Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.)
With the aim of developing additional genomic resources in safflower, a set of 41,011 ESTs of safflower were mined for the presence of SSRs. 18,773 SSR containing ESTs (SSR-ESTs) were identified and were analyzed to remove redundant sequences leading to identification of 8,810 non-redundant SSR-ESTs...
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| Veröffentlicht in: | Journal of plant biochemistry and biotechnology 2013, Vol.22 (1), p.90-102 |
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| container_title | Journal of plant biochemistry and biotechnology |
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| creator | Yamini, Kalinati Narasimhan Ramesh, Kamtam Naresh, Vasupalli Rajendrakumar, Passoupathy Anjani, Kammili Dinesh Kumar, Viswanathaswamy |
| description | With the aim of developing additional genomic resources in safflower, a set of 41,011 ESTs of safflower were mined for the presence of SSRs. 18,773 SSR containing ESTs (SSR-ESTs) were identified and were analyzed to remove redundant sequences leading to identification of 8,810 non-redundant SSR-ESTs (categorized into 6104 singletons and 2,706 contigs) having 13,085 non-redundant SSRs. The average number of non-redundant SSRs per EST was 0.32 and they predominantly consisted of dinucleotide (57.7 %), and trinucleotide (37.7 %) repeat motifs. 500 primer pairs were designed for the non-redundant EST-SSRs of which, 151 were tested. 60 markers which gave robust amplicons, were validated in a set of 19 Carthamus lines. A subset of EST-SSR markers, having average polymorphism information content (PIC) ≥0.4 could precisely elucidate the pedigree relatedness among these lines. Further, these markers exhibited high cross-species transferability to five other wild species of Carthamus. The markers reported here would be a valuable addition to existing safflower marker resources aiding in hastening its improvement. |
| doi_str_mv | 10.1007/s13562-012-0115-4 |
| format | Article |
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The average number of non-redundant SSRs per EST was 0.32 and they predominantly consisted of dinucleotide (57.7 %), and trinucleotide (37.7 %) repeat motifs. 500 primer pairs were designed for the non-redundant EST-SSRs of which, 151 were tested. 60 markers which gave robust amplicons, were validated in a set of 19 Carthamus lines. A subset of EST-SSR markers, having average polymorphism information content (PIC) ≥0.4 could precisely elucidate the pedigree relatedness among these lines. Further, these markers exhibited high cross-species transferability to five other wild species of Carthamus. 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Plant Biochem. Biotechnol</addtitle><description>With the aim of developing additional genomic resources in safflower, a set of 41,011 ESTs of safflower were mined for the presence of SSRs. 18,773 SSR containing ESTs (SSR-ESTs) were identified and were analyzed to remove redundant sequences leading to identification of 8,810 non-redundant SSR-ESTs (categorized into 6104 singletons and 2,706 contigs) having 13,085 non-redundant SSRs. The average number of non-redundant SSRs per EST was 0.32 and they predominantly consisted of dinucleotide (57.7 %), and trinucleotide (37.7 %) repeat motifs. 500 primer pairs were designed for the non-redundant EST-SSRs of which, 151 were tested. 60 markers which gave robust amplicons, were validated in a set of 19 Carthamus lines. A subset of EST-SSR markers, having average polymorphism information content (PIC) ≥0.4 could precisely elucidate the pedigree relatedness among these lines. Further, these markers exhibited high cross-species transferability to five other wild species of Carthamus. The markers reported here would be a valuable addition to existing safflower marker resources aiding in hastening its improvement.</description><subject>Biomedical and Life Sciences</subject><subject>Carthamus tinctorius</subject><subject>Cell Biology</subject><subject>expressed sequence tags</subject><subject>Life Sciences</subject><subject>microsatellite repeats</subject><subject>Original Article</subject><subject>pedigree</subject><subject>Plant Biochemistry</subject><subject>Protein Science</subject><subject>Receptors</subject><issn>0971-7811</issn><issn>0974-1275</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><recordid>eNp9kMFu1DAQhiMEEqXwAJzwsRxSZpxJvD6ipUCllZDY9mw5sb11ycaL7Wy1b4-X9FxLI4_G_zeSv6r6iHCNAOJLwqbteA14LmxrelVdgBRUIxft6_891mKF-LZ6l9IjALUC6KI6frNHO4bD3k6ZBcdutnf1dvub7XX8Y2NiejIsP1gf2Zz96POJ-YnFwujRTzs2xNMh-4EZfyzp5-eknRvDk43saq1jftD7ObHspyGH6Eu7uf78vnrj9Jjsh-f7srr_fnO3_llvfv24XX_d1ENDba65oJ4bI6EXIB2SJiE7coYLXaaG28b0vQQC6s3QNdJJs9JkdEutBLSiuayulr2HGP7ONmW192mw46gnG-akkBpYdSiJlygu0SGGlKJ16hB90XBSCOrsWC2OVXGszo4VFYYvTCrZaWejegxznMqPXoQ-LZDTQeld9EndbzkgQTkt8q75B8EgiRY</recordid><startdate>2013</startdate><enddate>2013</enddate><creator>Yamini, Kalinati Narasimhan</creator><creator>Ramesh, Kamtam</creator><creator>Naresh, Vasupalli</creator><creator>Rajendrakumar, Passoupathy</creator><creator>Anjani, Kammili</creator><creator>Dinesh Kumar, Viswanathaswamy</creator><general>Springer-Verlag</general><scope>FBQ</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope></search><sort><creationdate>2013</creationdate><title>Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.)</title><author>Yamini, Kalinati Narasimhan ; Ramesh, Kamtam ; Naresh, Vasupalli ; Rajendrakumar, Passoupathy ; Anjani, Kammili ; Dinesh Kumar, Viswanathaswamy</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c345t-274b2dd90b709f14a47964fd27add9d2e3dbb90404bdc639f9d8a4da545901e73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Biomedical and Life Sciences</topic><topic>Carthamus tinctorius</topic><topic>Cell Biology</topic><topic>expressed sequence tags</topic><topic>Life Sciences</topic><topic>microsatellite repeats</topic><topic>Original Article</topic><topic>pedigree</topic><topic>Plant Biochemistry</topic><topic>Protein Science</topic><topic>Receptors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yamini, Kalinati Narasimhan</creatorcontrib><creatorcontrib>Ramesh, Kamtam</creatorcontrib><creatorcontrib>Naresh, Vasupalli</creatorcontrib><creatorcontrib>Rajendrakumar, Passoupathy</creatorcontrib><creatorcontrib>Anjani, Kammili</creatorcontrib><creatorcontrib>Dinesh Kumar, Viswanathaswamy</creatorcontrib><collection>AGRIS</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><jtitle>Journal of plant biochemistry and biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yamini, Kalinati Narasimhan</au><au>Ramesh, Kamtam</au><au>Naresh, Vasupalli</au><au>Rajendrakumar, Passoupathy</au><au>Anjani, Kammili</au><au>Dinesh Kumar, Viswanathaswamy</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.)</atitle><jtitle>Journal of plant biochemistry and biotechnology</jtitle><stitle>J. 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| subjects | Biomedical and Life Sciences Carthamus tinctorius Cell Biology expressed sequence tags Life Sciences microsatellite repeats Original Article pedigree Plant Biochemistry Protein Science Receptors |
| title | Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.) |
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