Genome‑wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice
Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice g...
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| Veröffentlicht in: | Planta 2021-05, Vol.253 (5), p.1-16, Article 94 |
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| creator | Jiang, Nan Fu, Jun Zeng, Qin Liang, Yi Shi, Yanlong Li, Zhouwei Xiao, Youlun He, Zhizhou Wu, Yuntian Long, Yu Wang, Kai Yang, Yuanzhu Liu, Xionglun Peng, Junhua |
| description | Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R
2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance. |
| doi_str_mv | 10.1007/s00425-021-03612-5 |
| format | Article |
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2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-021-03612-5</identifier><identifier>PMID: 33830376</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Science + Business Media</publisher><subject>Agriculture ; Bacteria ; Biomedical and Life Sciences ; Blight ; Crop production ; Disease resistance ; Disease Resistance - genetics ; Ecology ; Economic importance ; Forestry ; Gene loci ; Gene mapping ; Gene pool ; Genes ; Genes, Plant - genetics ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Germplasm ; Gram-negative bacteria ; Humans ; Leaf streak ; Leaves ; Life Sciences ; Mapping ; ORIGINAL ARTICLE ; Oryza - genetics ; Oryza - microbiology ; Phenotypic variations ; Plant Breeding ; Plant Diseases - genetics ; Plant Diseases - microbiology ; Plant Sciences ; Polymorphism, Single Nucleotide - genetics ; Quantitative trait loci ; Rice ; Single-nucleotide polymorphism ; Subgroups ; Xanthomonas - pathogenicity</subject><ispartof>Planta, 2021-05, Vol.253 (5), p.1-16, Article 94</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021</rights><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c397t-671a2e50729af9914e59b9c92ac0f47282130d7008933901c134a21c9e38e1ed3</citedby><cites>FETCH-LOGICAL-c397t-671a2e50729af9914e59b9c92ac0f47282130d7008933901c134a21c9e38e1ed3</cites><orcidid>0000-0002-8428-3137</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/s00425-021-03612-5$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00425-021-03612-5$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33830376$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jiang, Nan</creatorcontrib><creatorcontrib>Fu, Jun</creatorcontrib><creatorcontrib>Zeng, Qin</creatorcontrib><creatorcontrib>Liang, Yi</creatorcontrib><creatorcontrib>Shi, Yanlong</creatorcontrib><creatorcontrib>Li, Zhouwei</creatorcontrib><creatorcontrib>Xiao, Youlun</creatorcontrib><creatorcontrib>He, Zhizhou</creatorcontrib><creatorcontrib>Wu, Yuntian</creatorcontrib><creatorcontrib>Long, Yu</creatorcontrib><creatorcontrib>Wang, Kai</creatorcontrib><creatorcontrib>Yang, Yuanzhu</creatorcontrib><creatorcontrib>Liu, Xionglun</creatorcontrib><creatorcontrib>Peng, Junhua</creatorcontrib><title>Genome‑wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice</title><title>Planta</title><addtitle>Planta</addtitle><addtitle>Planta</addtitle><description>Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R
2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.</description><subject>Agriculture</subject><subject>Bacteria</subject><subject>Biomedical and Life Sciences</subject><subject>Blight</subject><subject>Crop production</subject><subject>Disease resistance</subject><subject>Disease Resistance - genetics</subject><subject>Ecology</subject><subject>Economic importance</subject><subject>Forestry</subject><subject>Gene loci</subject><subject>Gene mapping</subject><subject>Gene pool</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Germplasm</subject><subject>Gram-negative bacteria</subject><subject>Humans</subject><subject>Leaf streak</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>Mapping</subject><subject>ORIGINAL ARTICLE</subject><subject>Oryza - genetics</subject><subject>Oryza - microbiology</subject><subject>Phenotypic variations</subject><subject>Plant Breeding</subject><subject>Plant Diseases - genetics</subject><subject>Plant Diseases - microbiology</subject><subject>Plant Sciences</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Quantitative trait loci</subject><subject>Rice</subject><subject>Single-nucleotide polymorphism</subject><subject>Subgroups</subject><subject>Xanthomonas - pathogenicity</subject><issn>0032-0935</issn><issn>1432-2048</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kcGKFDEQhoMo7rj6AoIS8OKltZJKJp2jLLoKC170HDLp6jFjd2dMMog3X8FX9EmM9rqKB08Vqr7_r1A_Yw8FPBMA5nkBUFJ3IEUHuBWy07fYRiiUnQTV32YbgPYGi_qM3SvlANCGxtxlZ4g9Aprtho2XtKSZvn_99jkOxH0pKURfY1r47I_HuOz5mDLPVGKpfgnEa-I7Hyrl6Ce-m-L-Q-V-Gf5qTuRHXmom_5HHhecY6D67M_qp0IPres7ev3r57uJ1d_X28s3Fi6suoDW12xrhJWkw0vrRWqFI250NVvoAozKylwJhMAC9RbQggkDlpQiWsCdBA56zp6vvMadPJyrVzbEEmia_UDoVJ7UAqbVG09An_6CHdMpL-12jwFqwosdGyZUKOZWSaXTHHGefvzgB7mcKbk3BtRTcrxScbqLH19an3UzDjeT32RuAK1DaaNlT_rP7v7aPVtWh1JRvXGW7llKg8Ae_95uE</recordid><startdate>20210501</startdate><enddate>20210501</enddate><creator>Jiang, Nan</creator><creator>Fu, Jun</creator><creator>Zeng, Qin</creator><creator>Liang, Yi</creator><creator>Shi, Yanlong</creator><creator>Li, Zhouwei</creator><creator>Xiao, Youlun</creator><creator>He, Zhizhou</creator><creator>Wu, Yuntian</creator><creator>Long, Yu</creator><creator>Wang, Kai</creator><creator>Yang, Yuanzhu</creator><creator>Liu, Xionglun</creator><creator>Peng, Junhua</creator><general>Springer Science + Business Media</general><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</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>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</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>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-8428-3137</orcidid></search><sort><creationdate>20210501</creationdate><title>Genome‑wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice</title><author>Jiang, Nan ; Fu, Jun ; Zeng, Qin ; Liang, Yi ; Shi, Yanlong ; Li, Zhouwei ; Xiao, Youlun ; He, Zhizhou ; Wu, Yuntian ; Long, Yu ; Wang, Kai ; Yang, Yuanzhu ; Liu, Xionglun ; Peng, Junhua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c397t-671a2e50729af9914e59b9c92ac0f47282130d7008933901c134a21c9e38e1ed3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Agriculture</topic><topic>Bacteria</topic><topic>Biomedical and Life Sciences</topic><topic>Blight</topic><topic>Crop production</topic><topic>Disease resistance</topic><topic>Disease Resistance - genetics</topic><topic>Ecology</topic><topic>Economic importance</topic><topic>Forestry</topic><topic>Gene loci</topic><topic>Gene mapping</topic><topic>Gene pool</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genome-wide association studies</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Germplasm</topic><topic>Gram-negative bacteria</topic><topic>Humans</topic><topic>Leaf streak</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>Mapping</topic><topic>ORIGINAL ARTICLE</topic><topic>Oryza - genetics</topic><topic>Oryza - microbiology</topic><topic>Phenotypic variations</topic><topic>Plant Breeding</topic><topic>Plant Diseases - genetics</topic><topic>Plant Diseases - microbiology</topic><topic>Plant Sciences</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Quantitative trait loci</topic><topic>Rice</topic><topic>Single-nucleotide polymorphism</topic><topic>Subgroups</topic><topic>Xanthomonas - pathogenicity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jiang, Nan</creatorcontrib><creatorcontrib>Fu, Jun</creatorcontrib><creatorcontrib>Zeng, Qin</creatorcontrib><creatorcontrib>Liang, Yi</creatorcontrib><creatorcontrib>Shi, Yanlong</creatorcontrib><creatorcontrib>Li, Zhouwei</creatorcontrib><creatorcontrib>Xiao, Youlun</creatorcontrib><creatorcontrib>He, Zhizhou</creatorcontrib><creatorcontrib>Wu, Yuntian</creatorcontrib><creatorcontrib>Long, Yu</creatorcontrib><creatorcontrib>Wang, Kai</creatorcontrib><creatorcontrib>Yang, Yuanzhu</creatorcontrib><creatorcontrib>Liu, Xionglun</creatorcontrib><creatorcontrib>Peng, Junhua</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</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>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Planta</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jiang, Nan</au><au>Fu, Jun</au><au>Zeng, Qin</au><au>Liang, Yi</au><au>Shi, Yanlong</au><au>Li, Zhouwei</au><au>Xiao, Youlun</au><au>He, Zhizhou</au><au>Wu, Yuntian</au><au>Long, Yu</au><au>Wang, Kai</au><au>Yang, Yuanzhu</au><au>Liu, Xionglun</au><au>Peng, Junhua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome‑wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice</atitle><jtitle>Planta</jtitle><stitle>Planta</stitle><addtitle>Planta</addtitle><date>2021-05-01</date><risdate>2021</risdate><volume>253</volume><issue>5</issue><spage>1</spage><epage>16</epage><pages>1-16</pages><artnum>94</artnum><issn>0032-0935</issn><eissn>1432-2048</eissn><abstract>Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R
2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Science + Business Media</pub><pmid>33830376</pmid><doi>10.1007/s00425-021-03612-5</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-8428-3137</orcidid></addata></record> |
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| source | MEDLINE; Springer Nature - Complete Springer Journals |
| subjects | Agriculture Bacteria Biomedical and Life Sciences Blight Crop production Disease resistance Disease Resistance - genetics Ecology Economic importance Forestry Gene loci Gene mapping Gene pool Genes Genes, Plant - genetics Genome-wide association studies Genome-Wide Association Study Genomes Germplasm Gram-negative bacteria Humans Leaf streak Leaves Life Sciences Mapping ORIGINAL ARTICLE Oryza - genetics Oryza - microbiology Phenotypic variations Plant Breeding Plant Diseases - genetics Plant Diseases - microbiology Plant Sciences Polymorphism, Single Nucleotide - genetics Quantitative trait loci Rice Single-nucleotide polymorphism Subgroups Xanthomonas - pathogenicity |
| title | Genome‑wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice |
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