Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.)
To get rice varieties with specific germination activity (GA) suitable for production and breeding, the genetic characteristics of GA were revealed by measuring the seed weight (SW), germination rate (GR), coleoptile length (CL) and radicle length (RL) of seeds at 5, 6 and 7 weeks after heading with...
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| Veröffentlicht in: | Genetic resources and crop evolution 2023-03, Vol.70 (3), p.1007-1022 |
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| creator | Li, Pen Liu, Hualong Wen, Haoran Yang, Luomiao Chen, Ziqi Zheng, Hongliang Xin, Wei Zhang, Dezhuang Wang, Jingguo Zou, Detang |
| description | To get rice varieties with specific germination activity (GA) suitable for production and breeding, the genetic characteristics of GA were revealed by measuring the seed weight (SW), germination rate (GR), coleoptile length (CL) and radicle length (RL) of seeds at 5, 6 and 7 weeks after heading with the recombinant inbred line (RIL) as the material. A total of 10 unconditional QTLs were detected, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, 10 unconditional QTLs were detected at three different developmental stages, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, qGR-7,
qSW7-1
, qSW7-2,
qCL7-1
, and
qRL3-1
played an important role in seed activity. In addition, a total of 295 epistatic QTLs were detected, of which 4 were located in the qRL3-1 and qGR-7 intervals. Three RIL lines (RIL18, RIL106, and RIL155) were further screened through genotype and phenotype identification. These three lines contain 3–6 additive QTLs, which can aggregate 6–8 excellent alleles, and have an important theoretical value of resistance to pre-harvest sprouting breeding. In addition, a total of 41 Mqtls was detected by meta-analysis, of which 15 Mqtls had physical intervals less than 1.0 Mb. And
qSW2-2
,
qSW2-3
,
qSW2-1
,
qCL2-1
, and
qRL3-1
were located in the
Mqtl2-2
,
Mqtl2-4
,
Mqtl3-3
, and
Mqtl4-2
intervals. A further prediction of candidate genes, expression level determination, and variation analysis showed that
Os01g0813100
was a candidate gene affecting seed activity. |
| doi_str_mv | 10.1007/s10722-022-01484-6 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_2777941460</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2777941460</sourcerecordid><originalsourceid>FETCH-LOGICAL-c270t-6f4c60626984b5378903a61d91ea6e6e62d0731698d15449ad2ae454e247fff23</originalsourceid><addsrcrecordid>eNp9kE9LxDAQxYMouK5-AU8BL3qITtI0aY6y-A8Ki7CeS2ynmmXbrkm3UD-9KRW8yTAM4b3fgzxCLjnccgB9FzhoIRhMy2UmmToiC57qhKUczDFZgBEpM5mSp-QshC0AGK2yBQmrrtl7_MQ2uAHpB7bYu5La1u7G4AL1OKDdBRoQq6j6xrW2d11Lbdm7wfUj87izfRRfN3nEKtpgb9n0cC31rkR6vfbjt6UhcoOl-e3NOTmpYyZe_N4leXt82KyeWb5-elnd56wUGnqmalkqUEKZTL6nic4MJFbxynC0CuOICnTCo1zxVEpjK2FRphKF1HVdi2RJrubcve--Dhj6YtsdfPxZKITW2kguFUSXmF2l70LwWBd77xrrx4JDMZVbzOUWMO1UbqEilMxQiOY29vIX_Q_1A_yNfA8</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2777941460</pqid></control><display><type>article</type><title>Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.)</title><source>SpringerLink Journals - AutoHoldings</source><creator>Li, Pen ; Liu, Hualong ; Wen, Haoran ; Yang, Luomiao ; Chen, Ziqi ; Zheng, Hongliang ; Xin, Wei ; Zhang, Dezhuang ; Wang, Jingguo ; Zou, Detang</creator><creatorcontrib>Li, Pen ; Liu, Hualong ; Wen, Haoran ; Yang, Luomiao ; Chen, Ziqi ; Zheng, Hongliang ; Xin, Wei ; Zhang, Dezhuang ; Wang, Jingguo ; Zou, Detang</creatorcontrib><description>To get rice varieties with specific germination activity (GA) suitable for production and breeding, the genetic characteristics of GA were revealed by measuring the seed weight (SW), germination rate (GR), coleoptile length (CL) and radicle length (RL) of seeds at 5, 6 and 7 weeks after heading with the recombinant inbred line (RIL) as the material. A total of 10 unconditional QTLs were detected, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, 10 unconditional QTLs were detected at three different developmental stages, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, qGR-7,
qSW7-1
, qSW7-2,
qCL7-1
, and
qRL3-1
played an important role in seed activity. In addition, a total of 295 epistatic QTLs were detected, of which 4 were located in the qRL3-1 and qGR-7 intervals. Three RIL lines (RIL18, RIL106, and RIL155) were further screened through genotype and phenotype identification. These three lines contain 3–6 additive QTLs, which can aggregate 6–8 excellent alleles, and have an important theoretical value of resistance to pre-harvest sprouting breeding. In addition, a total of 41 Mqtls was detected by meta-analysis, of which 15 Mqtls had physical intervals less than 1.0 Mb. And
qSW2-2
,
qSW2-3
,
qSW2-1
,
qCL2-1
, and
qRL3-1
were located in the
Mqtl2-2
,
Mqtl2-4
,
Mqtl3-3
, and
Mqtl4-2
intervals. A further prediction of candidate genes, expression level determination, and variation analysis showed that
Os01g0813100
was a candidate gene affecting seed activity.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-022-01484-6</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Biomedical and Life Sciences ; Coleoptile ; Developmental stages ; Epistasis ; Gene expression ; Genes ; Genetic analysis ; Genotypes ; Germination ; Harvest ; Inbreeding ; Intervals ; Life Sciences ; Meta-analysis ; Monte Carlo simulation ; Oryza sativa ; Phenotypes ; Phenotypic variations ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant Systematics/Taxonomy/Biogeography ; Quantitative trait loci ; Research Article ; Rice ; Seed germination ; Seeds</subject><ispartof>Genetic resources and crop evolution, 2023-03, Vol.70 (3), p.1007-1022</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2022. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c270t-6f4c60626984b5378903a61d91ea6e6e62d0731698d15449ad2ae454e247fff23</cites><orcidid>0000-0003-0835-0753</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/s10722-022-01484-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-022-01484-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27922,27923,41486,42555,51317</link.rule.ids></links><search><creatorcontrib>Li, Pen</creatorcontrib><creatorcontrib>Liu, Hualong</creatorcontrib><creatorcontrib>Wen, Haoran</creatorcontrib><creatorcontrib>Yang, Luomiao</creatorcontrib><creatorcontrib>Chen, Ziqi</creatorcontrib><creatorcontrib>Zheng, Hongliang</creatorcontrib><creatorcontrib>Xin, Wei</creatorcontrib><creatorcontrib>Zhang, Dezhuang</creatorcontrib><creatorcontrib>Wang, Jingguo</creatorcontrib><creatorcontrib>Zou, Detang</creatorcontrib><title>Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.)</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>To get rice varieties with specific germination activity (GA) suitable for production and breeding, the genetic characteristics of GA were revealed by measuring the seed weight (SW), germination rate (GR), coleoptile length (CL) and radicle length (RL) of seeds at 5, 6 and 7 weeks after heading with the recombinant inbred line (RIL) as the material. A total of 10 unconditional QTLs were detected, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, 10 unconditional QTLs were detected at three different developmental stages, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, qGR-7,
qSW7-1
, qSW7-2,
qCL7-1
, and
qRL3-1
played an important role in seed activity. In addition, a total of 295 epistatic QTLs were detected, of which 4 were located in the qRL3-1 and qGR-7 intervals. Three RIL lines (RIL18, RIL106, and RIL155) were further screened through genotype and phenotype identification. These three lines contain 3–6 additive QTLs, which can aggregate 6–8 excellent alleles, and have an important theoretical value of resistance to pre-harvest sprouting breeding. In addition, a total of 41 Mqtls was detected by meta-analysis, of which 15 Mqtls had physical intervals less than 1.0 Mb. And
qSW2-2
,
qSW2-3
,
qSW2-1
,
qCL2-1
, and
qRL3-1
were located in the
Mqtl2-2
,
Mqtl2-4
,
Mqtl3-3
, and
Mqtl4-2
intervals. A further prediction of candidate genes, expression level determination, and variation analysis showed that
Os01g0813100
was a candidate gene affecting seed activity.</description><subject>Agriculture</subject><subject>Biomedical and Life Sciences</subject><subject>Coleoptile</subject><subject>Developmental stages</subject><subject>Epistasis</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic analysis</subject><subject>Genotypes</subject><subject>Germination</subject><subject>Harvest</subject><subject>Inbreeding</subject><subject>Intervals</subject><subject>Life Sciences</subject><subject>Meta-analysis</subject><subject>Monte Carlo simulation</subject><subject>Oryza sativa</subject><subject>Phenotypes</subject><subject>Phenotypic variations</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Quantitative trait loci</subject><subject>Research Article</subject><subject>Rice</subject><subject>Seed germination</subject><subject>Seeds</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kE9LxDAQxYMouK5-AU8BL3qITtI0aY6y-A8Ki7CeS2ynmmXbrkm3UD-9KRW8yTAM4b3fgzxCLjnccgB9FzhoIRhMy2UmmToiC57qhKUczDFZgBEpM5mSp-QshC0AGK2yBQmrrtl7_MQ2uAHpB7bYu5La1u7G4AL1OKDdBRoQq6j6xrW2d11Lbdm7wfUj87izfRRfN3nEKtpgb9n0cC31rkR6vfbjt6UhcoOl-e3NOTmpYyZe_N4leXt82KyeWb5-elnd56wUGnqmalkqUEKZTL6nic4MJFbxynC0CuOICnTCo1zxVEpjK2FRphKF1HVdi2RJrubcve--Dhj6YtsdfPxZKITW2kguFUSXmF2l70LwWBd77xrrx4JDMZVbzOUWMO1UbqEilMxQiOY29vIX_Q_1A_yNfA8</recordid><startdate>20230301</startdate><enddate>20230301</enddate><creator>Li, Pen</creator><creator>Liu, Hualong</creator><creator>Wen, Haoran</creator><creator>Yang, Luomiao</creator><creator>Chen, Ziqi</creator><creator>Zheng, Hongliang</creator><creator>Xin, Wei</creator><creator>Zhang, Dezhuang</creator><creator>Wang, Jingguo</creator><creator>Zou, Detang</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/0000-0003-0835-0753</orcidid></search><sort><creationdate>20230301</creationdate><title>Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.)</title><author>Li, Pen ; Liu, Hualong ; Wen, Haoran ; Yang, Luomiao ; Chen, Ziqi ; Zheng, Hongliang ; Xin, Wei ; Zhang, Dezhuang ; Wang, Jingguo ; Zou, Detang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c270t-6f4c60626984b5378903a61d91ea6e6e62d0731698d15449ad2ae454e247fff23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Agriculture</topic><topic>Biomedical and Life Sciences</topic><topic>Coleoptile</topic><topic>Developmental stages</topic><topic>Epistasis</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genetic analysis</topic><topic>Genotypes</topic><topic>Germination</topic><topic>Harvest</topic><topic>Inbreeding</topic><topic>Intervals</topic><topic>Life Sciences</topic><topic>Meta-analysis</topic><topic>Monte Carlo simulation</topic><topic>Oryza sativa</topic><topic>Phenotypes</topic><topic>Phenotypic variations</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Quantitative trait loci</topic><topic>Research Article</topic><topic>Rice</topic><topic>Seed germination</topic><topic>Seeds</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Pen</creatorcontrib><creatorcontrib>Liu, Hualong</creatorcontrib><creatorcontrib>Wen, Haoran</creatorcontrib><creatorcontrib>Yang, Luomiao</creatorcontrib><creatorcontrib>Chen, Ziqi</creatorcontrib><creatorcontrib>Zheng, Hongliang</creatorcontrib><creatorcontrib>Xin, Wei</creatorcontrib><creatorcontrib>Zhang, Dezhuang</creatorcontrib><creatorcontrib>Wang, Jingguo</creatorcontrib><creatorcontrib>Zou, Detang</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>Li, Pen</au><au>Liu, Hualong</au><au>Wen, Haoran</au><au>Yang, Luomiao</au><au>Chen, Ziqi</au><au>Zheng, Hongliang</au><au>Xin, Wei</au><au>Zhang, Dezhuang</au><au>Wang, Jingguo</au><au>Zou, Detang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.)</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2023-03-01</date><risdate>2023</risdate><volume>70</volume><issue>3</issue><spage>1007</spage><epage>1022</epage><pages>1007-1022</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>To get rice varieties with specific germination activity (GA) suitable for production and breeding, the genetic characteristics of GA were revealed by measuring the seed weight (SW), germination rate (GR), coleoptile length (CL) and radicle length (RL) of seeds at 5, 6 and 7 weeks after heading with the recombinant inbred line (RIL) as the material. A total of 10 unconditional QTLs were detected, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, 10 unconditional QTLs were detected at three different developmental stages, and the phenotypic variation explained by a single QTL ranged from 3.97 to 14.16%. Among them, qGR-7,
qSW7-1
, qSW7-2,
qCL7-1
, and
qRL3-1
played an important role in seed activity. In addition, a total of 295 epistatic QTLs were detected, of which 4 were located in the qRL3-1 and qGR-7 intervals. Three RIL lines (RIL18, RIL106, and RIL155) were further screened through genotype and phenotype identification. These three lines contain 3–6 additive QTLs, which can aggregate 6–8 excellent alleles, and have an important theoretical value of resistance to pre-harvest sprouting breeding. In addition, a total of 41 Mqtls was detected by meta-analysis, of which 15 Mqtls had physical intervals less than 1.0 Mb. And
qSW2-2
,
qSW2-3
,
qSW2-1
,
qCL2-1
, and
qRL3-1
were located in the
Mqtl2-2
,
Mqtl2-4
,
Mqtl3-3
, and
Mqtl4-2
intervals. A further prediction of candidate genes, expression level determination, and variation analysis showed that
Os01g0813100
was a candidate gene affecting seed activity.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10722-022-01484-6</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0003-0835-0753</orcidid></addata></record> |
| fulltext | fulltext |
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| ispartof | Genetic resources and crop evolution, 2023-03, Vol.70 (3), p.1007-1022 |
| issn | 0925-9864 1573-5109 |
| language | eng |
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| source | SpringerLink Journals - AutoHoldings |
| subjects | Agriculture Biomedical and Life Sciences Coleoptile Developmental stages Epistasis Gene expression Genes Genetic analysis Genotypes Germination Harvest Inbreeding Intervals Life Sciences Meta-analysis Monte Carlo simulation Oryza sativa Phenotypes Phenotypic variations Plant Genetics and Genomics Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Quantitative trait loci Research Article Rice Seed germination Seeds |
| title | Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.) |
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