Identification of bakanae disease resistance loci in japonica rice through genome wide association study
Abstract Background Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. Results A germplasm collection of japonica rice was screened for...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2017-06-01
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| Series: | Rice |
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| Online Access: | http://link.springer.com/article/10.1186/s12284-017-0168-z |
| _version_ | 1818931239014367232 |
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| author | Andrea Volante Alessandro Tondelli Maria Aragona Maria Teresa Valente Chiara Biselli Francesca Desiderio Paolo Bagnaresi Slavica Matic Maria Lodovica Gullino Alessandro Infantino Davide Spadaro Giampiero Valè |
| author_facet | Andrea Volante Alessandro Tondelli Maria Aragona Maria Teresa Valente Chiara Biselli Francesca Desiderio Paolo Bagnaresi Slavica Matic Maria Lodovica Gullino Alessandro Infantino Davide Spadaro Giampiero Valè |
| author_sort | Andrea Volante |
| collection | DOAJ |
| description | Abstract Background Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. Results A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci. Conclusions New effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided. |
| first_indexed | 2024-12-20T04:13:25Z |
| format | Article |
| id | doaj.art-6afab4cedb984c7982cd49fb208bcd89 |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-12-20T04:13:25Z |
| publishDate | 2017-06-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-6afab4cedb984c7982cd49fb208bcd892022-12-21T19:53:50ZengSpringerOpenRice1939-84251939-84332017-06-0110111610.1186/s12284-017-0168-zIdentification of bakanae disease resistance loci in japonica rice through genome wide association studyAndrea Volante0Alessandro Tondelli1Maria Aragona2Maria Teresa Valente3Chiara Biselli4Francesca Desiderio5Paolo Bagnaresi6Slavica Matic7Maria Lodovica Gullino8Alessandro Infantino9Davide Spadaro10Giampiero Valè11Council for Agricultural Research and Economics (CREA), Rice Research UnitCouncil for Agricultural Research and Economics (CREA), Genomics Research CentreCouncil for Agricultural Research and Economics (CREA), Plant Pathology Research CentreCouncil for Agricultural Research and Economics (CREA), Plant Pathology Research CentreCouncil for Agricultural Research and Economics (CREA), Genomics Research CentreCouncil for Agricultural Research and Economics (CREA), Genomics Research CentreCouncil for Agricultural Research and Economics (CREA), Genomics Research CentreAGROINNOVA, Università di TorinoAGROINNOVA, Università di TorinoCouncil for Agricultural Research and Economics (CREA), Plant Pathology Research CentreAGROINNOVA, Università di TorinoCouncil for Agricultural Research and Economics (CREA), Rice Research UnitAbstract Background Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. Results A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci. Conclusions New effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided.http://link.springer.com/article/10.1186/s12284-017-0168-zBakanaeDisease resistance lociGenome wide association study (GWAS)Candidate genes |
| spellingShingle | Andrea Volante Alessandro Tondelli Maria Aragona Maria Teresa Valente Chiara Biselli Francesca Desiderio Paolo Bagnaresi Slavica Matic Maria Lodovica Gullino Alessandro Infantino Davide Spadaro Giampiero Valè Identification of bakanae disease resistance loci in japonica rice through genome wide association study Rice Bakanae Disease resistance loci Genome wide association study (GWAS) Candidate genes |
| title | Identification of bakanae disease resistance loci in japonica rice through genome wide association study |
| title_full | Identification of bakanae disease resistance loci in japonica rice through genome wide association study |
| title_fullStr | Identification of bakanae disease resistance loci in japonica rice through genome wide association study |
| title_full_unstemmed | Identification of bakanae disease resistance loci in japonica rice through genome wide association study |
| title_short | Identification of bakanae disease resistance loci in japonica rice through genome wide association study |
| title_sort | identification of bakanae disease resistance loci in japonica rice through genome wide association study |
| topic | Bakanae Disease resistance loci Genome wide association study (GWAS) Candidate genes |
| url | http://link.springer.com/article/10.1186/s12284-017-0168-z |
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