Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum
Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can b...
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| creator | Adhikari, Pragya Goodrich, Emma Fernandes, Samuel B Lipka, Alexander E Tranel, Patrick Brown, Patrick Jamann, Tiffany M |
| description | Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. In this study, we observed sorghum tolerance to residual fomesafen. To investigate the underlying tolerance mechanism a genome-wide association mapping study was conducted using field-collected sorghum biomass panel (SBP) data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR |
| doi_str_mv | 10.1371/journal.pone.0233254 |
| format | Article |
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Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. In this study, we observed sorghum tolerance to residual fomesafen. To investigate the underlying tolerance mechanism a genome-wide association mapping study was conducted using field-collected sorghum biomass panel (SBP) data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region on chromosome 3, were detected. The ten most significant SNPs included two in genic regions (Sobic.003G136800, and Sobic.003G136900) and eight SNPs in the intergenic region encompassing the genes Sobic.003G136700, Sobic.003G136800, Sobic.003G137000, Sobic.003G136900, and Sobic.003G137100. The gene Sobic.003G137100 (PPXI), which encodes the PPO1 enzyme, one of the targets of PPO-inhibiting herbicides, was located 12kb downstream of the significant SNP S03_13152838. We found that PPXI is highly conserved in sorghum and expression does not significantly differ between tolerant and sensitive sorghum lines. Our results suggest that PPXI most likely does not underlie the observed herbicide tolerance. Instead, the mechanism underlying herbicide tolerance in the SBP is likely metabolism-based resistance, possibly regulated by the action of multiple genes. Further research is necessary to confirm candidate genes and their functions.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0233254</identifier><identifier>PMID: 33052910</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Agricultural production ; Analysis ; BASIC BIOLOGICAL SCIENCES ; Biology and Life Sciences ; Chloroplasts ; Chromosome 3 ; Chromosomes ; Crop production ; Crop production systems ; Crop science ; Data analysis ; Enzymes ; Gene mapping ; Genes ; Genetic aspects ; Genetic diversity ; Genomes ; Grain ; Growth ; Herbicide resistance ; Herbicides ; Mapping ; Metabolism ; Mitochondria ; Phenotypes ; Physiological aspects ; Plant genetics ; Protoporphyrinogen oxidase ; Research and Analysis Methods ; Single-nucleotide polymorphism ; Sorghum ; Soybeans ; Weed control</subject><ispartof>PloS one, 2020-10, Vol.15 (10), p.e0233254-e0233254</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Adhikari et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. In this study, we observed sorghum tolerance to residual fomesafen. To investigate the underlying tolerance mechanism a genome-wide association mapping study was conducted using field-collected sorghum biomass panel (SBP) data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region on chromosome 3, were detected. 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Further research is necessary to confirm candidate genes and their functions.</description><subject>Agricultural production</subject><subject>Analysis</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biology and Life Sciences</subject><subject>Chloroplasts</subject><subject>Chromosome 3</subject><subject>Chromosomes</subject><subject>Crop production</subject><subject>Crop production systems</subject><subject>Crop science</subject><subject>Data analysis</subject><subject>Enzymes</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Grain</subject><subject>Growth</subject><subject>Herbicide resistance</subject><subject>Herbicides</subject><subject>Mapping</subject><subject>Metabolism</subject><subject>Mitochondria</subject><subject>Phenotypes</subject><subject>Physiological aspects</subject><subject>Plant genetics</subject><subject>Protoporphyrinogen 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variation associated with PPO-inhibiting herbicide tolerance in sorghum</title><author>Adhikari, Pragya ; Goodrich, Emma ; Fernandes, Samuel B ; Lipka, Alexander E ; Tranel, Patrick ; Brown, Patrick ; Jamann, Tiffany M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c626t-5f97a922d05e7ce6856c2c60d12241ad51a4b517a9cb1c3c11f36aa4c7b33fb03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agricultural production</topic><topic>Analysis</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Biology and Life Sciences</topic><topic>Chloroplasts</topic><topic>Chromosome 3</topic><topic>Chromosomes</topic><topic>Crop production</topic><topic>Crop production systems</topic><topic>Crop science</topic><topic>Data analysis</topic><topic>Enzymes</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Genomes</topic><topic>Grain</topic><topic>Growth</topic><topic>Herbicide resistance</topic><topic>Herbicides</topic><topic>Mapping</topic><topic>Metabolism</topic><topic>Mitochondria</topic><topic>Phenotypes</topic><topic>Physiological aspects</topic><topic>Plant genetics</topic><topic>Protoporphyrinogen oxidase</topic><topic>Research and Analysis Methods</topic><topic>Single-nucleotide polymorphism</topic><topic>Sorghum</topic><topic>Soybeans</topic><topic>Weed control</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Adhikari, Pragya</creatorcontrib><creatorcontrib>Goodrich, Emma</creatorcontrib><creatorcontrib>Fernandes, Samuel B</creatorcontrib><creatorcontrib>Lipka, Alexander E</creatorcontrib><creatorcontrib>Tranel, Patrick</creatorcontrib><creatorcontrib>Brown, Patrick</creatorcontrib><creatorcontrib>Jamann, Tiffany M</creatorcontrib><creatorcontrib>Univ. of Illinois at Urbana-Champaign, IL (United 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States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum</atitle><jtitle>PloS one</jtitle><date>2020-10-14</date><risdate>2020</risdate><volume>15</volume><issue>10</issue><spage>e0233254</spage><epage>e0233254</epage><pages>e0233254-e0233254</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. In this study, we observed sorghum tolerance to residual fomesafen. To investigate the underlying tolerance mechanism a genome-wide association mapping study was conducted using field-collected sorghum biomass panel (SBP) data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region on chromosome 3, were detected. The ten most significant SNPs included two in genic regions (Sobic.003G136800, and Sobic.003G136900) and eight SNPs in the intergenic region encompassing the genes Sobic.003G136700, Sobic.003G136800, Sobic.003G137000, Sobic.003G136900, and Sobic.003G137100. The gene Sobic.003G137100 (PPXI), which encodes the PPO1 enzyme, one of the targets of PPO-inhibiting herbicides, was located 12kb downstream of the significant SNP S03_13152838. We found that PPXI is highly conserved in sorghum and expression does not significantly differ between tolerant and sensitive sorghum lines. Our results suggest that PPXI most likely does not underlie the observed herbicide tolerance. Instead, the mechanism underlying herbicide tolerance in the SBP is likely metabolism-based resistance, possibly regulated by the action of multiple genes. Further research is necessary to confirm candidate genes and their functions.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>33052910</pmid><doi>10.1371/journal.pone.0233254</doi><tpages>e0233254</tpages><orcidid>https://orcid.org/0000-0002-1059-096X</orcidid><orcidid>https://orcid.org/0000-0001-8269-535X</orcidid><orcidid>https://orcid.org/0000-0002-7288-0866</orcidid><orcidid>https://orcid.org/000000021059096X</orcidid><orcidid>https://orcid.org/0000000272880866</orcidid><orcidid>https://orcid.org/000000018269535X</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2020-10, Vol.15 (10), p.e0233254-e0233254 |
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| subjects | Agricultural production Analysis BASIC BIOLOGICAL SCIENCES Biology and Life Sciences Chloroplasts Chromosome 3 Chromosomes Crop production Crop production systems Crop science Data analysis Enzymes Gene mapping Genes Genetic aspects Genetic diversity Genomes Grain Growth Herbicide resistance Herbicides Mapping Metabolism Mitochondria Phenotypes Physiological aspects Plant genetics Protoporphyrinogen oxidase Research and Analysis Methods Single-nucleotide polymorphism Sorghum Soybeans Weed control |
| title | Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-04T06%3A09%3A16IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genetic%20variation%20associated%20with%20PPO-inhibiting%20herbicide%20tolerance%20in%20sorghum&rft.jtitle=PloS%20one&rft.au=Adhikari,%20Pragya&rft.aucorp=Univ.%20of%20Illinois%20at%20Urbana-Champaign,%20IL%20(United%20States)&rft.date=2020-10-14&rft.volume=15&rft.issue=10&rft.spage=e0233254&rft.epage=e0233254&rft.pages=e0233254-e0233254&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0233254&rft_dat=%3Cgale_plos_%3EA638372431%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2451126784&rft_id=info:pmid/33052910&rft_galeid=A638372431&rft_doaj_id=oai_doaj_org_article_6b1b276612e94a6fa8ca2fc8f7e32a7c&rfr_iscdi=true |