Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice
Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome‐wide association study using an indica‐predominant diversity panel, we identified quanti...
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| Veröffentlicht in: | Plant, cell and environment cell and environment, 2018-12, Vol.41 (12), p.2731-2743 |
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| creator | Wang, Fanmiao Longkumer, Toshisangba Catausan, Sheryl C. Calumpang, Carla Lenore F. Tarun, Jeshurun A. Cattin‐Ortola, Jerome Ishizaki, Takuma Pariasca Tanaka, Juan Rose, Terry Wissuwa, Matthias Kretzschmar, Tobias |
| description | Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome‐wide association study using an indica‐predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS‐11, was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds, and a predicted glycosyl hydrolase, TIPS‐11‐9, was identified as the causal gene for observed phenotypic differences. TIPS‐11‐9 was differentially expressed in emerging lateral roots of contrasting qTIPS‐11 haplotypes, which was likely due to differences in cis‐regulatory elements and auxin responsiveness. Abolishment of Tips‐11‐9 function through T‐DNA insertion in a qTIPS‐11‐positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous‐limiting conditions.
Marker‐assisted introgression of qTIPS‐11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia. |
| doi_str_mv | 10.1111/pce.13400 |
| format | Article |
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Marker‐assisted introgression of qTIPS‐11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia.</description><identifier>ISSN: 0140-7791</identifier><identifier>EISSN: 1365-3040</identifier><identifier>DOI: 10.1111/pce.13400</identifier><identifier>PMID: 29981171</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Breeding ; Chromosome 11 ; Chromosomes ; Chromosomes, Plant - genetics ; Crop Production ; Deoxyribonucleic acid ; DNA ; early vigour ; Genes, Plant - genetics ; Genes, Plant - physiology ; Genetic control ; genetic variation ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Glycosyl hydrolase ; growth ; Haplotypes ; Hydrolase ; Insertion ; Linkage Disequilibrium - genetics ; Oryza - genetics ; Oryza - growth & development ; Oryza - physiology ; Oryza sativa indica ; Plant Breeding - methods ; Plant Roots - growth & development ; Plant Roots - physiology ; Quantitative trait loci ; Quantitative Trait Loci - genetics ; Quantitative Trait, Heritable ; Regulatory sequences ; Rice ; root ; Seeding ; Seedlings</subject><ispartof>Plant, cell and environment, 2018-12, Vol.41 (12), p.2731-2743</ispartof><rights>2018 John Wiley & Sons Ltd</rights><rights>2018 John Wiley & Sons Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3880-b7e740cb63be77dc607724d8d81ad09f4faa674e1bd6092564d053a18708b793</citedby><cites>FETCH-LOGICAL-c3880-b7e740cb63be77dc607724d8d81ad09f4faa674e1bd6092564d053a18708b793</cites><orcidid>0000-0002-8227-0746 ; 0000-0001-5386-6818</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fpce.13400$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fpce.13400$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,1433,27924,27925,45574,45575,46409,46833</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29981171$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Fanmiao</creatorcontrib><creatorcontrib>Longkumer, Toshisangba</creatorcontrib><creatorcontrib>Catausan, Sheryl C.</creatorcontrib><creatorcontrib>Calumpang, Carla Lenore F.</creatorcontrib><creatorcontrib>Tarun, Jeshurun A.</creatorcontrib><creatorcontrib>Cattin‐Ortola, Jerome</creatorcontrib><creatorcontrib>Ishizaki, Takuma</creatorcontrib><creatorcontrib>Pariasca Tanaka, Juan</creatorcontrib><creatorcontrib>Rose, Terry</creatorcontrib><creatorcontrib>Wissuwa, Matthias</creatorcontrib><creatorcontrib>Kretzschmar, Tobias</creatorcontrib><title>Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice</title><title>Plant, cell and environment</title><addtitle>Plant Cell Environ</addtitle><description>Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome‐wide association study using an indica‐predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS‐11, was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds, and a predicted glycosyl hydrolase, TIPS‐11‐9, was identified as the causal gene for observed phenotypic differences. TIPS‐11‐9 was differentially expressed in emerging lateral roots of contrasting qTIPS‐11 haplotypes, which was likely due to differences in cis‐regulatory elements and auxin responsiveness. Abolishment of Tips‐11‐9 function through T‐DNA insertion in a qTIPS‐11‐positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous‐limiting conditions.
Marker‐assisted introgression of qTIPS‐11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia.</description><subject>Breeding</subject><subject>Chromosome 11</subject><subject>Chromosomes</subject><subject>Chromosomes, Plant - genetics</subject><subject>Crop Production</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>early vigour</subject><subject>Genes, Plant - genetics</subject><subject>Genes, Plant - physiology</subject><subject>Genetic control</subject><subject>genetic variation</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Glycosyl hydrolase</subject><subject>growth</subject><subject>Haplotypes</subject><subject>Hydrolase</subject><subject>Insertion</subject><subject>Linkage Disequilibrium - genetics</subject><subject>Oryza - genetics</subject><subject>Oryza - growth & development</subject><subject>Oryza - physiology</subject><subject>Oryza sativa indica</subject><subject>Plant Breeding - methods</subject><subject>Plant Roots - growth & development</subject><subject>Plant Roots - physiology</subject><subject>Quantitative trait loci</subject><subject>Quantitative Trait Loci - genetics</subject><subject>Quantitative Trait, Heritable</subject><subject>Regulatory sequences</subject><subject>Rice</subject><subject>root</subject><subject>Seeding</subject><subject>Seedlings</subject><issn>0140-7791</issn><issn>1365-3040</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kcFu1DAQhi1ERZfCgRdAlriUQ9qZxLGTI1q1BalSOfRuOfZk5SqJFzvZam99BJ6RJ8GQwgGJuYz069Ovf-Zn7B3CBea53Fu6wEoAvGAbrGRdVCDgJdsACiiUavGUvU7pASALqn3FTsu2bRAVbth4Q1MY6cfT90fviJuUgvVm9mHiZnJ8RxPxgxm8W7U0L85T4n2InEwcjjyGMPOD34Ul8jlwP-5jOBB3PpKdeSJyftrx0PPoLb1hJ70ZEr193mfs_vrqfvu5uL27-bL9dFvYqmmg6BQpAbaTVUdKOStBqVK4xjVoHLS96I2RShB2TkJb1lI4qCuDjYKmU211xs5X25zl20Jp1qNPlobBTBSWpEuQUjS1xDqjH_5BH_IlUw6nS6xqwLJFmamPK2VjSClSr_fRjyYeNYL-VYHOFejfFWT2_bPj0o3k_pJ_fp6ByxV49AMd_--kv26vVsufMcOQwA</recordid><startdate>201812</startdate><enddate>201812</enddate><creator>Wang, Fanmiao</creator><creator>Longkumer, Toshisangba</creator><creator>Catausan, Sheryl C.</creator><creator>Calumpang, Carla Lenore F.</creator><creator>Tarun, Jeshurun A.</creator><creator>Cattin‐Ortola, Jerome</creator><creator>Ishizaki, Takuma</creator><creator>Pariasca Tanaka, Juan</creator><creator>Rose, Terry</creator><creator>Wissuwa, Matthias</creator><creator>Kretzschmar, Tobias</creator><general>Wiley Subscription Services, Inc</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>7QP</scope><scope>7ST</scope><scope>C1K</scope><scope>SOI</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-8227-0746</orcidid><orcidid>https://orcid.org/0000-0001-5386-6818</orcidid></search><sort><creationdate>201812</creationdate><title>Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice</title><author>Wang, Fanmiao ; Longkumer, Toshisangba ; Catausan, Sheryl C. ; Calumpang, Carla Lenore F. ; Tarun, Jeshurun A. ; Cattin‐Ortola, Jerome ; Ishizaki, Takuma ; Pariasca Tanaka, Juan ; Rose, Terry ; Wissuwa, Matthias ; Kretzschmar, Tobias</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3880-b7e740cb63be77dc607724d8d81ad09f4faa674e1bd6092564d053a18708b793</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Breeding</topic><topic>Chromosome 11</topic><topic>Chromosomes</topic><topic>Chromosomes, Plant - genetics</topic><topic>Crop Production</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>early vigour</topic><topic>Genes, Plant - genetics</topic><topic>Genes, Plant - physiology</topic><topic>Genetic control</topic><topic>genetic variation</topic><topic>Genome-wide association studies</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Glycosyl hydrolase</topic><topic>growth</topic><topic>Haplotypes</topic><topic>Hydrolase</topic><topic>Insertion</topic><topic>Linkage Disequilibrium - genetics</topic><topic>Oryza - genetics</topic><topic>Oryza - growth & development</topic><topic>Oryza - physiology</topic><topic>Oryza sativa indica</topic><topic>Plant Breeding - methods</topic><topic>Plant Roots - growth & development</topic><topic>Plant Roots - physiology</topic><topic>Quantitative trait loci</topic><topic>Quantitative Trait Loci - genetics</topic><topic>Quantitative Trait, Heritable</topic><topic>Regulatory sequences</topic><topic>Rice</topic><topic>root</topic><topic>Seeding</topic><topic>Seedlings</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Fanmiao</creatorcontrib><creatorcontrib>Longkumer, Toshisangba</creatorcontrib><creatorcontrib>Catausan, Sheryl C.</creatorcontrib><creatorcontrib>Calumpang, Carla Lenore F.</creatorcontrib><creatorcontrib>Tarun, Jeshurun A.</creatorcontrib><creatorcontrib>Cattin‐Ortola, Jerome</creatorcontrib><creatorcontrib>Ishizaki, Takuma</creatorcontrib><creatorcontrib>Pariasca Tanaka, Juan</creatorcontrib><creatorcontrib>Rose, Terry</creatorcontrib><creatorcontrib>Wissuwa, Matthias</creatorcontrib><creatorcontrib>Kretzschmar, Tobias</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Environment Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Plant, cell and environment</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Fanmiao</au><au>Longkumer, Toshisangba</au><au>Catausan, Sheryl C.</au><au>Calumpang, Carla Lenore F.</au><au>Tarun, Jeshurun A.</au><au>Cattin‐Ortola, Jerome</au><au>Ishizaki, Takuma</au><au>Pariasca Tanaka, Juan</au><au>Rose, Terry</au><au>Wissuwa, Matthias</au><au>Kretzschmar, Tobias</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice</atitle><jtitle>Plant, cell and environment</jtitle><addtitle>Plant Cell Environ</addtitle><date>2018-12</date><risdate>2018</risdate><volume>41</volume><issue>12</issue><spage>2731</spage><epage>2743</epage><pages>2731-2743</pages><issn>0140-7791</issn><eissn>1365-3040</eissn><abstract>Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome‐wide association study using an indica‐predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS‐11, was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds, and a predicted glycosyl hydrolase, TIPS‐11‐9, was identified as the causal gene for observed phenotypic differences. TIPS‐11‐9 was differentially expressed in emerging lateral roots of contrasting qTIPS‐11 haplotypes, which was likely due to differences in cis‐regulatory elements and auxin responsiveness. Abolishment of Tips‐11‐9 function through T‐DNA insertion in a qTIPS‐11‐positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous‐limiting conditions.
Marker‐assisted introgression of qTIPS‐11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>29981171</pmid><doi>10.1111/pce.13400</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-8227-0746</orcidid><orcidid>https://orcid.org/0000-0001-5386-6818</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Breeding Chromosome 11 Chromosomes Chromosomes, Plant - genetics Crop Production Deoxyribonucleic acid DNA early vigour Genes, Plant - genetics Genes, Plant - physiology Genetic control genetic variation Genome-wide association studies Genome-Wide Association Study Genomes Glycosyl hydrolase growth Haplotypes Hydrolase Insertion Linkage Disequilibrium - genetics Oryza - genetics Oryza - growth & development Oryza - physiology Oryza sativa indica Plant Breeding - methods Plant Roots - growth & development Plant Roots - physiology Quantitative trait loci Quantitative Trait Loci - genetics Quantitative Trait, Heritable Regulatory sequences Rice root Seeding Seedlings |
| title | Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice |
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