Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum
The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of comprising high species diversity, morphological overlap and weak genetic barrier. In present study, expressed sequence tag (EST) data fro...
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| description | The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of comprising high species diversity, morphological overlap and weak genetic barrier. In present study, expressed sequence tag (EST) data from
Rhododendron catawbiense
Michx (Subgenus Hymenanthes, Section Ponticum) and
Rhododendron mucronatum
var.
ripense
(Makino) E.H. Wilson (Subgenus Tsutsusi, Section Tsutsusi) were utilized for mining and identification of the SSRs for genetic diversity analysis of
R. arboreum
Smith (Subgenus Tsutsusi, Section Tsutsusi). A total of 249 SSRs were developed from 1767 contigs. Di-nucleotide was found to be most abundant repeat followed by tri- and tetra-nucleotide repeats. The motif AG/CT was most common di-nucleotide motif (31.73%), whereas, AAC/GTT (8.43%), ACG/CGT (8.03%), AAG/CTT (7.23%) and AGG/CCT (6.43%) were most abundant tri-nucleotide repeat motif. Among these SSRs, 168 sequences were only fit into the criteria to design flanking primer pairs. A total of 30 randomly selected primer pairs were utilized for validation and genetic diversity study in 36 genotypes of
R. arboreum
collected from western Himalayan region. In aggregate, 26 SSR markers (86.66%) produced good and repeatable amplifications. Expected heterozygosity (
H
E
) ranged from 0.322 to 0.841 and observed heterozygosity (
H
O
) ranged from 0.327 to 1.000 and PIC value ranged from 0.008 to 0.786. These primers were able to distinguish the geographic differences of occurrence based on cluster analysis. These developed EST-SSRs can be useful in future population genetics analysis and micro-evolutionary studies in
Rhododendron
species. |
| doi_str_mv | 10.1007/s11033-020-05300-1 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2370532028</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2370532028</sourcerecordid><originalsourceid>FETCH-LOGICAL-c375t-d0687cfc64e8927ea95302f157d7cacf6fb8b938405d38a7634e5adc7843e18b3</originalsourceid><addsrcrecordid>eNp9kUtv1DAUhS0EokPhD7BAltiwCfgZe5aoLQ-pUqVOu7Yc-6bjktjBTkYa8efxdApILLqy7Pudc33vQegtJR8pIepToZRw3hBGGiI5IQ19hlZUKt6ItdLP0YpwQhuhJT1Br0q5J4QIquRLdMIZZYK2aoV-ncMOhjSNEGecejylYT-mPG2Dwxebm2azucajzT8gF2yjx_MWQsZ2mobgbBeGMO9xiPgOIsxV4sOukodH2NlhsXNI8VC_3iafPESf693mLmVYxtfoRW-HAm8ez1N0--Xi5uxbc3n19fvZ58vGcSXnxpNWK9e7VoBeMwV2XYdlfR3UK2dd3_ad7tZcCyI911a1XIC03iktOFDd8VP04eg75fRzgTKbMRQHw2AjpKUYxlXdHyNMV_T9f-h9WnKsvzNMKqWEFIJVih0pl1MpGXoz5VC3tDeUmEM05hiNqdGYh2gMraJ3j9ZLN4L_K_mTRQX4ESi1FO8g_-v9hO1vwwGajg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2577745442</pqid></control><display><type>article</type><title>Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum</title><source>MEDLINE</source><source>SpringerLink Journals - AutoHoldings</source><creator>Sharma, Himanshu ; Kumar, Pankaj ; Singh, Abhishek ; Aggarwal, Kanika ; Roy, Joy ; Sharma, Vikas ; Rawat, Sandeep</creator><creatorcontrib>Sharma, Himanshu ; Kumar, Pankaj ; Singh, Abhishek ; Aggarwal, Kanika ; Roy, Joy ; Sharma, Vikas ; Rawat, Sandeep</creatorcontrib><description>The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of comprising high species diversity, morphological overlap and weak genetic barrier. In present study, expressed sequence tag (EST) data from
Rhododendron catawbiense
Michx (Subgenus Hymenanthes, Section Ponticum) and
Rhododendron mucronatum
var.
ripense
(Makino) E.H. Wilson (Subgenus Tsutsusi, Section Tsutsusi) were utilized for mining and identification of the SSRs for genetic diversity analysis of
R. arboreum
Smith (Subgenus Tsutsusi, Section Tsutsusi). A total of 249 SSRs were developed from 1767 contigs. Di-nucleotide was found to be most abundant repeat followed by tri- and tetra-nucleotide repeats. The motif AG/CT was most common di-nucleotide motif (31.73%), whereas, AAC/GTT (8.43%), ACG/CGT (8.03%), AAG/CTT (7.23%) and AGG/CCT (6.43%) were most abundant tri-nucleotide repeat motif. Among these SSRs, 168 sequences were only fit into the criteria to design flanking primer pairs. A total of 30 randomly selected primer pairs were utilized for validation and genetic diversity study in 36 genotypes of
R. arboreum
collected from western Himalayan region. In aggregate, 26 SSR markers (86.66%) produced good and repeatable amplifications. Expected heterozygosity (
H
E
) ranged from 0.322 to 0.841 and observed heterozygosity (
H
O
) ranged from 0.327 to 1.000 and PIC value ranged from 0.008 to 0.786. These primers were able to distinguish the geographic differences of occurrence based on cluster analysis. These developed EST-SSRs can be useful in future population genetics analysis and micro-evolutionary studies in
Rhododendron
species.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-020-05300-1</identifier><identifier>PMID: 32124167</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Biomedical and Life Sciences ; DNA, Plant - genetics ; Evolution ; Expressed sequence tags ; Expressed Sequence Tags - metabolism ; Flowers ; Genetic analysis ; Genetic diversity ; Genetic Markers - genetics ; Genetic Variation - genetics ; Genome, Plant - genetics ; Genotype ; Genotypes ; Heterozygosity ; Histology ; Life Sciences ; Microsatellite Repeats - genetics ; Morphology ; Nucleotide Motifs - genetics ; Original Article ; Polymorphism, Genetic - genetics ; Population genetics ; Rhododendron ; Rhododendron - genetics ; Sequence Analysis, DNA - methods ; Species diversity</subject><ispartof>Molecular biology reports, 2020-04, Vol.47 (4), p.2447-2457</ispartof><rights>Springer Nature B.V. 2020</rights><rights>Springer Nature B.V. 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-d0687cfc64e8927ea95302f157d7cacf6fb8b938405d38a7634e5adc7843e18b3</citedby><cites>FETCH-LOGICAL-c375t-d0687cfc64e8927ea95302f157d7cacf6fb8b938405d38a7634e5adc7843e18b3</cites><orcidid>0000-0001-7991-2878</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-020-05300-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-020-05300-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32124167$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sharma, Himanshu</creatorcontrib><creatorcontrib>Kumar, Pankaj</creatorcontrib><creatorcontrib>Singh, Abhishek</creatorcontrib><creatorcontrib>Aggarwal, Kanika</creatorcontrib><creatorcontrib>Roy, Joy</creatorcontrib><creatorcontrib>Sharma, Vikas</creatorcontrib><creatorcontrib>Rawat, Sandeep</creatorcontrib><title>Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of comprising high species diversity, morphological overlap and weak genetic barrier. In present study, expressed sequence tag (EST) data from
Rhododendron catawbiense
Michx (Subgenus Hymenanthes, Section Ponticum) and
Rhododendron mucronatum
var.
ripense
(Makino) E.H. Wilson (Subgenus Tsutsusi, Section Tsutsusi) were utilized for mining and identification of the SSRs for genetic diversity analysis of
R. arboreum
Smith (Subgenus Tsutsusi, Section Tsutsusi). A total of 249 SSRs were developed from 1767 contigs. Di-nucleotide was found to be most abundant repeat followed by tri- and tetra-nucleotide repeats. The motif AG/CT was most common di-nucleotide motif (31.73%), whereas, AAC/GTT (8.43%), ACG/CGT (8.03%), AAG/CTT (7.23%) and AGG/CCT (6.43%) were most abundant tri-nucleotide repeat motif. Among these SSRs, 168 sequences were only fit into the criteria to design flanking primer pairs. A total of 30 randomly selected primer pairs were utilized for validation and genetic diversity study in 36 genotypes of
R. arboreum
collected from western Himalayan region. In aggregate, 26 SSR markers (86.66%) produced good and repeatable amplifications. Expected heterozygosity (
H
E
) ranged from 0.322 to 0.841 and observed heterozygosity (
H
O
) ranged from 0.327 to 1.000 and PIC value ranged from 0.008 to 0.786. These primers were able to distinguish the geographic differences of occurrence based on cluster analysis. These developed EST-SSRs can be useful in future population genetics analysis and micro-evolutionary studies in
Rhododendron
species.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>DNA, Plant - genetics</subject><subject>Evolution</subject><subject>Expressed sequence tags</subject><subject>Expressed Sequence Tags - metabolism</subject><subject>Flowers</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic Markers - genetics</subject><subject>Genetic Variation - genetics</subject><subject>Genome, Plant - genetics</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Heterozygosity</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Microsatellite Repeats - genetics</subject><subject>Morphology</subject><subject>Nucleotide Motifs - genetics</subject><subject>Original Article</subject><subject>Polymorphism, Genetic - genetics</subject><subject>Population genetics</subject><subject>Rhododendron</subject><subject>Rhododendron - genetics</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Species diversity</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kUtv1DAUhS0EokPhD7BAltiwCfgZe5aoLQ-pUqVOu7Yc-6bjktjBTkYa8efxdApILLqy7Pudc33vQegtJR8pIepToZRw3hBGGiI5IQ19hlZUKt6ItdLP0YpwQhuhJT1Br0q5J4QIquRLdMIZZYK2aoV-ncMOhjSNEGecejylYT-mPG2Dwxebm2azucajzT8gF2yjx_MWQsZ2mobgbBeGMO9xiPgOIsxV4sOukodH2NlhsXNI8VC_3iafPESf693mLmVYxtfoRW-HAm8ez1N0--Xi5uxbc3n19fvZ58vGcSXnxpNWK9e7VoBeMwV2XYdlfR3UK2dd3_ad7tZcCyI911a1XIC03iktOFDd8VP04eg75fRzgTKbMRQHw2AjpKUYxlXdHyNMV_T9f-h9WnKsvzNMKqWEFIJVih0pl1MpGXoz5VC3tDeUmEM05hiNqdGYh2gMraJ3j9ZLN4L_K_mTRQX4ESi1FO8g_-v9hO1vwwGajg</recordid><startdate>20200401</startdate><enddate>20200401</enddate><creator>Sharma, Himanshu</creator><creator>Kumar, Pankaj</creator><creator>Singh, Abhishek</creator><creator>Aggarwal, Kanika</creator><creator>Roy, Joy</creator><creator>Sharma, Vikas</creator><creator>Rawat, Sandeep</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-7991-2878</orcidid></search><sort><creationdate>20200401</creationdate><title>Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum</title><author>Sharma, Himanshu ; Kumar, Pankaj ; Singh, Abhishek ; Aggarwal, Kanika ; Roy, Joy ; Sharma, Vikas ; Rawat, Sandeep</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-d0687cfc64e8927ea95302f157d7cacf6fb8b938405d38a7634e5adc7843e18b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>DNA, Plant - genetics</topic><topic>Evolution</topic><topic>Expressed sequence tags</topic><topic>Expressed Sequence Tags - metabolism</topic><topic>Flowers</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genetic Markers - genetics</topic><topic>Genetic Variation - genetics</topic><topic>Genome, Plant - genetics</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Heterozygosity</topic><topic>Histology</topic><topic>Life Sciences</topic><topic>Microsatellite Repeats - genetics</topic><topic>Morphology</topic><topic>Nucleotide Motifs - genetics</topic><topic>Original Article</topic><topic>Polymorphism, Genetic - genetics</topic><topic>Population genetics</topic><topic>Rhododendron</topic><topic>Rhododendron - genetics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Species diversity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sharma, Himanshu</creatorcontrib><creatorcontrib>Kumar, Pankaj</creatorcontrib><creatorcontrib>Singh, Abhishek</creatorcontrib><creatorcontrib>Aggarwal, Kanika</creatorcontrib><creatorcontrib>Roy, Joy</creatorcontrib><creatorcontrib>Sharma, Vikas</creatorcontrib><creatorcontrib>Rawat, Sandeep</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids 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>Science 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>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sharma, Himanshu</au><au>Kumar, Pankaj</au><au>Singh, Abhishek</au><au>Aggarwal, Kanika</au><au>Roy, Joy</au><au>Sharma, Vikas</au><au>Rawat, Sandeep</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>47</volume><issue>4</issue><spage>2447</spage><epage>2457</epage><pages>2447-2457</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of comprising high species diversity, morphological overlap and weak genetic barrier. In present study, expressed sequence tag (EST) data from
Rhododendron catawbiense
Michx (Subgenus Hymenanthes, Section Ponticum) and
Rhododendron mucronatum
var.
ripense
(Makino) E.H. Wilson (Subgenus Tsutsusi, Section Tsutsusi) were utilized for mining and identification of the SSRs for genetic diversity analysis of
R. arboreum
Smith (Subgenus Tsutsusi, Section Tsutsusi). A total of 249 SSRs were developed from 1767 contigs. Di-nucleotide was found to be most abundant repeat followed by tri- and tetra-nucleotide repeats. The motif AG/CT was most common di-nucleotide motif (31.73%), whereas, AAC/GTT (8.43%), ACG/CGT (8.03%), AAG/CTT (7.23%) and AGG/CCT (6.43%) were most abundant tri-nucleotide repeat motif. Among these SSRs, 168 sequences were only fit into the criteria to design flanking primer pairs. A total of 30 randomly selected primer pairs were utilized for validation and genetic diversity study in 36 genotypes of
R. arboreum
collected from western Himalayan region. In aggregate, 26 SSR markers (86.66%) produced good and repeatable amplifications. Expected heterozygosity (
H
E
) ranged from 0.322 to 0.841 and observed heterozygosity (
H
O
) ranged from 0.327 to 1.000 and PIC value ranged from 0.008 to 0.786. These primers were able to distinguish the geographic differences of occurrence based on cluster analysis. These developed EST-SSRs can be useful in future population genetics analysis and micro-evolutionary studies in
Rhododendron
species.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>32124167</pmid><doi>10.1007/s11033-020-05300-1</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0001-7991-2878</orcidid></addata></record> |
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| subjects | Animal Anatomy Animal Biochemistry Biomedical and Life Sciences DNA, Plant - genetics Evolution Expressed sequence tags Expressed Sequence Tags - metabolism Flowers Genetic analysis Genetic diversity Genetic Markers - genetics Genetic Variation - genetics Genome, Plant - genetics Genotype Genotypes Heterozygosity Histology Life Sciences Microsatellite Repeats - genetics Morphology Nucleotide Motifs - genetics Original Article Polymorphism, Genetic - genetics Population genetics Rhododendron Rhododendron - genetics Sequence Analysis, DNA - methods Species diversity |
| title | Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum |
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