Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR
The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple se...
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| Veröffentlicht in: | Theoretical and applied genetics 2005-03, Vol.110 (5), p.819-831 |
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| creator | Tam, S.M Mhiri, C Vogelaar, A Kerkveld, M Pearce, S.R Grandbastien, M.A |
| description | The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group. |
| doi_str_mv | 10.1007/s00122-004-1837-z |
| format | Article |
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The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-004-1837-z</identifier><identifier>PMID: 15700147</identifier><identifier>CODEN: THAGA6</identifier><language>eng</language><publisher>Heidelberg: Springer</publisher><subject>amplified fragment length polymorphism ; Biological and medical sciences ; Biological diversity ; Capsicum ; Capsicum - genetics ; Capsicum annuum ; Classical genetics, quantitative genetics, hybrids ; Cluster Analysis ; DNA Primers ; Evaluation Studies as Topic ; Fundamental and applied biological sciences. Psychology ; Genetic aspects ; Genetic diversity ; genetic markers ; Genetic Variation ; Genetics of eukaryotes. Biological and molecular evolution ; Genic rearrangement. Recombination. Transposable element ; germplasm ; lines ; Lycopersicon esculentum ; Lycopersicon esculentum - genetics ; microsatellite repeats ; Minisatellite Repeats - genetics ; Molecular and cellular biology ; Molecular genetics ; Nucleic Acid Amplification Techniques - methods ; peppers ; Phylogeny ; plant genetic resources ; Polymorphism, Restriction Fragment Length ; Pteridophyta, spermatophyta ; retrotransposons ; sequence-specific amplification polymorphism ; Solanum lycopersicum var. lycopersicum ; tomatoes ; Vegetals</subject><ispartof>Theoretical and applied genetics, 2005-03, Vol.110 (5), p.819-831</ispartof><rights>2005 INIST-CNRS</rights><rights>COPYRIGHT 2005 Springer</rights><rights>Springer-Verlag 2005</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c445t-7b5d9e43fabc20673ce9d4c2790f4ec73109838ee0efb89c13c7aff72c639cc83</citedby><cites>FETCH-LOGICAL-c445t-7b5d9e43fabc20673ce9d4c2790f4ec73109838ee0efb89c13c7aff72c639cc83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16647559$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15700147$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tam, S.M</creatorcontrib><creatorcontrib>Mhiri, C</creatorcontrib><creatorcontrib>Vogelaar, A</creatorcontrib><creatorcontrib>Kerkveld, M</creatorcontrib><creatorcontrib>Pearce, S.R</creatorcontrib><creatorcontrib>Grandbastien, M.A</creatorcontrib><title>Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><description>The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group.</description><subject>amplified fragment length polymorphism</subject><subject>Biological and medical sciences</subject><subject>Biological diversity</subject><subject>Capsicum</subject><subject>Capsicum - genetics</subject><subject>Capsicum annuum</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>Cluster Analysis</subject><subject>DNA Primers</subject><subject>Evaluation Studies as Topic</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>genetic markers</subject><subject>Genetic Variation</subject><subject>Genetics of eukaryotes. 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Psychology</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>genetic markers</topic><topic>Genetic Variation</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genic rearrangement. Recombination. Transposable element</topic><topic>germplasm</topic><topic>lines</topic><topic>Lycopersicon esculentum</topic><topic>Lycopersicon esculentum - genetics</topic><topic>microsatellite repeats</topic><topic>Minisatellite Repeats - genetics</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Nucleic Acid Amplification Techniques - methods</topic><topic>peppers</topic><topic>Phylogeny</topic><topic>plant genetic resources</topic><topic>Polymorphism, Restriction Fragment Length</topic><topic>Pteridophyta, spermatophyta</topic><topic>retrotransposons</topic><topic>sequence-specific amplification polymorphism</topic><topic>Solanum lycopersicum var. lycopersicum</topic><topic>tomatoes</topic><topic>Vegetals</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tam, S.M</creatorcontrib><creatorcontrib>Mhiri, C</creatorcontrib><creatorcontrib>Vogelaar, A</creatorcontrib><creatorcontrib>Kerkveld, M</creatorcontrib><creatorcontrib>Pearce, S.R</creatorcontrib><creatorcontrib>Grandbastien, M.A</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>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>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 Edition)</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>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>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>ProQuest Health & Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health & Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied & Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tam, S.M</au><au>Mhiri, C</au><au>Vogelaar, A</au><au>Kerkveld, M</au><au>Pearce, S.R</au><au>Grandbastien, M.A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR</atitle><jtitle>Theoretical and applied genetics</jtitle><addtitle>Theor Appl Genet</addtitle><date>2005-03-01</date><risdate>2005</risdate><volume>110</volume><issue>5</issue><spage>819</spage><epage>831</epage><pages>819-831</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><coden>THAGA6</coden><abstract>The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group.</abstract><cop>Heidelberg</cop><cop>Berlin</cop><pub>Springer</pub><pmid>15700147</pmid><doi>10.1007/s00122-004-1837-z</doi><tpages>13</tpages></addata></record> |
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| subjects | amplified fragment length polymorphism Biological and medical sciences Biological diversity Capsicum Capsicum - genetics Capsicum annuum Classical genetics, quantitative genetics, hybrids Cluster Analysis DNA Primers Evaluation Studies as Topic Fundamental and applied biological sciences. Psychology Genetic aspects Genetic diversity genetic markers Genetic Variation Genetics of eukaryotes. Biological and molecular evolution Genic rearrangement. Recombination. Transposable element germplasm lines Lycopersicon esculentum Lycopersicon esculentum - genetics microsatellite repeats Minisatellite Repeats - genetics Molecular and cellular biology Molecular genetics Nucleic Acid Amplification Techniques - methods peppers Phylogeny plant genetic resources Polymorphism, Restriction Fragment Length Pteridophyta, spermatophyta retrotransposons sequence-specific amplification polymorphism Solanum lycopersicum var. lycopersicum tomatoes Vegetals |
| title | Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR |
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