Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers
This study was conducted to understand variation patterns and establish the population structure in the wild rice species, Oryza officinalis , using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the Intern...
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| Veröffentlicht in: | Genetic resources and crop evolution 2017-04, Vol.64 (4), p.733-744 |
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| creator | Naredo, Maria Elizabeth Boncodin Mercado, Sheila Mae Quilloy Banaticla-Hilario, Maria Celeste Naynes Berdos, Myrricar Loren Rodriguez, Mario Alcantara McNally, Kenneth Lee Hamilton, Ruaraidh Sackville |
| description | This study was conducted to understand variation patterns and establish the population structure in the wild rice species,
Oryza officinalis
, using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the International Rice Research Institute. Morphological and microsatellite data detected a tendency for latitudinal divergence in
O. officinalis
and divided the accessions into (1) Malesian and (2) South and East Asian populations. Cluster and ordination analyses of morphological characters revealed that accessions from Malesia (Regions 1–6), Vietnam (Region 7), and Central Thailand (Region 8) showed short (16.19 ± 3.70 cm) and slender (1.53 ± 2.06 cm) flag leaves that are erect to almost horizontal, short panicles (25.19 ± 3.02 cm) and mainly purple internodes; and (3) accessions from Northern Thailand and Myanmar (Region 9), India (Region 10) and China (Region 11) characterized by long (29.57 ± 4.94 cm) and broad (2.18 ± 3.33 cm) flag leaves that are horizontal to drooping, long panicles (35.26 ± 2.63 cm) and green internodes. With 79.3 % of the SSR markers being polymorphic, molecular analyses detected an average of 5.31 alleles per marker with a total of 154 alleles. Differentiation was evident among the regions with FST = 0.2173, although there is an apparent loss of heterozygosity across regions indicated by an over-all positive FIS. Based on the results, issues related to the management of
O. officinalis
, specifically filling gaps in the collection and the formulation of seed multiplication practices are addressed. |
| doi_str_mv | 10.1007/s10722-016-0396-x |
| format | Article |
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Oryza officinalis
, using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the International Rice Research Institute. Morphological and microsatellite data detected a tendency for latitudinal divergence in
O. officinalis
and divided the accessions into (1) Malesian and (2) South and East Asian populations. Cluster and ordination analyses of morphological characters revealed that accessions from Malesia (Regions 1–6), Vietnam (Region 7), and Central Thailand (Region 8) showed short (16.19 ± 3.70 cm) and slender (1.53 ± 2.06 cm) flag leaves that are erect to almost horizontal, short panicles (25.19 ± 3.02 cm) and mainly purple internodes; and (3) accessions from Northern Thailand and Myanmar (Region 9), India (Region 10) and China (Region 11) characterized by long (29.57 ± 4.94 cm) and broad (2.18 ± 3.33 cm) flag leaves that are horizontal to drooping, long panicles (35.26 ± 2.63 cm) and green internodes. With 79.3 % of the SSR markers being polymorphic, molecular analyses detected an average of 5.31 alleles per marker with a total of 154 alleles. Differentiation was evident among the regions with FST = 0.2173, although there is an apparent loss of heterozygosity across regions indicated by an over-all positive FIS. Based on the results, issues related to the management of
O. officinalis
, specifically filling gaps in the collection and the formulation of seed multiplication practices are addressed.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-016-0396-x</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Alleles ; Biomedical and Life Sciences ; Data collection ; Differentiation ; Divergence ; Endemism ; Genetic diversity ; Genetic markers ; Heterozygosity ; Leaves ; Life Sciences ; Loss of heterozygosity ; Markers ; Microsatellites ; Morphology ; Multiplication ; Ordination ; Oryza officinalis ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant Systematics/Taxonomy/Biogeography ; Population structure ; Research Article ; Rice</subject><ispartof>Genetic resources and crop evolution, 2017-04, Vol.64 (4), p.733-744</ispartof><rights>Springer Science+Business Media Dordrecht 2016</rights><rights>Copyright Springer Science & Business Media 2017</rights><rights>Genetic Resources and Crop Evolution is a copyright of Springer, (2016). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c344t-6e5e2996511a63c26afdd226c74cbbbb1c8d5fcb79a3c8cd50a489327ecc04783</citedby><cites>FETCH-LOGICAL-c344t-6e5e2996511a63c26afdd226c74cbbbb1c8d5fcb79a3c8cd50a489327ecc04783</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/s10722-016-0396-x$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-016-0396-x$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Naredo, Maria Elizabeth Boncodin</creatorcontrib><creatorcontrib>Mercado, Sheila Mae Quilloy</creatorcontrib><creatorcontrib>Banaticla-Hilario, Maria Celeste Naynes</creatorcontrib><creatorcontrib>Berdos, Myrricar Loren</creatorcontrib><creatorcontrib>Rodriguez, Mario Alcantara</creatorcontrib><creatorcontrib>McNally, Kenneth Lee</creatorcontrib><creatorcontrib>Hamilton, Ruaraidh Sackville</creatorcontrib><title>Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>This study was conducted to understand variation patterns and establish the population structure in the wild rice species,
Oryza officinalis
, using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the International Rice Research Institute. Morphological and microsatellite data detected a tendency for latitudinal divergence in
O. officinalis
and divided the accessions into (1) Malesian and (2) South and East Asian populations. Cluster and ordination analyses of morphological characters revealed that accessions from Malesia (Regions 1–6), Vietnam (Region 7), and Central Thailand (Region 8) showed short (16.19 ± 3.70 cm) and slender (1.53 ± 2.06 cm) flag leaves that are erect to almost horizontal, short panicles (25.19 ± 3.02 cm) and mainly purple internodes; and (3) accessions from Northern Thailand and Myanmar (Region 9), India (Region 10) and China (Region 11) characterized by long (29.57 ± 4.94 cm) and broad (2.18 ± 3.33 cm) flag leaves that are horizontal to drooping, long panicles (35.26 ± 2.63 cm) and green internodes. With 79.3 % of the SSR markers being polymorphic, molecular analyses detected an average of 5.31 alleles per marker with a total of 154 alleles. Differentiation was evident among the regions with FST = 0.2173, although there is an apparent loss of heterozygosity across regions indicated by an over-all positive FIS. Based on the results, issues related to the management of
O. officinalis
, specifically filling gaps in the collection and the formulation of seed multiplication practices are addressed.</description><subject>Agriculture</subject><subject>Alleles</subject><subject>Biomedical and Life Sciences</subject><subject>Data collection</subject><subject>Differentiation</subject><subject>Divergence</subject><subject>Endemism</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Heterozygosity</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>Loss of heterozygosity</subject><subject>Markers</subject><subject>Microsatellites</subject><subject>Morphology</subject><subject>Multiplication</subject><subject>Ordination</subject><subject>Oryza officinalis</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Population structure</subject><subject>Research Article</subject><subject>Rice</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp9kc9qGzEQxkVJoY7bB-hNkPO6knb171hM4gQMvjTkKGTtrCtXXjmSbOw-Qx-6Mu6hl2QuMwy_b4aPD6GvlMwoIfJbpkQy1hAqGtJq0Zw-oAnlsm04JfoGTYhmvNFKdJ_Qbc5bQoiWQk3QnwWMULzDvT9Cyr6c8d6WAmnM2I8YTrjuDtjFEMAVH-s6DniVzr9tHQbv_GiDz_jFhjC74ItZnUvBCY5gA_R4fca7mPY_Y4gb72zAduzxzrsUsy0Qgi-Adzb9qt8_o4-DDRm-_OtT9Pxw_2P-2CxXi6f592Xj2q4rjQAOTGvBKbWidUzYoe8ZE052bl2LOtXzwa2ltq1TrufEdkq3TIJzpJOqnaK76919iq8HyMVs4yFVI9kwxrXkSjHyHkWVIrITreoqRa_UxVBOMJh98tXP2VBiLtGYazSmRmMu0ZhT1bCrJld23ED67_Kbor9_cJQF</recordid><startdate>20170401</startdate><enddate>20170401</enddate><creator>Naredo, Maria Elizabeth Boncodin</creator><creator>Mercado, Sheila Mae Quilloy</creator><creator>Banaticla-Hilario, Maria Celeste Naynes</creator><creator>Berdos, Myrricar Loren</creator><creator>Rodriguez, Mario Alcantara</creator><creator>McNally, Kenneth Lee</creator><creator>Hamilton, Ruaraidh Sackville</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>20170401</creationdate><title>Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers</title><author>Naredo, Maria Elizabeth Boncodin ; Mercado, Sheila Mae Quilloy ; Banaticla-Hilario, Maria Celeste Naynes ; Berdos, Myrricar Loren ; Rodriguez, Mario Alcantara ; McNally, Kenneth Lee ; Hamilton, Ruaraidh Sackville</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c344t-6e5e2996511a63c26afdd226c74cbbbb1c8d5fcb79a3c8cd50a489327ecc04783</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Agriculture</topic><topic>Alleles</topic><topic>Biomedical and Life Sciences</topic><topic>Data collection</topic><topic>Differentiation</topic><topic>Divergence</topic><topic>Endemism</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Heterozygosity</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>Loss of heterozygosity</topic><topic>Markers</topic><topic>Microsatellites</topic><topic>Morphology</topic><topic>Multiplication</topic><topic>Ordination</topic><topic>Oryza officinalis</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Population structure</topic><topic>Research Article</topic><topic>Rice</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Naredo, Maria Elizabeth Boncodin</creatorcontrib><creatorcontrib>Mercado, Sheila Mae Quilloy</creatorcontrib><creatorcontrib>Banaticla-Hilario, Maria Celeste Naynes</creatorcontrib><creatorcontrib>Berdos, Myrricar Loren</creatorcontrib><creatorcontrib>Rodriguez, Mario Alcantara</creatorcontrib><creatorcontrib>McNally, Kenneth Lee</creatorcontrib><creatorcontrib>Hamilton, Ruaraidh Sackville</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>Naredo, Maria Elizabeth Boncodin</au><au>Mercado, Sheila Mae Quilloy</au><au>Banaticla-Hilario, Maria Celeste Naynes</au><au>Berdos, Myrricar Loren</au><au>Rodriguez, Mario Alcantara</au><au>McNally, Kenneth Lee</au><au>Hamilton, Ruaraidh Sackville</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2017-04-01</date><risdate>2017</risdate><volume>64</volume><issue>4</issue><spage>733</spage><epage>744</epage><pages>733-744</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>This study was conducted to understand variation patterns and establish the population structure in the wild rice species,
Oryza officinalis
, using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the International Rice Research Institute. Morphological and microsatellite data detected a tendency for latitudinal divergence in
O. officinalis
and divided the accessions into (1) Malesian and (2) South and East Asian populations. Cluster and ordination analyses of morphological characters revealed that accessions from Malesia (Regions 1–6), Vietnam (Region 7), and Central Thailand (Region 8) showed short (16.19 ± 3.70 cm) and slender (1.53 ± 2.06 cm) flag leaves that are erect to almost horizontal, short panicles (25.19 ± 3.02 cm) and mainly purple internodes; and (3) accessions from Northern Thailand and Myanmar (Region 9), India (Region 10) and China (Region 11) characterized by long (29.57 ± 4.94 cm) and broad (2.18 ± 3.33 cm) flag leaves that are horizontal to drooping, long panicles (35.26 ± 2.63 cm) and green internodes. With 79.3 % of the SSR markers being polymorphic, molecular analyses detected an average of 5.31 alleles per marker with a total of 154 alleles. Differentiation was evident among the regions with FST = 0.2173, although there is an apparent loss of heterozygosity across regions indicated by an over-all positive FIS. Based on the results, issues related to the management of
O. officinalis
, specifically filling gaps in the collection and the formulation of seed multiplication practices are addressed.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10722-016-0396-x</doi><tpages>12</tpages></addata></record> |
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| source | Springer Nature - Complete Springer Journals |
| subjects | Agriculture Alleles Biomedical and Life Sciences Data collection Differentiation Divergence Endemism Genetic diversity Genetic markers Heterozygosity Leaves Life Sciences Loss of heterozygosity Markers Microsatellites Morphology Multiplication Ordination Oryza officinalis Plant Genetics and Genomics Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Population structure Research Article Rice |
| title | Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers |
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