S0044-8486(02)00667-1.
Sun G H,Liu X Q,Yang J M,Zhang X J,Liu A Y,Tan F Y.2010.Genetic diversity of ITS sequences in farmed and natural Rhopilema esculentum populations.Marine Sciences,34(10):90-95.(in Chinese with English abstract)
Waits L P,Luikart G,Taberlet P.2001.Estimating the probability of identity among genotypes in natural populations:cautions and guidelines.Molecular Ecology,10(1):249-256,http://dx.doi.org/10.1046/j.1365-294X.2001.01185.x.
Wang G S,Yu Z G,Mi T Z,Yao Q Z,Zhen Y,Chen S Q,Wang J Y.2014b.The research progress of environmental factors on the growth and development in Rhopilema esculenta.Marine Sciences,38(1):85-90.(in Chinese with English abstract)
Wang W J,Zhang K,Luo K,Xiao G X,Song W P,Kong J,Jin X S.2014a.Assessment of recapture rates after hatchery release of Chinese shrimp Fenneropenaeus chinensis in Jiaozhou Bay and Bohai Bay in 2012 using pedigree tracing based on SSR markers.Fisheries Science,80(4):749-755,http://dx.doi.org/10.1007/s12562-014-0743-9.
You K,Chi X P,Ma C H,Liu X T,Mu Y C,Han Z Q,Gao Z X,Ding M L,Luo C Y.2012.The analysis of jellyfi sh industry development in China.Chinese Fisheries Economics,30(5):108-112.(in Chinese with English abstract)
You K,Ma C H,Wang S J,Gao T X,Li J X,Wang X W.2010.Eff ects of aeration and feeding on podocyst germination of jellyfi sh,Rhopolema esculentum Kishinouye.Journal of Fishery Sciences of China,17(6):1 352-1 357.(in Chinese with English abstract)
Yu D H,Chu K H.2006.Genetic variation in wild and cultured populations of the pearl oyster Pinctada fucata from southern China.Aquaculture,258(1-4):220-227,http://dx.doi.org/10.1016/j.aquaculture.2006.03.024.
Zhang J H.2013.The enhancement eff ect evaluation of jellyfi sh in southern Shandong peninsula.Yantai University,Yantai.63p.(in Chinese with English abstract)
Zhao B,Zhang X M,Chen S Q,Cheng Y X,Zhang Y.2006.Eff ect of diff erent environmental factors on early development of jellyfi sh,Rhopilema esculenta.Marine Fisheries Research,27(1):87-92.(in Chinese with English abstract)
Zhu L,Yang A A,Zhou C Y,Yang H,Luo X R,Chen S Q,Zhuang Z M.2015.Characterization of 15 polymorphic microsatellite loci for the jellyfi sh Rhopilema esculentum.Conservation Genetics Resources,7(2):551-556,http://dx.doi.org/10.1007/s12686-015-0422-x.