First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree
Platonia insignis is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic ma...
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| Veröffentlicht in: | Molecular biology reports 2020-04, Vol.47 (4), p.2985-2989 |
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| description | Platonia insignis
is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic markers such as microsatellite are the most suitable, but they need to be developed for this species. Thus, the aim of this work was to develop and validate microsatellite markers for
P. insignis
. We used Roche 454 GS FLX sequencing platform of a single
P. insignis
genotype and 1702 microsatellite sequences were identified. Based on some pre-requisites, we could develop 50 primer pairs to be tested. Twenty-two primer pairs successfully amplified fragments and they were tested in 31 genotypes of
P. insignis
that belong to a germplasm bank and were sampled in the northeast of Pará State, Brazil. Thirteen primers were polymorphic and the number of alleles per loci varied from 5 (PI18 and PI27) to 2 (PI08, PI25, PI31, PI33 and PI 37). Expected heterozygosity (H
E
) varied from 0.74 (PI27) to 0.12 (PI31) and observed heterozygosity (H
O
) varied from 1.00 (PI25) to 0.00 (PI08, PI31, PI33 and PI37). Principal coordinates could separate the genotypes of
P. insignis
in clusters and we can conclude that the primers can estimate the genetic diversity of
P. insignis
populations. |
| doi_str_mv | 10.1007/s11033-020-05301-0 |
| format | Article |
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is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic markers such as microsatellite are the most suitable, but they need to be developed for this species. Thus, the aim of this work was to develop and validate microsatellite markers for
P. insignis
. We used Roche 454 GS FLX sequencing platform of a single
P. insignis
genotype and 1702 microsatellite sequences were identified. Based on some pre-requisites, we could develop 50 primer pairs to be tested. Twenty-two primer pairs successfully amplified fragments and they were tested in 31 genotypes of
P. insignis
that belong to a germplasm bank and were sampled in the northeast of Pará State, Brazil. Thirteen primers were polymorphic and the number of alleles per loci varied from 5 (PI18 and PI27) to 2 (PI08, PI25, PI31, PI33 and PI 37). Expected heterozygosity (H
E
) varied from 0.74 (PI27) to 0.12 (PI31) and observed heterozygosity (H
O
) varied from 1.00 (PI25) to 0.00 (PI08, PI31, PI33 and PI37). Principal coordinates could separate the genotypes of
P. insignis
in clusters and we can conclude that the primers can estimate the genetic diversity of
P. insignis
populations.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-020-05301-0</identifier><identifier>PMID: 32034625</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Alleles ; Animal Anatomy ; Animal Biochemistry ; Asexual reproduction ; Asexuality ; Biomedical and Life Sciences ; Brazil ; Clusiaceae - genetics ; DNA Primers - genetics ; DNA, Plant - genetics ; Fruit - genetics ; Fruits ; Genetic diversity ; Genetic markers ; Genomics - methods ; Genotype ; Genotypes ; Germplasm ; Heterozygosity ; High-Throughput Nucleotide Sequencing - methods ; Histology ; Life Sciences ; Microsatellite Repeats - genetics ; Microsatellites ; Molecular biology ; Morphology ; Platonia ; Polymorphism ; Polymorphism, Genetic - genetics ; Short Communication ; Trees - genetics</subject><ispartof>Molecular biology reports, 2020-04, Vol.47 (4), p.2985-2989</ispartof><rights>Springer Nature B.V. 2020</rights><rights>Springer Nature B.V. 2020.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c419t-10175016d22add3dead4a2612e12b6ff6d1c7ab6014aac637ffb2cdb96ed523</citedby><cites>FETCH-LOGICAL-c419t-10175016d22add3dead4a2612e12b6ff6d1c7ab6014aac637ffb2cdb96ed523</cites><orcidid>0000-0003-3470-405X</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/s11033-020-05301-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-020-05301-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32034625$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Paraense, Luany Caroline Ribeiro</creatorcontrib><creatorcontrib>Pena, Dayane Nascimento</creatorcontrib><creatorcontrib>Darnet, Sylvain Henri</creatorcontrib><creatorcontrib>de Miranda Rodrigues, Simone</creatorcontrib><creatorcontrib>de Menezes, Ilmarina Campos</creatorcontrib><creatorcontrib>Moura, Elisa Ferreira</creatorcontrib><title>First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Platonia insignis
is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic markers such as microsatellite are the most suitable, but they need to be developed for this species. Thus, the aim of this work was to develop and validate microsatellite markers for
P. insignis
. We used Roche 454 GS FLX sequencing platform of a single
P. insignis
genotype and 1702 microsatellite sequences were identified. Based on some pre-requisites, we could develop 50 primer pairs to be tested. Twenty-two primer pairs successfully amplified fragments and they were tested in 31 genotypes of
P. insignis
that belong to a germplasm bank and were sampled in the northeast of Pará State, Brazil. Thirteen primers were polymorphic and the number of alleles per loci varied from 5 (PI18 and PI27) to 2 (PI08, PI25, PI31, PI33 and PI 37). Expected heterozygosity (H
E
) varied from 0.74 (PI27) to 0.12 (PI31) and observed heterozygosity (H
O
) varied from 1.00 (PI25) to 0.00 (PI08, PI31, PI33 and PI37). Principal coordinates could separate the genotypes of
P. insignis
in clusters and we can conclude that the primers can estimate the genetic diversity of
P. insignis
populations.</description><subject>Alleles</subject><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Asexual reproduction</subject><subject>Asexuality</subject><subject>Biomedical and Life Sciences</subject><subject>Brazil</subject><subject>Clusiaceae - genetics</subject><subject>DNA Primers - genetics</subject><subject>DNA, Plant - genetics</subject><subject>Fruit - genetics</subject><subject>Fruits</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genomics - methods</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Germplasm</subject><subject>Heterozygosity</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Microsatellite Repeats - genetics</subject><subject>Microsatellites</subject><subject>Molecular biology</subject><subject>Morphology</subject><subject>Platonia</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic - genetics</subject><subject>Short Communication</subject><subject>Trees - genetics</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kU9r3DAQxUVoaDZpv0APRdBLCnU6-u89JkvTFgIJtHcxtsaLUq-9lexC8umjzSYt5NCDGJB-8zTzHmPvBJwJAPc5CwFKVSChAqNAVHDAFsI4Vemlq1-xBewudW3EETvO-RYAtHDmNTtSEpS20ixYvIwpT3xNw7iJLS8njRkn6vs4Ed9g-kUp80B_qB-3FHg3Jn7T4zQOEXkcclwPMfPTVT_niC0hffzEkV8kvI99xIF3aY4TnxLRG3bYYZ_p7VM9YT8uv_xcfauurr9-X51fVa0Wy6kSUEYEYYOUGIIKhEGjtEKSkI3tOhtE67CxIDRia5Xruka2oVlaCkaqE3a6V92m8fdMefKbmNuyDg40ztlLZaQ1ta5FQT-8QG_HOQ1lNi-Nc04bq-tCyT21MyYn6vw2xeLLnRfgdzH4fQy-xOAfY_BQmt4_Sc_NhsLflmffC6D2QC5Pw5rSv7__I_sA5pyTRA</recordid><startdate>20200401</startdate><enddate>20200401</enddate><creator>Paraense, Luany Caroline Ribeiro</creator><creator>Pena, Dayane Nascimento</creator><creator>Darnet, Sylvain Henri</creator><creator>de Miranda Rodrigues, Simone</creator><creator>de Menezes, Ilmarina Campos</creator><creator>Moura, Elisa Ferreira</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-3470-405X</orcidid></search><sort><creationdate>20200401</creationdate><title>First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree</title><author>Paraense, Luany Caroline Ribeiro ; Pena, Dayane Nascimento ; Darnet, Sylvain Henri ; de Miranda Rodrigues, Simone ; de Menezes, Ilmarina Campos ; Moura, Elisa Ferreira</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c419t-10175016d22add3dead4a2612e12b6ff6d1c7ab6014aac637ffb2cdb96ed523</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Alleles</topic><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Asexual reproduction</topic><topic>Asexuality</topic><topic>Biomedical and Life Sciences</topic><topic>Brazil</topic><topic>Clusiaceae - genetics</topic><topic>DNA Primers - genetics</topic><topic>DNA, Plant - genetics</topic><topic>Fruit - genetics</topic><topic>Fruits</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Genomics - methods</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Germplasm</topic><topic>Heterozygosity</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Histology</topic><topic>Life Sciences</topic><topic>Microsatellite Repeats - genetics</topic><topic>Microsatellites</topic><topic>Molecular biology</topic><topic>Morphology</topic><topic>Platonia</topic><topic>Polymorphism</topic><topic>Polymorphism, Genetic - genetics</topic><topic>Short Communication</topic><topic>Trees - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Paraense, Luany Caroline Ribeiro</creatorcontrib><creatorcontrib>Pena, Dayane Nascimento</creatorcontrib><creatorcontrib>Darnet, Sylvain Henri</creatorcontrib><creatorcontrib>de Miranda Rodrigues, Simone</creatorcontrib><creatorcontrib>de Menezes, Ilmarina Campos</creatorcontrib><creatorcontrib>Moura, Elisa Ferreira</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>ProQuest_Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Science Database (ProQuest)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</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><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Paraense, Luany Caroline Ribeiro</au><au>Pena, Dayane Nascimento</au><au>Darnet, Sylvain Henri</au><au>de Miranda Rodrigues, Simone</au><au>de Menezes, Ilmarina Campos</au><au>Moura, Elisa Ferreira</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>47</volume><issue>4</issue><spage>2985</spage><epage>2989</epage><pages>2985-2989</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Platonia insignis
is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic markers such as microsatellite are the most suitable, but they need to be developed for this species. Thus, the aim of this work was to develop and validate microsatellite markers for
P. insignis
. We used Roche 454 GS FLX sequencing platform of a single
P. insignis
genotype and 1702 microsatellite sequences were identified. Based on some pre-requisites, we could develop 50 primer pairs to be tested. Twenty-two primer pairs successfully amplified fragments and they were tested in 31 genotypes of
P. insignis
that belong to a germplasm bank and were sampled in the northeast of Pará State, Brazil. Thirteen primers were polymorphic and the number of alleles per loci varied from 5 (PI18 and PI27) to 2 (PI08, PI25, PI31, PI33 and PI 37). Expected heterozygosity (H
E
) varied from 0.74 (PI27) to 0.12 (PI31) and observed heterozygosity (H
O
) varied from 1.00 (PI25) to 0.00 (PI08, PI31, PI33 and PI37). Principal coordinates could separate the genotypes of
P. insignis
in clusters and we can conclude that the primers can estimate the genetic diversity of
P. insignis
populations.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>32034625</pmid><doi>10.1007/s11033-020-05301-0</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0003-3470-405X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Alleles Animal Anatomy Animal Biochemistry Asexual reproduction Asexuality Biomedical and Life Sciences Brazil Clusiaceae - genetics DNA Primers - genetics DNA, Plant - genetics Fruit - genetics Fruits Genetic diversity Genetic markers Genomics - methods Genotype Genotypes Germplasm Heterozygosity High-Throughput Nucleotide Sequencing - methods Histology Life Sciences Microsatellite Repeats - genetics Microsatellites Molecular biology Morphology Platonia Polymorphism Polymorphism, Genetic - genetics Short Communication Trees - genetics |
| title | First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree |
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