Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species
Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of...
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| Veröffentlicht in: | Applied biochemistry and biotechnology 2012-11, Vol.168 (6), p.1594-1607 |
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| creator | Spandana, B. Reddy, V. Prathap Prasanna, G. John Anuradha, G. Sivaramakrishnan, S. |
| description | Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in
Sesamum
(
Sesamum indicum
L.). More than 200 SSR motifs were detected (SSR motifs ≥2 repeat units or 6 bp); 80 % of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10 bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60
Sesamum
germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs. |
| doi_str_mv | 10.1007/s12010-012-9881-7 |
| format | Article |
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Sesamum
(
Sesamum indicum
L.). More than 200 SSR motifs were detected (SSR motifs ≥2 repeat units or 6 bp); 80 % of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10 bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60
Sesamum
germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.</description><identifier>ISSN: 0273-2289</identifier><identifier>EISSN: 1559-0291</identifier><identifier>DOI: 10.1007/s12010-012-9881-7</identifier><identifier>PMID: 22971833</identifier><identifier>CODEN: ABIBDL</identifier><language>eng</language><publisher>New York: Springer-Verlag</publisher><subject>Agricultural biotechnology ; Animal species ; Biochemistry ; Biological and medical sciences ; Biotechnology ; Chemistry ; Chemistry and Materials Science ; Cultivars ; DNA, Plant - genetics ; Fundamental and applied biological sciences. Psychology ; Genetic diversity ; Genetic Variation ; Genetics ; Genome, Plant ; Microsatellite Repeats ; Plant populations ; Plant propagation ; Polymerase Chain Reaction - methods ; Polymorphism ; Polymorphism, Genetic ; Seeds ; Sesamum ; Sesamum - classification ; Sesamum - genetics ; Sesamum indicum</subject><ispartof>Applied biochemistry and biotechnology, 2012-11, Vol.168 (6), p.1594-1607</ispartof><rights>Springer Science+Business Media, LLC 2012</rights><rights>2014 INIST-CNRS</rights><rights>Springer Science+Business Media New York 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c435t-1c5cd09459c388c9dd95b1ed9c3df69b90b9c2852aa6254e1e9f3123dfc3a7d33</citedby><cites>FETCH-LOGICAL-c435t-1c5cd09459c388c9dd95b1ed9c3df69b90b9c2852aa6254e1e9f3123dfc3a7d33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12010-012-9881-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12010-012-9881-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26701967$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22971833$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Spandana, B.</creatorcontrib><creatorcontrib>Reddy, V. Prathap</creatorcontrib><creatorcontrib>Prasanna, G. John</creatorcontrib><creatorcontrib>Anuradha, G.</creatorcontrib><creatorcontrib>Sivaramakrishnan, S.</creatorcontrib><title>Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species</title><title>Applied biochemistry and biotechnology</title><addtitle>Appl Biochem Biotechnol</addtitle><addtitle>Appl Biochem Biotechnol</addtitle><description>Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in
Sesamum
(
Sesamum indicum
L.). More than 200 SSR motifs were detected (SSR motifs ≥2 repeat units or 6 bp); 80 % of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10 bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60
Sesamum
germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.</description><subject>Agricultural biotechnology</subject><subject>Animal species</subject><subject>Biochemistry</subject><subject>Biological and medical sciences</subject><subject>Biotechnology</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Cultivars</subject><subject>DNA, Plant - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>Genetics</subject><subject>Genome, Plant</subject><subject>Microsatellite Repeats</subject><subject>Plant populations</subject><subject>Plant propagation</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Seeds</subject><subject>Sesamum</subject><subject>Sesamum - classification</subject><subject>Sesamum - genetics</subject><subject>Sesamum indicum</subject><issn>0273-2289</issn><issn>1559-0291</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</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>eNqFkU2LFDEQhoMo7rj6A7xIQITdQ6-ppNPpHGX8hFkER88hk1S7WbvTs0m3sPvrTTPjB4J4qiT11FtVeQl5CuwCGFMvM3AGrGLAK922UKl7ZAVS6opxDffJinElKs5bfUIe5XzNCthK9ZCccK4VtEKsyNVr_I79uB8wTtRGT9dXNlk3YQp3dgpjpGNHL4NLY7YT9n2YkF7a9A1Tpmfb7adzGiLdYrbDPJSH4yFEH1yJm4tzut2jC5gfkwed7TM-OcZT8uXtm8_r99Xm47sP61ebytVCThU46TzTtdROtK3T3mu5A_Tl6rtG7zTbaVe24NY2XNYIqDsBvCSdsMoLcUrODrr7NN7MmCczhOzK5DbiOGcDXCrVcFDN_1FQbaOhaeqCPv8LvR7nFMsiC8Ukr2UNhYIDtXxXTtiZfQqDTbcGmFkcMwfHTDHCLI4ZVWqeHZXn3YD-V8VPiwrw4gjY7GzfJRtdyL-5RjHQzSLED1wuqfgV0x8j_rP7D4aWrBU</recordid><startdate>20121101</startdate><enddate>20121101</enddate><creator>Spandana, B.</creator><creator>Reddy, V. 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Psychology</topic><topic>Genetic diversity</topic><topic>Genetic Variation</topic><topic>Genetics</topic><topic>Genome, Plant</topic><topic>Microsatellite Repeats</topic><topic>Plant populations</topic><topic>Plant propagation</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymorphism</topic><topic>Polymorphism, Genetic</topic><topic>Seeds</topic><topic>Sesamum</topic><topic>Sesamum - classification</topic><topic>Sesamum - genetics</topic><topic>Sesamum indicum</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Spandana, B.</creatorcontrib><creatorcontrib>Reddy, V. Prathap</creatorcontrib><creatorcontrib>Prasanna, G. 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Prathap</au><au>Prasanna, G. John</au><au>Anuradha, G.</au><au>Sivaramakrishnan, S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species</atitle><jtitle>Applied biochemistry and biotechnology</jtitle><stitle>Appl Biochem Biotechnol</stitle><addtitle>Appl Biochem Biotechnol</addtitle><date>2012-11-01</date><risdate>2012</risdate><volume>168</volume><issue>6</issue><spage>1594</spage><epage>1607</epage><pages>1594-1607</pages><issn>0273-2289</issn><eissn>1559-0291</eissn><coden>ABIBDL</coden><abstract>Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in
Sesamum
(
Sesamum indicum
L.). More than 200 SSR motifs were detected (SSR motifs ≥2 repeat units or 6 bp); 80 % of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10 bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60
Sesamum
germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.</abstract><cop>New York</cop><pub>Springer-Verlag</pub><pmid>22971833</pmid><doi>10.1007/s12010-012-9881-7</doi><tpages>14</tpages></addata></record> |
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| ispartof | Applied biochemistry and biotechnology, 2012-11, Vol.168 (6), p.1594-1607 |
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| language | eng |
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| source | MEDLINE; Springer Nature - Complete Springer Journals |
| subjects | Agricultural biotechnology Animal species Biochemistry Biological and medical sciences Biotechnology Chemistry Chemistry and Materials Science Cultivars DNA, Plant - genetics Fundamental and applied biological sciences. Psychology Genetic diversity Genetic Variation Genetics Genome, Plant Microsatellite Repeats Plant populations Plant propagation Polymerase Chain Reaction - methods Polymorphism Polymorphism, Genetic Seeds Sesamum Sesamum - classification Sesamum - genetics Sesamum indicum |
| title | Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species |
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