SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr
Simple sequence repeat (SSR) markers provide a reliable tool for the identification of accessions and the construction of genetic linkage maps because of their co-dominant inheritance. In the present study, we developed new SSR markers with next-generation sequencing using the Roche 454 GS FLX+ plat...
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| Veröffentlicht in: | Breeding Science 2020, Vol.70(3), pp.415-421 |
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| creator | Nashima, Kenji Hosaka, Fumiko Terakami, Shingo Kunihisa, Miyuki Nishitani, Chikako Moromizato, Chie Takeuchi, Makoto Shoda, Moriyuki Tarora, Kazuhiko Urasaki, Naoya Yamamoto, Toshiya |
| description | Simple sequence repeat (SSR) markers provide a reliable tool for the identification of accessions and the construction of genetic linkage maps because of their co-dominant inheritance. In the present study, we developed new SSR markers with next-generation sequencing using the Roche 454 GS FLX+ platform. Five hundred SSR primer sets were tested for the genetic identification of pineapple, including 100 each for the di-, tri-, tetra-, penta-, and hexa-nucleotide motif SSRs. In total, 160 SSR markers successfully amplified fragments and exhibited polymorphism among accessions. The SSR markers revealed the number of alleles per locus (ranging from 2 to 13), the expected heterozygosity (ranging from 0.041 to 0.823), and the observed heterozygosity (ranging from 0 to 0.875). A total of 117 SSR markers with tri- or greater nucleotide motifs were shown to be effective at facilitating accurate genotyping. Using the SSR markers, 25 accessions were distinguished genetically, with the exception of accessions ‘MD-2’ and ‘Yonekura’. The developed SSR markers could facilitate the establishment of efficient and accurate genetic identification systems and the construction of genetic linkage maps in the future. |
| doi_str_mv | 10.1270/jsbbs.19158 |
| format | Article |
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Five hundred SSR primer sets were tested for the genetic identification of pineapple, including 100 each for the di-, tri-, tetra-, penta-, and hexa-nucleotide motif SSRs. In total, 160 SSR markers successfully amplified fragments and exhibited polymorphism among accessions. The SSR markers revealed the number of alleles per locus (ranging from 2 to 13), the expected heterozygosity (ranging from 0.041 to 0.823), and the observed heterozygosity (ranging from 0 to 0.875). A total of 117 SSR markers with tri- or greater nucleotide motifs were shown to be effective at facilitating accurate genotyping. Using the SSR markers, 25 accessions were distinguished genetically, with the exception of accessions ‘MD-2’ and ‘Yonekura’. The developed SSR markers could facilitate the establishment of efficient and accurate genetic identification systems and the construction of genetic linkage maps in the future.</description><identifier>ISSN: 1344-7610</identifier><identifier>EISSN: 1347-3735</identifier><identifier>DOI: 10.1270/jsbbs.19158</identifier><identifier>PMID: 32714066</identifier><language>eng</language><publisher>Tokyo: Japanese Society of Breeding</publisher><subject>Ananas comosus ; Construction ; Gene mapping ; Genotyping ; Heredity ; Heterozygosity ; identification of accessions ; Markers ; Next-generation sequencing ; NGS ; Nucleotides ; Pineapples ; Polymorphism ; SSR marker</subject><ispartof>Breeding Science, 2020, Vol.70(3), pp.415-421</ispartof><rights>2020 by JAPANESE SOCIETY OF BREEDING</rights><rights>Copyright Japan Science and Technology Agency 2020</rights><rights>Copyright © 2020 by JAPANESE SOCIETY OF BREEDING 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c594t-c8b2856848900a6a572a756feacdad72a2c3466a1123ebc63a04b42d7b0666f23</citedby><cites>FETCH-LOGICAL-c594t-c8b2856848900a6a572a756feacdad72a2c3466a1123ebc63a04b42d7b0666f23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372017/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372017/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,1877,27901,27902,53766,53768</link.rule.ids></links><search><creatorcontrib>Nashima, Kenji</creatorcontrib><creatorcontrib>Hosaka, Fumiko</creatorcontrib><creatorcontrib>Terakami, Shingo</creatorcontrib><creatorcontrib>Kunihisa, Miyuki</creatorcontrib><creatorcontrib>Nishitani, Chikako</creatorcontrib><creatorcontrib>Moromizato, Chie</creatorcontrib><creatorcontrib>Takeuchi, Makoto</creatorcontrib><creatorcontrib>Shoda, Moriyuki</creatorcontrib><creatorcontrib>Tarora, Kazuhiko</creatorcontrib><creatorcontrib>Urasaki, Naoya</creatorcontrib><creatorcontrib>Yamamoto, Toshiya</creatorcontrib><title>SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr</title><title>Breeding Science</title><addtitle>Breeding Science</addtitle><description>Simple sequence repeat (SSR) markers provide a reliable tool for the identification of accessions and the construction of genetic linkage maps because of their co-dominant inheritance. In the present study, we developed new SSR markers with next-generation sequencing using the Roche 454 GS FLX+ platform. Five hundred SSR primer sets were tested for the genetic identification of pineapple, including 100 each for the di-, tri-, tetra-, penta-, and hexa-nucleotide motif SSRs. In total, 160 SSR markers successfully amplified fragments and exhibited polymorphism among accessions. The SSR markers revealed the number of alleles per locus (ranging from 2 to 13), the expected heterozygosity (ranging from 0.041 to 0.823), and the observed heterozygosity (ranging from 0 to 0.875). A total of 117 SSR markers with tri- or greater nucleotide motifs were shown to be effective at facilitating accurate genotyping. Using the SSR markers, 25 accessions were distinguished genetically, with the exception of accessions ‘MD-2’ and ‘Yonekura’. The developed SSR markers could facilitate the establishment of efficient and accurate genetic identification systems and the construction of genetic linkage maps in the future.</description><subject>Ananas comosus</subject><subject>Construction</subject><subject>Gene mapping</subject><subject>Genotyping</subject><subject>Heredity</subject><subject>Heterozygosity</subject><subject>identification of accessions</subject><subject>Markers</subject><subject>Next-generation sequencing</subject><subject>NGS</subject><subject>Nucleotides</subject><subject>Pineapples</subject><subject>Polymorphism</subject><subject>SSR marker</subject><issn>1344-7610</issn><issn>1347-3735</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNpdkUtrFEEUhRtRTIyu_AMFbhK0x3pXz0YYQhKFCQGj6-J29Z2eHnuq2qruYP69NQ8GdFMPzncP93CK4j2jM8YN_bxJdZ1mbM5U9aI4Z0KaUhihXu7fsjSa0bPiTUobSrmiUr0uzgQ3TFKtz4v14-N3soX4C2MiDT5hHwZsyJQ63xKPf8ayRY8Rxi54kvD3hN7tpBHd2oc-tM-k82ToPMIw9PiJLDx4SMSFbUhTIpfL2RW5xxjfFq9W0Cd8d7wvip-3Nz-uv5bLh7tv14tl6dRcjqWral4pXclqTiloUIaDUXqF4Bpo8oc7IbUGxrjA2mkBVNaSN6bOcfSKi4viy8F3mOotNg79GKG3Q-xyymcboLP_Kr5b2zY8WSMMp8xkg8ujQQw5bhrttksO-x48hilZLrlRXKpKZ_TDf-gmTNHneJlic6krbnYbfTxQLoaUIq5OyzBqdw3afYN232CmFwd6k0Zo8cRCHDvX45HNQ2J37GdOmltDtOjFXwUzpiI</recordid><startdate>20200101</startdate><enddate>20200101</enddate><creator>Nashima, Kenji</creator><creator>Hosaka, Fumiko</creator><creator>Terakami, Shingo</creator><creator>Kunihisa, Miyuki</creator><creator>Nishitani, Chikako</creator><creator>Moromizato, Chie</creator><creator>Takeuchi, Makoto</creator><creator>Shoda, Moriyuki</creator><creator>Tarora, Kazuhiko</creator><creator>Urasaki, Naoya</creator><creator>Yamamoto, Toshiya</creator><general>Japanese Society of Breeding</general><general>Japan Science and Technology Agency</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200101</creationdate><title>SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr</title><author>Nashima, Kenji ; Hosaka, Fumiko ; Terakami, Shingo ; Kunihisa, Miyuki ; Nishitani, Chikako ; Moromizato, Chie ; Takeuchi, Makoto ; Shoda, Moriyuki ; Tarora, Kazuhiko ; Urasaki, Naoya ; Yamamoto, Toshiya</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c594t-c8b2856848900a6a572a756feacdad72a2c3466a1123ebc63a04b42d7b0666f23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Ananas comosus</topic><topic>Construction</topic><topic>Gene mapping</topic><topic>Genotyping</topic><topic>Heredity</topic><topic>Heterozygosity</topic><topic>identification of accessions</topic><topic>Markers</topic><topic>Next-generation sequencing</topic><topic>NGS</topic><topic>Nucleotides</topic><topic>Pineapples</topic><topic>Polymorphism</topic><topic>SSR marker</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nashima, Kenji</creatorcontrib><creatorcontrib>Hosaka, Fumiko</creatorcontrib><creatorcontrib>Terakami, Shingo</creatorcontrib><creatorcontrib>Kunihisa, Miyuki</creatorcontrib><creatorcontrib>Nishitani, Chikako</creatorcontrib><creatorcontrib>Moromizato, Chie</creatorcontrib><creatorcontrib>Takeuchi, Makoto</creatorcontrib><creatorcontrib>Shoda, Moriyuki</creatorcontrib><creatorcontrib>Tarora, Kazuhiko</creatorcontrib><creatorcontrib>Urasaki, Naoya</creatorcontrib><creatorcontrib>Yamamoto, Toshiya</creatorcontrib><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Breeding Science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nashima, Kenji</au><au>Hosaka, Fumiko</au><au>Terakami, Shingo</au><au>Kunihisa, Miyuki</au><au>Nishitani, Chikako</au><au>Moromizato, Chie</au><au>Takeuchi, Makoto</au><au>Shoda, Moriyuki</au><au>Tarora, Kazuhiko</au><au>Urasaki, Naoya</au><au>Yamamoto, Toshiya</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) 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| subjects | Ananas comosus Construction Gene mapping Genotyping Heredity Heterozygosity identification of accessions Markers Next-generation sequencing NGS Nucleotides Pineapples Polymorphism SSR marker |
| title | SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr |
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