CEL I Nuclease Digestion for SNP Discovery and Marker Development in Common Bean (Phaseolus vulgaris L.)
Single nucleotide polymorphisms (SNPs) are the most common sequence difference found in plant genomes, yet they have not been widely exploited for producing molecular markers in common bean (Phaseolus vulgaris L.). The objective of this study was to develop a SNP assay based on a type of heteroduple...
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| Veröffentlicht in: | Crop science 2009-03, Vol.49 (2), p.381-394 |
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| creator | Galeano, Carlos H. Gomez, Marcela Rodriguez, Lina M. Blair, Matthew W. |
| description | Single nucleotide polymorphisms (SNPs) are the most common sequence difference found in plant genomes, yet they have not been widely exploited for producing molecular markers in common bean (Phaseolus vulgaris L.). The objective of this study was to develop a SNP assay based on a type of heteroduplex mismatch cleavage called EcoTILLING for molecular marker development in this important legume, and apply the assay (i) to the conversion of a sequence‐characterized amplified region (SCAR) marker useful for selecting virus resistance (SR2) and (ii) to the screening of SNP polymorphisms in newly developed expressed sequence tag (EST)–based markers. The SNP assay involved heteroduplex mismatch cleavage by a single‐strand specific nuclease ‘CEL I’ which was used to uncover two SNPs in the SR2 fragment and 22 SNPs in 37 candidate ESTs, some of which were used in segregation analysis. While developing the SNP techniques we tested several platforms, including LI‐COR, nondenaturing polyacrylamide, and agarose gel detection. The agarose gel system was used for SNP genetic mapping in two common bean mapping populations, showing that heteroduplex cleavage is a useful technique for increasing molecular marker number for the crop. Examples are given of mapped SNP markers for the phytic acid pathway gene for myo‐inositol‐1‐phosphate synthase and a drought tolerance–related gene, S‐adenosylmethionine decarboxylase. |
| doi_str_mv | 10.2135/cropsci2008.07.0413 |
| format | Article |
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The objective of this study was to develop a SNP assay based on a type of heteroduplex mismatch cleavage called EcoTILLING for molecular marker development in this important legume, and apply the assay (i) to the conversion of a sequence‐characterized amplified region (SCAR) marker useful for selecting virus resistance (SR2) and (ii) to the screening of SNP polymorphisms in newly developed expressed sequence tag (EST)–based markers. The SNP assay involved heteroduplex mismatch cleavage by a single‐strand specific nuclease ‘CEL I’ which was used to uncover two SNPs in the SR2 fragment and 22 SNPs in 37 candidate ESTs, some of which were used in segregation analysis. While developing the SNP techniques we tested several platforms, including LI‐COR, nondenaturing polyacrylamide, and agarose gel detection. The agarose gel system was used for SNP genetic mapping in two common bean mapping populations, showing that heteroduplex cleavage is a useful technique for increasing molecular marker number for the crop. Examples are given of mapped SNP markers for the phytic acid pathway gene for myo‐inositol‐1‐phosphate synthase and a drought tolerance–related gene, S‐adenosylmethionine decarboxylase.</description><identifier>ISSN: 0011-183X</identifier><identifier>EISSN: 1435-0653</identifier><identifier>DOI: 10.2135/cropsci2008.07.0413</identifier><identifier>CODEN: CRPSAY</identifier><language>eng</language><publisher>Madison: Crop Science Society of America</publisher><subject>Agronomy. Soil science and plant productions ; Biological and medical sciences ; Drought resistance ; Fundamental and applied biological sciences. 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Psychology</subject><subject>Genetics</subject><subject>Genetics and breeding of economic plants</subject><subject>Genomics</subject><subject>Methods</subject><subject>Mutation</subject><subject>Phaseolus vulgaris</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism</subject><subject>Rice</subject><subject>Studies</subject><issn>0011-183X</issn><issn>1435-0653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqNkEtvEzEUhS1EJULhF7CxkECwmPT6OeMlTF-R0jYiILGzHMdup3jGwe4E5d_jkKpCrFhd6eg75957EHpDYEoJEyc2xU22HQVoplBPgRP2DE0IZ6ICKdhzNAEgpCIN-_4Cvcz5HgBqVYsJumvP5niGr0cbnMkOn3a3Lj90ccA-Jry8XhQl27h1aYfNsMZXJv1wCZ-6rQtx07vhAXcDbmPfF8tnZwb8YXFXgmIYM96O4dakLuP59OMrdORNyO714zxG387PvraX1fzmYtZ-mleWM8Yqs1JCek-VNWu1slxIsSYUVq621HviGyk9h8Yr5ZQtsnTGSrWmUlFDmsawY_T-kLtJ8edYftF9ecCFYAYXx6wpcCUU5wV8-w94H8c0lNs0owIaziQrEDtApeGck_N6k7repJ0moPfV67-q11DrffXF9e4x2mRrgk9msF1-shYfEaSWhTs_cL-64Hb_E63bZUvbLzeLZTvb61D_WfgbtqKaCg</recordid><startdate>200903</startdate><enddate>200903</enddate><creator>Galeano, Carlos H.</creator><creator>Gomez, Marcela</creator><creator>Rodriguez, Lina M.</creator><creator>Blair, Matthew W.</creator><general>Crop Science Society of America</general><general>American Society of Agronomy</general><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8AF</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>M0K</scope><scope>M2O</scope><scope>M2P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>R05</scope><scope>S0X</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>200903</creationdate><title>CEL I Nuclease Digestion for SNP Discovery and Marker Development in Common Bean (Phaseolus vulgaris L.)</title><author>Galeano, Carlos H. ; Gomez, Marcela ; Rodriguez, Lina M. ; Blair, Matthew W.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4333-ab956ff29cad9bc4565d120be7c2ff1f866f408f99e9c0be6eac69d2692a188a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Agronomy. Soil science and plant productions</topic><topic>Biological and medical sciences</topic><topic>Drought resistance</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genetics</topic><topic>Genetics and breeding of economic plants</topic><topic>Genomics</topic><topic>Methods</topic><topic>Mutation</topic><topic>Phaseolus vulgaris</topic><topic>Polymerase chain reaction</topic><topic>Polymorphism</topic><topic>Rice</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Galeano, Carlos H.</creatorcontrib><creatorcontrib>Gomez, Marcela</creatorcontrib><creatorcontrib>Rodriguez, Lina M.</creatorcontrib><creatorcontrib>Blair, Matthew W.</creatorcontrib><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Engineering Collection</collection><collection>Agricultural Science Database</collection><collection>ProQuest research library</collection><collection>ProQuest Science Journals</collection><collection>Engineering Database</collection><collection>Research Library (Corporate)</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>University of Michigan</collection><collection>SIRS Editorial</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Crop science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Galeano, Carlos H.</au><au>Gomez, Marcela</au><au>Rodriguez, Lina M.</au><au>Blair, Matthew W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CEL I Nuclease Digestion for SNP Discovery and Marker Development in Common Bean (Phaseolus vulgaris L.)</atitle><jtitle>Crop science</jtitle><date>2009-03</date><risdate>2009</risdate><volume>49</volume><issue>2</issue><spage>381</spage><epage>394</epage><pages>381-394</pages><issn>0011-183X</issn><eissn>1435-0653</eissn><coden>CRPSAY</coden><abstract>Single nucleotide polymorphisms (SNPs) are the most common sequence difference found in plant genomes, yet they have not been widely exploited for producing molecular markers in common bean (Phaseolus vulgaris L.). The objective of this study was to develop a SNP assay based on a type of heteroduplex mismatch cleavage called EcoTILLING for molecular marker development in this important legume, and apply the assay (i) to the conversion of a sequence‐characterized amplified region (SCAR) marker useful for selecting virus resistance (SR2) and (ii) to the screening of SNP polymorphisms in newly developed expressed sequence tag (EST)–based markers. The SNP assay involved heteroduplex mismatch cleavage by a single‐strand specific nuclease ‘CEL I’ which was used to uncover two SNPs in the SR2 fragment and 22 SNPs in 37 candidate ESTs, some of which were used in segregation analysis. While developing the SNP techniques we tested several platforms, including LI‐COR, nondenaturing polyacrylamide, and agarose gel detection. The agarose gel system was used for SNP genetic mapping in two common bean mapping populations, showing that heteroduplex cleavage is a useful technique for increasing molecular marker number for the crop. Examples are given of mapped SNP markers for the phytic acid pathway gene for myo‐inositol‐1‐phosphate synthase and a drought tolerance–related gene, S‐adenosylmethionine decarboxylase.</abstract><cop>Madison</cop><pub>Crop Science Society of America</pub><doi>10.2135/cropsci2008.07.0413</doi><tpages>14</tpages></addata></record> |
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| ispartof | Crop science, 2009-03, Vol.49 (2), p.381-394 |
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| language | eng |
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| source | Wiley-Blackwell Journals; Alma/SFX Local Collection |
| subjects | Agronomy. Soil science and plant productions Biological and medical sciences Drought resistance Fundamental and applied biological sciences. Psychology Genetics Genetics and breeding of economic plants Genomics Methods Mutation Phaseolus vulgaris Polymerase chain reaction Polymorphism Rice Studies |
| title | CEL I Nuclease Digestion for SNP Discovery and Marker Development in Common Bean (Phaseolus vulgaris L.) |
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