Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers
The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucle...
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| Veröffentlicht in: | Euphytica 2021-07, Vol.217 (7), Article 135 |
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| description | The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the
Perilla
crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. In total, 130 alleles were detected segregating in nine
Perilla
accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of
Perilla
crop, 40 individuals from an F
2
population of
Perilla
were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F
2
population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. Therefore, the new
Perilla
SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for
Perilla
crop breeding programs, and allowing
Perilla
breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs. |
| doi_str_mv | 10.1007/s10681-021-02867-z |
| format | Article |
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Perilla
crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. In total, 130 alleles were detected segregating in nine
Perilla
accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of
Perilla
crop, 40 individuals from an F
2
population of
Perilla
were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F
2
population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. Therefore, the new
Perilla
SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for
Perilla
crop breeding programs, and allowing
Perilla
breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.</description><identifier>ISSN: 0014-2336</identifier><identifier>EISSN: 1573-5060</identifier><identifier>DOI: 10.1007/s10681-021-02867-z</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Alleles ; Association analysis ; Biomarkers ; Biomedical and Life Sciences ; Biotechnology ; Corn ; Crops ; Gene expression ; Gene mapping ; Gene sequencing ; Genetic diversity ; Leaves ; Life Sciences ; Marker-assisted selection ; Morphology ; Physical characteristics ; Plant breeding ; Plant Genetics and Genomics ; Plant Pathology ; Plant Physiology ; Plant reproduction ; Plant Sciences ; Plants ; Population ; Quantitative trait loci ; Ribonucleic acid ; RNA ; Seeds ; Transcription ; Transcriptomes ; Trinucleotide repeats</subject><ispartof>Euphytica, 2021-07, Vol.217 (7), Article 135</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><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c278z-bace8461ff3f2421162448a625754ccaf7dcdabfab3513a0f61fb3a400b292a13</citedby><cites>FETCH-LOGICAL-c278z-bace8461ff3f2421162448a625754ccaf7dcdabfab3513a0f61fb3a400b292a13</cites><orcidid>0000-0002-2769-0799</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/s10681-021-02867-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10681-021-02867-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Kim, Ju Yeon</creatorcontrib><creatorcontrib>Sa, Kyu Jin</creatorcontrib><creatorcontrib>Ha, Ye Ju</creatorcontrib><creatorcontrib>Lee, Ju Kyong</creatorcontrib><title>Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers</title><title>Euphytica</title><addtitle>Euphytica</addtitle><description>The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the
Perilla
crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. In total, 130 alleles were detected segregating in nine
Perilla
accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of
Perilla
crop, 40 individuals from an F
2
population of
Perilla
were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F
2
population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. Therefore, the new
Perilla
SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for
Perilla
crop breeding programs, and allowing
Perilla
breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.</description><subject>Alleles</subject><subject>Association analysis</subject><subject>Biomarkers</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Corn</subject><subject>Crops</subject><subject>Gene expression</subject><subject>Gene mapping</subject><subject>Gene sequencing</subject><subject>Genetic diversity</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>Marker-assisted selection</subject><subject>Morphology</subject><subject>Physical characteristics</subject><subject>Plant breeding</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Pathology</subject><subject>Plant Physiology</subject><subject>Plant reproduction</subject><subject>Plant Sciences</subject><subject>Plants</subject><subject>Population</subject><subject>Quantitative trait loci</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Seeds</subject><subject>Transcription</subject><subject>Transcriptomes</subject><subject>Trinucleotide repeats</subject><issn>0014-2336</issn><issn>1573-5060</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp9UMtOwzAQtBBIlMIPcLLEBQ4pazuvHlFFC1IlEIWz5Th2SQl2sJMi-hl8MW7D48ZhtdrdmdndQeiUwIgAZJeeQJqTCOg28jSLNntoQJKMRQmksI8GACSOKGPpITryfgUA4yyBAfqcKaPaSuK1cJVoK2uwMCUW3lv5Xb-KpqnMElcGt88KTylubNPV_dDqXfNeuaquBZbONvj8p9Kua5WXyng8H13gzm9ljHrHpVqr2jaq_CUuFg9hkXtRzh-jAy1qr06-8xA9Ta8fJzfR_G52O7maR5Jm-SYqhFR5nBKtmaYxJSSlcZyLlCZZEkspdFbKUhRaFCwhTIAO0IKJGKCgYyoIG6KzXrdx9q1TvuUr2zkTVnKasAwgJXkeULRHhde8d0rzxlXh0g9OgG-95733PHjPd97zTSCxnuQD2CyV-5P-h_UFZjyJbQ</recordid><startdate>20210701</startdate><enddate>20210701</enddate><creator>Kim, Ju Yeon</creator><creator>Sa, Kyu Jin</creator><creator>Ha, Ye Ju</creator><creator>Lee, Ju Kyong</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7SS</scope><scope>7T7</scope><scope>7TM</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>M0K</scope><scope>M2P</scope><scope>M7N</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><orcidid>https://orcid.org/0000-0002-2769-0799</orcidid></search><sort><creationdate>20210701</creationdate><title>Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers</title><author>Kim, Ju Yeon ; Sa, Kyu Jin ; Ha, Ye Ju ; Lee, Ju Kyong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c278z-bace8461ff3f2421162448a625754ccaf7dcdabfab3513a0f61fb3a400b292a13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Alleles</topic><topic>Association analysis</topic><topic>Biomarkers</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Corn</topic><topic>Crops</topic><topic>Gene expression</topic><topic>Gene mapping</topic><topic>Gene sequencing</topic><topic>Genetic diversity</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>Marker-assisted selection</topic><topic>Morphology</topic><topic>Physical characteristics</topic><topic>Plant breeding</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Pathology</topic><topic>Plant Physiology</topic><topic>Plant reproduction</topic><topic>Plant Sciences</topic><topic>Plants</topic><topic>Population</topic><topic>Quantitative trait loci</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Seeds</topic><topic>Transcription</topic><topic>Transcriptomes</topic><topic>Trinucleotide repeats</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kim, Ju Yeon</creatorcontrib><creatorcontrib>Sa, Kyu Jin</creatorcontrib><creatorcontrib>Ha, Ye Ju</creatorcontrib><creatorcontrib>Lee, Ju Kyong</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>Agricultural Science Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</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>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><jtitle>Euphytica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kim, Ju Yeon</au><au>Sa, Kyu Jin</au><au>Ha, Ye Ju</au><au>Lee, Ju Kyong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers</atitle><jtitle>Euphytica</jtitle><stitle>Euphytica</stitle><date>2021-07-01</date><risdate>2021</risdate><volume>217</volume><issue>7</issue><artnum>135</artnum><issn>0014-2336</issn><eissn>1573-5060</eissn><abstract>The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the
Perilla
crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. In total, 130 alleles were detected segregating in nine
Perilla
accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of
Perilla
crop, 40 individuals from an F
2
population of
Perilla
were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F
2
population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. Therefore, the new
Perilla
SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for
Perilla
crop breeding programs, and allowing
Perilla
breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10681-021-02867-z</doi><orcidid>https://orcid.org/0000-0002-2769-0799</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Euphytica, 2021-07, Vol.217 (7), Article 135 |
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| language | eng |
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| source | Springer Nature - Complete Springer Journals |
| subjects | Alleles Association analysis Biomarkers Biomedical and Life Sciences Biotechnology Corn Crops Gene expression Gene mapping Gene sequencing Genetic diversity Leaves Life Sciences Marker-assisted selection Morphology Physical characteristics Plant breeding Plant Genetics and Genomics Plant Pathology Plant Physiology Plant reproduction Plant Sciences Plants Population Quantitative trait loci Ribonucleic acid RNA Seeds Transcription Transcriptomes Trinucleotide repeats |
| title | Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers |
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