Resequencing of a Core Rice Mutant Population Induced by Gamma-Ray Irradiation and Its Application in a Genome-Wide Association Study
A total of 2561 gamma ray-induced mutants (M 7 ) were evaluated in six abiotic stress treatments, and then principal component analysis was performed to score their phenotypes. Resequencing was performed on 123 selected rice mutants and wild-type rice to assess the structural changes in the genomes...
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| creator | Hwang, Sun-Goo Lee, Sang Cheol Lee, Junkyung Lee, Jae Woo Kim, Jin-Hyuk Choi, Seung Young Kim, Jin-Baek Choi, Hong-Il Jang, Cheol Seong |
| description | A total of 2561 gamma ray-induced mutants (M
7
) were evaluated in six abiotic stress treatments, and then principal component analysis was performed to score their phenotypes. Resequencing was performed on 123 selected rice mutants and wild-type rice to assess the structural changes in the genomes of these mutants, such as single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels). A total of 5160 (avg. 87.3 per plant) SNPs and 7195 (avg. 121.9) InDels were observed in the 200-Gy lines, whereas 5650 (avg. 88.3) SNPs and 7676 (avg. 119.9) InDels were found in the 300-Gy lines. We found that one candidate gene (
Os02g0528900
, which is similar to the gene for pleiotropic drug resistance (PDR)-like ATP-binding cassette (ABC) transporter) contained two SNPs that were included in principal component 4 via a genome-wide association study. The 300-42 line had the lowest phenotype score against heat, possibly suggesting the existence of a relationship between these SNPs and heat stress. Co-expression analysis of the candidate gene involved in responses to toxic substances and the chemical stimulation of significant biological processes. Therefore, the studied targeting induced local lesions in genome (TILLING) population could be a useful source of mutations in the breeding of new genetic resources for forward and reverse genetics. |
| doi_str_mv | 10.1007/s12374-020-09266-2 |
| format | Article |
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7
) were evaluated in six abiotic stress treatments, and then principal component analysis was performed to score their phenotypes. Resequencing was performed on 123 selected rice mutants and wild-type rice to assess the structural changes in the genomes of these mutants, such as single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels). A total of 5160 (avg. 87.3 per plant) SNPs and 7195 (avg. 121.9) InDels were observed in the 200-Gy lines, whereas 5650 (avg. 88.3) SNPs and 7676 (avg. 119.9) InDels were found in the 300-Gy lines. We found that one candidate gene (
Os02g0528900
, which is similar to the gene for pleiotropic drug resistance (PDR)-like ATP-binding cassette (ABC) transporter) contained two SNPs that were included in principal component 4 via a genome-wide association study. The 300-42 line had the lowest phenotype score against heat, possibly suggesting the existence of a relationship between these SNPs and heat stress. Co-expression analysis of the candidate gene involved in responses to toxic substances and the chemical stimulation of significant biological processes. Therefore, the studied targeting induced local lesions in genome (TILLING) population could be a useful source of mutations in the breeding of new genetic resources for forward and reverse genetics.</description><identifier>ISSN: 1226-9239</identifier><identifier>EISSN: 1867-0725</identifier><identifier>DOI: 10.1007/s12374-020-09266-2</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Abiotic stress ; Adenosine triphosphate ; Annotations ; Biological activity ; Biomedical and Life Sciences ; Drug resistance ; Food ; Gamma rays ; Gene deletion ; Gene expression ; Genetic resources ; Genetic testing ; Genetics ; Genome-wide association studies ; Genomes ; Heat stress ; Heat tolerance ; Irradiation ; Life Sciences ; Life Sciences & Biomedicine ; Mutagenesis ; Mutants ; Mutation ; Nucleotides ; Phenotypes ; Plant Breeding/Biotechnology ; Plant Ecology ; Plant Genetics and Genomics ; Plant Sciences ; Plant Systematics/Taxonomy/Biogeography ; Principal components analysis ; Radiation ; Research Article ; Rice ; Salinity ; Science & Technology ; Single-nucleotide polymorphism ; Software ; Toxic substances ; Wheat ; γ Radiation ; 생물학</subject><ispartof>Journal of Plant Biology(한국식물학회지), 2020, 63(6), , pp.463-472</ispartof><rights>Korean Society of Plant Biologist 2020</rights><rights>Korean Society of Plant Biologist 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>15</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000551001900001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c353t-f541db5b93fb376d563ed6d7fe10afc9e8fef5330b005b9b331a6e574dc329c03</citedby><cites>FETCH-LOGICAL-c353t-f541db5b93fb376d563ed6d7fe10afc9e8fef5330b005b9b331a6e574dc329c03</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/s12374-020-09266-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2919717206?pq-origsite=primo$$EHTML$$P50$$Gproquest$$H</linktohtml><link.rule.ids>315,781,785,21393,27929,27930,28253,33749,41493,42562,43810,51324,64390,64394,72474</link.rule.ids><backlink>$$Uhttps://www.kci.go.kr/kciportal/ci/sereArticleSearch/ciSereArtiView.kci?sereArticleSearchBean.artiId=ART002701002$$DAccess content in National Research Foundation of Korea (NRF)$$Hfree_for_read</backlink></links><search><creatorcontrib>Hwang, Sun-Goo</creatorcontrib><creatorcontrib>Lee, Sang Cheol</creatorcontrib><creatorcontrib>Lee, Junkyung</creatorcontrib><creatorcontrib>Lee, Jae Woo</creatorcontrib><creatorcontrib>Kim, Jin-Hyuk</creatorcontrib><creatorcontrib>Choi, Seung Young</creatorcontrib><creatorcontrib>Kim, Jin-Baek</creatorcontrib><creatorcontrib>Choi, Hong-Il</creatorcontrib><creatorcontrib>Jang, Cheol Seong</creatorcontrib><title>Resequencing of a Core Rice Mutant Population Induced by Gamma-Ray Irradiation and Its Application in a Genome-Wide Association Study</title><title>Journal of plant biology = Singmul Hakhoe chi</title><addtitle>J. Plant Biol</addtitle><addtitle>J PLANT BIOL</addtitle><description>A total of 2561 gamma ray-induced mutants (M
7
) were evaluated in six abiotic stress treatments, and then principal component analysis was performed to score their phenotypes. Resequencing was performed on 123 selected rice mutants and wild-type rice to assess the structural changes in the genomes of these mutants, such as single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels). A total of 5160 (avg. 87.3 per plant) SNPs and 7195 (avg. 121.9) InDels were observed in the 200-Gy lines, whereas 5650 (avg. 88.3) SNPs and 7676 (avg. 119.9) InDels were found in the 300-Gy lines. We found that one candidate gene (
Os02g0528900
, which is similar to the gene for pleiotropic drug resistance (PDR)-like ATP-binding cassette (ABC) transporter) contained two SNPs that were included in principal component 4 via a genome-wide association study. The 300-42 line had the lowest phenotype score against heat, possibly suggesting the existence of a relationship between these SNPs and heat stress. Co-expression analysis of the candidate gene involved in responses to toxic substances and the chemical stimulation of significant biological processes. Therefore, the studied targeting induced local lesions in genome (TILLING) population could be a useful source of mutations in the breeding of new genetic resources for forward and reverse genetics.</description><subject>Abiotic stress</subject><subject>Adenosine triphosphate</subject><subject>Annotations</subject><subject>Biological activity</subject><subject>Biomedical and Life Sciences</subject><subject>Drug resistance</subject><subject>Food</subject><subject>Gamma rays</subject><subject>Gene deletion</subject><subject>Gene expression</subject><subject>Genetic resources</subject><subject>Genetic testing</subject><subject>Genetics</subject><subject>Genome-wide association studies</subject><subject>Genomes</subject><subject>Heat stress</subject><subject>Heat tolerance</subject><subject>Irradiation</subject><subject>Life Sciences</subject><subject>Life Sciences & Biomedicine</subject><subject>Mutagenesis</subject><subject>Mutants</subject><subject>Mutation</subject><subject>Nucleotides</subject><subject>Phenotypes</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Ecology</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Sciences</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Principal components analysis</subject><subject>Radiation</subject><subject>Research Article</subject><subject>Rice</subject><subject>Salinity</subject><subject>Science & Technology</subject><subject>Single-nucleotide polymorphism</subject><subject>Software</subject><subject>Toxic substances</subject><subject>Wheat</subject><subject>γ Radiation</subject><subject>생물학</subject><issn>1226-9239</issn><issn>1867-0725</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>AOWDO</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkc-KFDEQhxtRcF19AU8BTyJx82c66RyHwR0bdlHGFY8hnVSG7M4kbdKNzAP43sbpRW_iqYri-0Klfk3zmpL3lBB5VSjjcoUJI5goJgRmT5oL2gmJiWTt09ozJrBiXD1vXpRyT4igrOsump87KPB9hmhD3KPkkUGblAHtggV0O08mTuhzGueDmUKKqI9utuDQcEJbczwavDMn1OdsXFgAEx3qp4LW43gIdpmFOkZbiOkI-FtwgNalJPsofJlmd3rZPPPmUODVY71svl5_uNt8xDeftv1mfYMtb_mEfbuibmgHxf3ApXCt4OCEkx4oMd4q6Dz4lnMyEFKpgXNqBLRy5SxnyhJ-2bxd3o3Z6wcbdDLhXPdJP2S93t31WkkhOV1V9s3CjjnVA5VJ36c5x7qeZooqSSUjolJsoWxOpWTweszhaPJJU6J_R6OXaHSNRp-j0axK7xbpBwzJFxvq-eGPSOrybVWpqh2hle7-n96E6XzXTZrjVFW-qKXicQ_57x_-sd4vyz6yIg</recordid><startdate>20201201</startdate><enddate>20201201</enddate><creator>Hwang, Sun-Goo</creator><creator>Lee, Sang Cheol</creator><creator>Lee, Junkyung</creator><creator>Lee, Jae Woo</creator><creator>Kim, Jin-Hyuk</creator><creator>Choi, Seung Young</creator><creator>Kim, Jin-Baek</creator><creator>Choi, Hong-Il</creator><creator>Jang, Cheol Seong</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature</general><general>Springer Nature B.V</general><general>한국식물학회</general><scope>AOWDO</scope><scope>BLEPL</scope><scope>DTL</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</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>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>ACYCR</scope></search><sort><creationdate>20201201</creationdate><title>Resequencing of a Core Rice Mutant Population Induced by Gamma-Ray Irradiation and Its Application in a Genome-Wide Association Study</title><author>Hwang, Sun-Goo ; Lee, Sang Cheol ; Lee, Junkyung ; Lee, Jae Woo ; Kim, Jin-Hyuk ; Choi, Seung Young ; Kim, Jin-Baek ; Choi, Hong-Il ; Jang, Cheol Seong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c353t-f541db5b93fb376d563ed6d7fe10afc9e8fef5330b005b9b331a6e574dc329c03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Abiotic stress</topic><topic>Adenosine triphosphate</topic><topic>Annotations</topic><topic>Biological activity</topic><topic>Biomedical and Life Sciences</topic><topic>Drug resistance</topic><topic>Food</topic><topic>Gamma rays</topic><topic>Gene deletion</topic><topic>Gene expression</topic><topic>Genetic resources</topic><topic>Genetic testing</topic><topic>Genetics</topic><topic>Genome-wide association studies</topic><topic>Genomes</topic><topic>Heat stress</topic><topic>Heat tolerance</topic><topic>Irradiation</topic><topic>Life Sciences</topic><topic>Life Sciences & Biomedicine</topic><topic>Mutagenesis</topic><topic>Mutants</topic><topic>Mutation</topic><topic>Nucleotides</topic><topic>Phenotypes</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Ecology</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Sciences</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Principal components analysis</topic><topic>Radiation</topic><topic>Research Article</topic><topic>Rice</topic><topic>Salinity</topic><topic>Science & Technology</topic><topic>Single-nucleotide polymorphism</topic><topic>Software</topic><topic>Toxic substances</topic><topic>Wheat</topic><topic>γ Radiation</topic><topic>생물학</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hwang, Sun-Goo</creatorcontrib><creatorcontrib>Lee, Sang Cheol</creatorcontrib><creatorcontrib>Lee, Junkyung</creatorcontrib><creatorcontrib>Lee, Jae Woo</creatorcontrib><creatorcontrib>Kim, Jin-Hyuk</creatorcontrib><creatorcontrib>Choi, Seung Young</creatorcontrib><creatorcontrib>Kim, Jin-Baek</creatorcontrib><creatorcontrib>Choi, Hong-Il</creatorcontrib><creatorcontrib>Jang, Cheol Seong</creatorcontrib><collection>Web of Science - Science Citation Index Expanded - 2020</collection><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><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 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>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>Korean Citation Index</collection><jtitle>Journal of plant biology = Singmul Hakhoe chi</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hwang, Sun-Goo</au><au>Lee, Sang Cheol</au><au>Lee, Junkyung</au><au>Lee, Jae Woo</au><au>Kim, Jin-Hyuk</au><au>Choi, Seung Young</au><au>Kim, Jin-Baek</au><au>Choi, Hong-Il</au><au>Jang, Cheol Seong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Resequencing of a Core Rice Mutant Population Induced by Gamma-Ray Irradiation and Its Application in a Genome-Wide Association Study</atitle><jtitle>Journal of plant biology = Singmul Hakhoe chi</jtitle><stitle>J. Plant Biol</stitle><stitle>J PLANT BIOL</stitle><date>2020-12-01</date><risdate>2020</risdate><volume>63</volume><issue>6</issue><spage>463</spage><epage>472</epage><pages>463-472</pages><issn>1226-9239</issn><eissn>1867-0725</eissn><abstract>A total of 2561 gamma ray-induced mutants (M
7
) were evaluated in six abiotic stress treatments, and then principal component analysis was performed to score their phenotypes. Resequencing was performed on 123 selected rice mutants and wild-type rice to assess the structural changes in the genomes of these mutants, such as single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels). A total of 5160 (avg. 87.3 per plant) SNPs and 7195 (avg. 121.9) InDels were observed in the 200-Gy lines, whereas 5650 (avg. 88.3) SNPs and 7676 (avg. 119.9) InDels were found in the 300-Gy lines. We found that one candidate gene (
Os02g0528900
, which is similar to the gene for pleiotropic drug resistance (PDR)-like ATP-binding cassette (ABC) transporter) contained two SNPs that were included in principal component 4 via a genome-wide association study. The 300-42 line had the lowest phenotype score against heat, possibly suggesting the existence of a relationship between these SNPs and heat stress. Co-expression analysis of the candidate gene involved in responses to toxic substances and the chemical stimulation of significant biological processes. Therefore, the studied targeting induced local lesions in genome (TILLING) population could be a useful source of mutations in the breeding of new genetic resources for forward and reverse genetics.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s12374-020-09266-2</doi><tpages>10</tpages></addata></record> |
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| subjects | Abiotic stress Adenosine triphosphate Annotations Biological activity Biomedical and Life Sciences Drug resistance Food Gamma rays Gene deletion Gene expression Genetic resources Genetic testing Genetics Genome-wide association studies Genomes Heat stress Heat tolerance Irradiation Life Sciences Life Sciences & Biomedicine Mutagenesis Mutants Mutation Nucleotides Phenotypes Plant Breeding/Biotechnology Plant Ecology Plant Genetics and Genomics Plant Sciences Plant Systematics/Taxonomy/Biogeography Principal components analysis Radiation Research Article Rice Salinity Science & Technology Single-nucleotide polymorphism Software Toxic substances Wheat γ Radiation 생물학 |
| title | Resequencing of a Core Rice Mutant Population Induced by Gamma-Ray Irradiation and Its Application in a Genome-Wide Association Study |
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