Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing
Taro [ Colocasia esculenta (L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-assoc...
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| Veröffentlicht in: | Genetic resources and crop evolution 2021-10, Vol.68 (7), p.2897-2905 |
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| creator | Dong, Weiqing He, Fanglian Wei, Shaolong Qiu, Zuyang Chen, Qi |
| description | Taro [
Colocasia esculenta
(L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-associated DNA sequencing (RAD-seq) was used to identify SSRs from a taro variety. PCR and capillary electrophoresis were applied to evaluate the efficiency of the primers. A phylogenetic tree was constructed to analyse the evolutionary relationship of 30 taro varieties. A total of 4438 SSRs (simple sequence repeats)were identified using RAD sequencing. A total of 3919 pairs of primers were designed based on the SSR data. Trinucleotide repeats (49.1%) were the most abundant type of SSR, while AT was the most common motif type (327 instances). Among 50 randomly selected primer pairs, 46 primer pairs were able to amplify the corresponding bands. A phylogenetic tree cluster analysis using SSR markers mainly supported the classification of taro varieties according to their phenotypes and ecological distribution. The SSR markers identified in this study provide a useful resource for taro genetic and germplasm research and genetic breeding. |
| doi_str_mv | 10.1007/s10722-021-01162-z |
| format | Article |
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Colocasia esculenta
(L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-associated DNA sequencing (RAD-seq) was used to identify SSRs from a taro variety. PCR and capillary electrophoresis were applied to evaluate the efficiency of the primers. A phylogenetic tree was constructed to analyse the evolutionary relationship of 30 taro varieties. A total of 4438 SSRs (simple sequence repeats)were identified using RAD sequencing. A total of 3919 pairs of primers were designed based on the SSR data. Trinucleotide repeats (49.1%) were the most abundant type of SSR, while AT was the most common motif type (327 instances). Among 50 randomly selected primer pairs, 46 primer pairs were able to amplify the corresponding bands. A phylogenetic tree cluster analysis using SSR markers mainly supported the classification of taro varieties according to their phenotypes and ecological distribution. The SSR markers identified in this study provide a useful resource for taro genetic and germplasm research and genetic breeding.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-021-01162-z</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Biomedical and Life Sciences ; Breeding ; Capillary electrophoresis ; Cluster analysis ; Colocasia esculenta ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Ecological distribution ; Electrophoresis ; Evolution ; Genetic diversity ; Genetic markers ; Germplasm ; Life Sciences ; Markers ; Phenotypes ; Phylogenetics ; Phylogeny ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant Systematics/Taxonomy/Biogeography ; Primers ; Research Article ; Resource management ; Simple sequence repeats ; Taro ; Trinucleotide repeats</subject><ispartof>Genetic resources and crop evolution, 2021-10, Vol.68 (7), p.2897-2905</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c270t-424de46c4cc0f84ccf6b1c63ac54b6b7b525168458af37c93684a3f8dcfa5dae3</cites><orcidid>0000-0002-8276-8181</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/s10722-021-01162-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-021-01162-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids></links><search><creatorcontrib>Dong, Weiqing</creatorcontrib><creatorcontrib>He, Fanglian</creatorcontrib><creatorcontrib>Wei, Shaolong</creatorcontrib><creatorcontrib>Qiu, Zuyang</creatorcontrib><creatorcontrib>Chen, Qi</creatorcontrib><title>Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>Taro [
Colocasia esculenta
(L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-associated DNA sequencing (RAD-seq) was used to identify SSRs from a taro variety. PCR and capillary electrophoresis were applied to evaluate the efficiency of the primers. A phylogenetic tree was constructed to analyse the evolutionary relationship of 30 taro varieties. A total of 4438 SSRs (simple sequence repeats)were identified using RAD sequencing. A total of 3919 pairs of primers were designed based on the SSR data. Trinucleotide repeats (49.1%) were the most abundant type of SSR, while AT was the most common motif type (327 instances). Among 50 randomly selected primer pairs, 46 primer pairs were able to amplify the corresponding bands. A phylogenetic tree cluster analysis using SSR markers mainly supported the classification of taro varieties according to their phenotypes and ecological distribution. The SSR markers identified in this study provide a useful resource for taro genetic and germplasm research and genetic breeding.</description><subject>Agriculture</subject><subject>Biomedical and Life Sciences</subject><subject>Breeding</subject><subject>Capillary electrophoresis</subject><subject>Cluster analysis</subject><subject>Colocasia esculenta</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Ecological distribution</subject><subject>Electrophoresis</subject><subject>Evolution</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Germplasm</subject><subject>Life Sciences</subject><subject>Markers</subject><subject>Phenotypes</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Primers</subject><subject>Research Article</subject><subject>Resource management</subject><subject>Simple sequence repeats</subject><subject>Taro</subject><subject>Trinucleotide repeats</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kE9LAzEQxYMoWKtfwFPAix5Sk-xms3ss9S8UhFZPIiGbTdrUmtQkPbSf3ugK3rzMDMN7b5gfAOcEjwjG_DoSzClFmBKECako2h-AAWG8QIzg5hAMcEMZauqqPAYnMa4wxg2v6gFwj512yRqrZLLeQek6qJYySJV0sPt-6Q2cz2fwQ4Z3HSK0DiYZPHyd-LVXMloJdVTbdQ6S8HI6uoJztfQpvcF2B2fjGxj151Y7Zd3iFBwZuY767LcPwcvd7fPkAU2f7h8n4ylSlOOESlp2uqxUqRQ2da6maomqCqlY2VYtbxllpKpLVktTcNUUeZaFqTtlJOukLobgos_dBJ9vxyRWfhtcPiko45TTJlPKKtqrVPAxBm3EJtj85U4QLL65ip6ryFzFD1exz6aiN8Usdgsd_qL_cX0BOY58Sw</recordid><startdate>20211001</startdate><enddate>20211001</enddate><creator>Dong, Weiqing</creator><creator>He, Fanglian</creator><creator>Wei, Shaolong</creator><creator>Qiu, Zuyang</creator><creator>Chen, Qi</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><orcidid>https://orcid.org/0000-0002-8276-8181</orcidid></search><sort><creationdate>20211001</creationdate><title>Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing</title><author>Dong, Weiqing ; He, Fanglian ; Wei, Shaolong ; Qiu, Zuyang ; Chen, Qi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c270t-424de46c4cc0f84ccf6b1c63ac54b6b7b525168458af37c93684a3f8dcfa5dae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Agriculture</topic><topic>Biomedical and Life Sciences</topic><topic>Breeding</topic><topic>Capillary electrophoresis</topic><topic>Cluster analysis</topic><topic>Colocasia esculenta</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Ecological distribution</topic><topic>Electrophoresis</topic><topic>Evolution</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Germplasm</topic><topic>Life Sciences</topic><topic>Markers</topic><topic>Phenotypes</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Primers</topic><topic>Research Article</topic><topic>Resource management</topic><topic>Simple sequence repeats</topic><topic>Taro</topic><topic>Trinucleotide repeats</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dong, Weiqing</creatorcontrib><creatorcontrib>He, Fanglian</creatorcontrib><creatorcontrib>Wei, Shaolong</creatorcontrib><creatorcontrib>Qiu, Zuyang</creatorcontrib><creatorcontrib>Chen, Qi</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</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>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Biological 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><jtitle>Genetic resources and crop evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dong, Weiqing</au><au>He, Fanglian</au><au>Wei, Shaolong</au><au>Qiu, Zuyang</au><au>Chen, Qi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2021-10-01</date><risdate>2021</risdate><volume>68</volume><issue>7</issue><spage>2897</spage><epage>2905</epage><pages>2897-2905</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>Taro [
Colocasia esculenta
(L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-associated DNA sequencing (RAD-seq) was used to identify SSRs from a taro variety. PCR and capillary electrophoresis were applied to evaluate the efficiency of the primers. A phylogenetic tree was constructed to analyse the evolutionary relationship of 30 taro varieties. A total of 4438 SSRs (simple sequence repeats)were identified using RAD sequencing. A total of 3919 pairs of primers were designed based on the SSR data. Trinucleotide repeats (49.1%) were the most abundant type of SSR, while AT was the most common motif type (327 instances). Among 50 randomly selected primer pairs, 46 primer pairs were able to amplify the corresponding bands. A phylogenetic tree cluster analysis using SSR markers mainly supported the classification of taro varieties according to their phenotypes and ecological distribution. The SSR markers identified in this study provide a useful resource for taro genetic and germplasm research and genetic breeding.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10722-021-01162-z</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-8276-8181</orcidid></addata></record> |
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| subjects | Agriculture Biomedical and Life Sciences Breeding Capillary electrophoresis Cluster analysis Colocasia esculenta Deoxyribonucleic acid DNA DNA sequencing Ecological distribution Electrophoresis Evolution Genetic diversity Genetic markers Germplasm Life Sciences Markers Phenotypes Phylogenetics Phylogeny Plant Genetics and Genomics Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Primers Research Article Resource management Simple sequence repeats Taro Trinucleotide repeats |
| title | Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing |
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