Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice
Deep rooting is a very important trait for plants’ drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association ma...
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| Veröffentlicht in: | Journal of experimental botany 2015-08, Vol.66 (15), p.4749-4757 |
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| container_title | Journal of experimental botany |
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| creator | Lou, Qiaojun Chen, Liang Mei, Hanwei Wei, Haibin Feng, Fangjun Wang, Pei Xia, Hui Li, Tiemei Luo, Lijun |
| description | Deep rooting is a very important trait for plants’ drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding. |
| doi_str_mv | 10.1093/jxb/erv246 |
| format | Article |
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Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. 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Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding.</description><subject>Chromosome Mapping</subject><subject>Genome-Wide Association Study</subject><subject>Oryza - genetics</subject><subject>Oryza - metabolism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative Trait Loci</subject><subject>RESEARCH PAPER</subject><issn>0022-0957</issn><issn>1460-2431</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9rFDEcxYNY7Fq9eFdyFGHa_JpkchFKUVsoFEFvQshkvrNmnU3GJLN0__umbFvqyVzCl_fJ--bxEHpHySklmp9tbvszSDsm5Au0okKShglOX6IVIYw1RLfqGL3OeUMIaUnbvkLHTFaFtXyFfn1fbCi-2OJ3gEuyvuApuiXjrZ1nH9Y4jngAmHGKsdzP_R5PPvyxa8A2DNjmHJ2vz2Oos5322WfsA07ewRt0NNopw9uH-wT9_Prlx8Vlc33z7eri_LpxQuvSgKBacSJAt3ZgNUBP7eCoUE6CACU6PlILstNcKqW7kVE5UiU16Hp67fgJ-nzwnZd-C4ODUINMZk5-a9PeROvNv0rwv8067oxoiVJKVoOPDwYp_l0gF7P12cE02QBxyYYqzjomNNf_R6XuCJcdJRX9dEBdijknGJ9-RIm5b87U5syhuQp_eJ7hCX2sqgLvD8Aml5ie6byrGyW_A48En9w</recordid><startdate>20150801</startdate><enddate>20150801</enddate><creator>Lou, Qiaojun</creator><creator>Chen, Liang</creator><creator>Mei, Hanwei</creator><creator>Wei, Haibin</creator><creator>Feng, Fangjun</creator><creator>Wang, Pei</creator><creator>Xia, Hui</creator><creator>Li, Tiemei</creator><creator>Luo, Lijun</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20150801</creationdate><title>Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice</title><author>Lou, Qiaojun ; Chen, Liang ; Mei, Hanwei ; Wei, Haibin ; Feng, Fangjun ; Wang, Pei ; Xia, Hui ; Li, Tiemei ; Luo, Lijun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c499t-e4197304e95ad2146b1adc147c6e4e7483f1ae689367798f216f1769e9999b9c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Chromosome Mapping</topic><topic>Genome-Wide Association Study</topic><topic>Oryza - genetics</topic><topic>Oryza - metabolism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Quantitative Trait Loci</topic><topic>RESEARCH PAPER</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lou, Qiaojun</creatorcontrib><creatorcontrib>Chen, Liang</creatorcontrib><creatorcontrib>Mei, Hanwei</creatorcontrib><creatorcontrib>Wei, Haibin</creatorcontrib><creatorcontrib>Feng, Fangjun</creatorcontrib><creatorcontrib>Wang, Pei</creatorcontrib><creatorcontrib>Xia, Hui</creatorcontrib><creatorcontrib>Li, Tiemei</creatorcontrib><creatorcontrib>Luo, Lijun</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of experimental botany</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lou, Qiaojun</au><au>Chen, Liang</au><au>Mei, Hanwei</au><au>Wei, Haibin</au><au>Feng, Fangjun</au><au>Wang, Pei</au><au>Xia, Hui</au><au>Li, Tiemei</au><au>Luo, Lijun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice</atitle><jtitle>Journal of experimental botany</jtitle><addtitle>J Exp Bot</addtitle><date>2015-08-01</date><risdate>2015</risdate><volume>66</volume><issue>15</issue><spage>4749</spage><epage>4757</epage><pages>4749-4757</pages><issn>0022-0957</issn><eissn>1460-2431</eissn><abstract>Deep rooting is a very important trait for plants’ drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>26022253</pmid><doi>10.1093/jxb/erv246</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Jstor Complete Legacy; Oxford University Press Journals All Titles (1996-Current); Alma/SFX Local Collection |
| subjects | Chromosome Mapping Genome-Wide Association Study Oryza - genetics Oryza - metabolism Polymorphism, Single Nucleotide Quantitative Trait Loci RESEARCH PAPER |
| title | Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice |
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