Diversity and differentiation of Oryza sativa and O. rufipogon in Indonesia
Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon . Accessions of O. sativa in this stu...
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| Veröffentlicht in: | Genetic resources and crop evolution 2017, Vol.64 (1), p.41-54 |
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| creator | Muhamad, Kadapi Ebana, Kaworu Fukuoka, Shuichi Okuno, Kazutoshi |
| description | Analysis of the genetic structure of Indonesian
Oryza sativa
and
O. rufipogon
using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that
O. sativa
in Indonesia is separated from
O. rufipogon
. Accessions of
O. sativa
in this study were differentiated into two major groups,
indica
and tropical
japonica,
excluding some varieties. SSR and SNP markers revealed the high value of differentiation (
F
ST
) and genetic distance (
D
) between
indica
and tropical
japonica
and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between
indica
and tropical
japonica
. Interestingly, genetic diversity (
H
) in
O. rufipogon
was lower than that in
O. sativa
, however
H
in
O. rufipogon
was the highest and
H
in tropical
japonica
was the lowest when
O. sativa
was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (
Nm
) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within
O. sativa
as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers. |
| doi_str_mv | 10.1007/s10722-015-0331-6 |
| format | Article |
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Oryza sativa
and
O. rufipogon
using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that
O. sativa
in Indonesia is separated from
O. rufipogon
. Accessions of
O. sativa
in this study were differentiated into two major groups,
indica
and tropical
japonica,
excluding some varieties. SSR and SNP markers revealed the high value of differentiation (
F
ST
) and genetic distance (
D
) between
indica
and tropical
japonica
and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between
indica
and tropical
japonica
. Interestingly, genetic diversity (
H
) in
O. rufipogon
was lower than that in
O. sativa
, however
H
in
O. rufipogon
was the highest and
H
in tropical
japonica
was the lowest when
O. sativa
was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (
Nm
) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within
O. sativa
as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-015-0331-6</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Biomedical and Life Sciences ; Differentiation ; Gene flow ; Genetic distance ; Genetic diversity ; Germplasm ; Inbreeding ; Life Sciences ; Loci ; Markers ; Nucleotides ; Oryza rufipogon ; Oryza sativa ; Oryza sativa indica ; Oryza sativa japonica ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant Systematics/Taxonomy/Biogeography ; Polymorphism ; Research Article ; Single-nucleotide polymorphism ; Species</subject><ispartof>Genetic resources and crop evolution, 2017, Vol.64 (1), p.41-54</ispartof><rights>Springer Science+Business Media Dordrecht 2015</rights><rights>Copyright Springer Science & Business Media 2017</rights><rights>Genetic Resources and Crop Evolution is a copyright of Springer, (2015). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c296t-26caae9af80a62588b633082e3ff29b351217f5b03bf02418790cb4a676a2eb83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10722-015-0331-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-015-0331-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids></links><search><creatorcontrib>Muhamad, Kadapi</creatorcontrib><creatorcontrib>Ebana, Kaworu</creatorcontrib><creatorcontrib>Fukuoka, Shuichi</creatorcontrib><creatorcontrib>Okuno, Kazutoshi</creatorcontrib><title>Diversity and differentiation of Oryza sativa and O. rufipogon in Indonesia</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>Analysis of the genetic structure of Indonesian
Oryza sativa
and
O. rufipogon
using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that
O. sativa
in Indonesia is separated from
O. rufipogon
. Accessions of
O. sativa
in this study were differentiated into two major groups,
indica
and tropical
japonica,
excluding some varieties. SSR and SNP markers revealed the high value of differentiation (
F
ST
) and genetic distance (
D
) between
indica
and tropical
japonica
and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between
indica
and tropical
japonica
. Interestingly, genetic diversity (
H
) in
O. rufipogon
was lower than that in
O. sativa
, however
H
in
O. rufipogon
was the highest and
H
in tropical
japonica
was the lowest when
O. sativa
was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (
Nm
) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within
O. sativa
as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.</description><subject>Agriculture</subject><subject>Biomedical and Life Sciences</subject><subject>Differentiation</subject><subject>Gene flow</subject><subject>Genetic distance</subject><subject>Genetic diversity</subject><subject>Germplasm</subject><subject>Inbreeding</subject><subject>Life Sciences</subject><subject>Loci</subject><subject>Markers</subject><subject>Nucleotides</subject><subject>Oryza rufipogon</subject><subject>Oryza sativa</subject><subject>Oryza sativa indica</subject><subject>Oryza sativa japonica</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Polymorphism</subject><subject>Research Article</subject><subject>Single-nucleotide polymorphism</subject><subject>Species</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kEtLAzEUhYMoWKs_wN2A69Sbm8lrKfVVLHSj65CZJiVFMzWZFuqvd7Qu3OjqcuA758JHyCWDCQNQ14WBQqTABAXOGZVHZMSE4lQwMMdkBAYFNVrWp-SslDUAGCX1iDzdxp3PJfb7yqVltYwh-OxTH10fu1R1oVrk_YerypB37ptZTKq8DXHTrQYgpmqWll3yJbpzchLca_EXP3dMXu7vnqePdL54mE1v5rRFI3uKsnXOGxc0OIlC60ZyDho9DwFNwwVDpoJogDcBsGZaGWib2kklHfpG8zG5Ouxucve-9aW3626b0_DSIgqjBCrN_qOY1qCMqQc_Y8IOVJu7UrIPdpPjm8t7y8B-mbUHs3Ywa7_MWjl08NApA5tWPv9a_rP0CUCZeYA</recordid><startdate>2017</startdate><enddate>2017</enddate><creator>Muhamad, Kadapi</creator><creator>Ebana, Kaworu</creator><creator>Fukuoka, Shuichi</creator><creator>Okuno, Kazutoshi</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></search><sort><creationdate>2017</creationdate><title>Diversity and differentiation of Oryza sativa and O. rufipogon in Indonesia</title><author>Muhamad, Kadapi ; Ebana, Kaworu ; Fukuoka, Shuichi ; Okuno, Kazutoshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c296t-26caae9af80a62588b633082e3ff29b351217f5b03bf02418790cb4a676a2eb83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Agriculture</topic><topic>Biomedical and Life Sciences</topic><topic>Differentiation</topic><topic>Gene flow</topic><topic>Genetic distance</topic><topic>Genetic diversity</topic><topic>Germplasm</topic><topic>Inbreeding</topic><topic>Life Sciences</topic><topic>Loci</topic><topic>Markers</topic><topic>Nucleotides</topic><topic>Oryza rufipogon</topic><topic>Oryza sativa</topic><topic>Oryza sativa indica</topic><topic>Oryza sativa japonica</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Polymorphism</topic><topic>Research Article</topic><topic>Single-nucleotide polymorphism</topic><topic>Species</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Muhamad, Kadapi</creatorcontrib><creatorcontrib>Ebana, Kaworu</creatorcontrib><creatorcontrib>Fukuoka, Shuichi</creatorcontrib><creatorcontrib>Okuno, Kazutoshi</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>Muhamad, Kadapi</au><au>Ebana, Kaworu</au><au>Fukuoka, Shuichi</au><au>Okuno, Kazutoshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Diversity and differentiation of Oryza sativa and O. rufipogon in Indonesia</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2017</date><risdate>2017</risdate><volume>64</volume><issue>1</issue><spage>41</spage><epage>54</epage><pages>41-54</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>Analysis of the genetic structure of Indonesian
Oryza sativa
and
O. rufipogon
using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that
O. sativa
in Indonesia is separated from
O. rufipogon
. Accessions of
O. sativa
in this study were differentiated into two major groups,
indica
and tropical
japonica,
excluding some varieties. SSR and SNP markers revealed the high value of differentiation (
F
ST
) and genetic distance (
D
) between
indica
and tropical
japonica
and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between
indica
and tropical
japonica
. Interestingly, genetic diversity (
H
) in
O. rufipogon
was lower than that in
O. sativa
, however
H
in
O. rufipogon
was the highest and
H
in tropical
japonica
was the lowest when
O. sativa
was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (
Nm
) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within
O. sativa
as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10722-015-0331-6</doi><tpages>14</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0925-9864 |
| ispartof | Genetic resources and crop evolution, 2017, Vol.64 (1), p.41-54 |
| issn | 0925-9864 1573-5109 |
| language | eng |
| recordid | cdi_proquest_journals_2259752781 |
| source | SpringerLink Journals - AutoHoldings |
| subjects | Agriculture Biomedical and Life Sciences Differentiation Gene flow Genetic distance Genetic diversity Germplasm Inbreeding Life Sciences Loci Markers Nucleotides Oryza rufipogon Oryza sativa Oryza sativa indica Oryza sativa japonica Plant Genetics and Genomics Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Polymorphism Research Article Single-nucleotide polymorphism Species |
| title | Diversity and differentiation of Oryza sativa and O. rufipogon in Indonesia |
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