Development of EST‐derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability
With 1 figure and 3 tables ABSTRACT: Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are important resources for gene discovery and mapping. In this study, we developed EST‐based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 8...
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| creator | Mishra, Raghvendra K Gangadhar, Baniekal H Nookaraju, Akula Kumar, Sushil Park, Se W |
| description | With 1 figure and 3 tables ABSTRACT: Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are important resources for gene discovery and mapping. In this study, we developed EST‐based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 800 unigenes were detected from 18 522 pea EST sequences (December 2009). Screening of 10 800 unigenes by MISA (MIcroSAtellite) revealed 2612 (14.1%) eSSRs in 2395 (12.9%) SSR‐containing ESTs from which 577 (24.1%) primer pairs were designed. The most abundant repeat motif identified in eSSR was mononucleotide (85.2%), followed by trinucleotide (10.6%) and dinucleotide (2.8%). Among 108 randomly selected primer pairs, 40 were assessed for mapping and 68 to test cross‐species transferability in six leguminous species. Out of 40 primer pairs, 85% produced amplicons, 60% showed polymorphism and 47.5% were mapped. Furthermore, 68 primer pairs revealed high rate of transferability (48–85%) in leguminous species. High levels of polymorphism, reproducibility, presence of alleles (3.8/locus) and transferability revealed the potential use of these eSSR markers in molecular mapping, quantitative trait loci (QTL) analysis and comparative mapping in pea and other legumes. |
| doi_str_mv | 10.1111/j.1439-0523.2011.01926.x |
| format | Article |
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In this study, we developed EST‐based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 800 unigenes were detected from 18 522 pea EST sequences (December 2009). Screening of 10 800 unigenes by MISA (MIcroSAtellite) revealed 2612 (14.1%) eSSRs in 2395 (12.9%) SSR‐containing ESTs from which 577 (24.1%) primer pairs were designed. The most abundant repeat motif identified in eSSR was mononucleotide (85.2%), followed by trinucleotide (10.6%) and dinucleotide (2.8%). Among 108 randomly selected primer pairs, 40 were assessed for mapping and 68 to test cross‐species transferability in six leguminous species. Out of 40 primer pairs, 85% produced amplicons, 60% showed polymorphism and 47.5% were mapped. Furthermore, 68 primer pairs revealed high rate of transferability (48–85%) in leguminous species. High levels of polymorphism, reproducibility, presence of alleles (3.8/locus) and transferability revealed the potential use of these eSSR markers in molecular mapping, quantitative trait loci (QTL) analysis and comparative mapping in pea and other legumes.</description><identifier>ISSN: 0179-9541</identifier><identifier>EISSN: 1439-0523</identifier><identifier>DOI: 10.1111/j.1439-0523.2011.01926.x</identifier><identifier>CODEN: PLABED</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Agronomy. Soil science and plant productions ; alleles ; Biological and medical sciences ; chromosome mapping ; Classical and quantitative genetics. Population genetics. Molecular genetics ; expressed sequence tags ; Fundamental and applied biological sciences. Psychology ; Gene mapping ; Generalities. Genetics. Plant material ; genetic markers ; Genetics and breeding of economic plants ; Legumes ; Medicago truncatula ; microsatellite repeats ; Microsatellites ; Molecular genetics ; peas ; Pisum sativum ; Plant breeding ; polymorphism ; Primers ; Quantitative trait loci ; screening ; Simple sequence repeats ; unigenes</subject><ispartof>Plant breeding, 2012-02, Vol.131 (1), p.118-124</ispartof><rights>2011 Blackwell Verlag GmbH</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4616-df1d0e17e567cf4984e81a7447e9820f0cff2fa7b19ce51029bdfea3fd489f723</citedby><cites>FETCH-LOGICAL-c4616-df1d0e17e567cf4984e81a7447e9820f0cff2fa7b19ce51029bdfea3fd489f723</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1439-0523.2011.01926.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1439-0523.2011.01926.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27915,27916,45565,45566</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=25353690$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Mishra, Raghvendra K</creatorcontrib><creatorcontrib>Gangadhar, Baniekal H</creatorcontrib><creatorcontrib>Nookaraju, Akula</creatorcontrib><creatorcontrib>Kumar, Sushil</creatorcontrib><creatorcontrib>Park, Se W</creatorcontrib><title>Development of EST‐derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability</title><title>Plant breeding</title><description>With 1 figure and 3 tables ABSTRACT: Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are important resources for gene discovery and mapping. In this study, we developed EST‐based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 800 unigenes were detected from 18 522 pea EST sequences (December 2009). Screening of 10 800 unigenes by MISA (MIcroSAtellite) revealed 2612 (14.1%) eSSRs in 2395 (12.9%) SSR‐containing ESTs from which 577 (24.1%) primer pairs were designed. The most abundant repeat motif identified in eSSR was mononucleotide (85.2%), followed by trinucleotide (10.6%) and dinucleotide (2.8%). Among 108 randomly selected primer pairs, 40 were assessed for mapping and 68 to test cross‐species transferability in six leguminous species. Out of 40 primer pairs, 85% produced amplicons, 60% showed polymorphism and 47.5% were mapped. Furthermore, 68 primer pairs revealed high rate of transferability (48–85%) in leguminous species. 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Plant material</subject><subject>genetic markers</subject><subject>Genetics and breeding of economic plants</subject><subject>Legumes</subject><subject>Medicago truncatula</subject><subject>microsatellite repeats</subject><subject>Microsatellites</subject><subject>Molecular genetics</subject><subject>peas</subject><subject>Pisum sativum</subject><subject>Plant breeding</subject><subject>polymorphism</subject><subject>Primers</subject><subject>Quantitative trait loci</subject><subject>screening</subject><subject>Simple sequence repeats</subject><subject>unigenes</subject><issn>0179-9541</issn><issn>1439-0523</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><recordid>eNqNkctu1DAYRiMEEkPhGfAGQRcJviWOFyxoKAVUYNRpxdLyJL8HD7lhJ8PMDokX4Bl5EpymmiUiG8fy-T7bx1GECE5I-F5uE8KZjHFKWUIxIQkmkmbJ_l60OC7cjxaYCBnLlJOH0SPvt3iaM7GIfr2BHdRd30A7oM6g89X1n5-_K3B2BxVara5Qo903cB7ZFvWg0Yul9WODvB7sbmxOkW4rNHwF61DfDaHE6hqNg63tcECmc2gDLQy2DDV9b9vNzDvdegNOr2-5x9EDo2sPT-7Gk-jm7fl18S6-_Hzxvnh9GZc8I1lcGVJhIALSTJSGy5xDTrTgXIDMKTa4NIYaLdZElpASTOW6MqCZqXgujaDsJHo-9_au-z6CH1RjfQl1rVvoRq8kxUJySrNA5jNZus57B0b1zgYRB0WwmrSrrZrsqsmumrSrW-1qH6LP7jbRvtS1CVctrT_macpSlkkcuFcz98PWcPjvfrU8u5r-Qj6e89YPsD_mw2OpTDCRqi-fLlReFGfF8uMHJQL_dOaN7pTeuHCmm1Vo5hhjThjL_klQhqVgfwHHM7nm</recordid><startdate>201202</startdate><enddate>201202</enddate><creator>Mishra, Raghvendra K</creator><creator>Gangadhar, Baniekal H</creator><creator>Nookaraju, Akula</creator><creator>Kumar, Sushil</creator><creator>Park, Se W</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><scope>FBQ</scope><scope>BSCLL</scope><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>201202</creationdate><title>Development of EST‐derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability</title><author>Mishra, Raghvendra K ; Gangadhar, Baniekal H ; Nookaraju, Akula ; Kumar, Sushil ; Park, Se W</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4616-df1d0e17e567cf4984e81a7447e9820f0cff2fa7b19ce51029bdfea3fd489f723</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Agronomy. Soil science and plant productions</topic><topic>alleles</topic><topic>Biological and medical sciences</topic><topic>chromosome mapping</topic><topic>Classical and quantitative genetics. Population genetics. Molecular genetics</topic><topic>expressed sequence tags</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene mapping</topic><topic>Generalities. Genetics. Plant material</topic><topic>genetic markers</topic><topic>Genetics and breeding of economic plants</topic><topic>Legumes</topic><topic>Medicago truncatula</topic><topic>microsatellite repeats</topic><topic>Microsatellites</topic><topic>Molecular genetics</topic><topic>peas</topic><topic>Pisum sativum</topic><topic>Plant breeding</topic><topic>polymorphism</topic><topic>Primers</topic><topic>Quantitative trait loci</topic><topic>screening</topic><topic>Simple sequence repeats</topic><topic>unigenes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mishra, Raghvendra K</creatorcontrib><creatorcontrib>Gangadhar, Baniekal H</creatorcontrib><creatorcontrib>Nookaraju, Akula</creatorcontrib><creatorcontrib>Kumar, Sushil</creatorcontrib><creatorcontrib>Park, Se W</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Plant breeding</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mishra, Raghvendra K</au><au>Gangadhar, Baniekal H</au><au>Nookaraju, Akula</au><au>Kumar, Sushil</au><au>Park, Se W</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of EST‐derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability</atitle><jtitle>Plant breeding</jtitle><date>2012-02</date><risdate>2012</risdate><volume>131</volume><issue>1</issue><spage>118</spage><epage>124</epage><pages>118-124</pages><issn>0179-9541</issn><eissn>1439-0523</eissn><coden>PLABED</coden><abstract>With 1 figure and 3 tables ABSTRACT: Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are important resources for gene discovery and mapping. In this study, we developed EST‐based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 800 unigenes were detected from 18 522 pea EST sequences (December 2009). Screening of 10 800 unigenes by MISA (MIcroSAtellite) revealed 2612 (14.1%) eSSRs in 2395 (12.9%) SSR‐containing ESTs from which 577 (24.1%) primer pairs were designed. The most abundant repeat motif identified in eSSR was mononucleotide (85.2%), followed by trinucleotide (10.6%) and dinucleotide (2.8%). Among 108 randomly selected primer pairs, 40 were assessed for mapping and 68 to test cross‐species transferability in six leguminous species. Out of 40 primer pairs, 85% produced amplicons, 60% showed polymorphism and 47.5% were mapped. Furthermore, 68 primer pairs revealed high rate of transferability (48–85%) in leguminous species. High levels of polymorphism, reproducibility, presence of alleles (3.8/locus) and transferability revealed the potential use of these eSSR markers in molecular mapping, quantitative trait loci (QTL) analysis and comparative mapping in pea and other legumes.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><doi>10.1111/j.1439-0523.2011.01926.x</doi><tpages>7</tpages></addata></record> |
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| subjects | Agronomy. Soil science and plant productions alleles Biological and medical sciences chromosome mapping Classical and quantitative genetics. Population genetics. Molecular genetics expressed sequence tags Fundamental and applied biological sciences. Psychology Gene mapping Generalities. Genetics. Plant material genetic markers Genetics and breeding of economic plants Legumes Medicago truncatula microsatellite repeats Microsatellites Molecular genetics peas Pisum sativum Plant breeding polymorphism Primers Quantitative trait loci screening Simple sequence repeats unigenes |
| title | Development of EST‐derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability |
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