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Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

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Title: Genome wide association studies for japonica rice resistance to blast in field and controlled conditions
Authors: Andrea Volante, Alessandro Tondelli, Francesca Desiderio, Pamela Abbruscato, Barbara Menin, Chiara Biselli, Laura Casella, Namrata Singh, Susan R. McCouch, Didier Tharreau, Elisa Zampieri, Luigi Cattivelli, Giampiero Valè
Source: Rice, Vol 13, Iss 1, Pp 1-17 (2020)
Publisher Information: SpringerOpen, 2020.
Publication Year: 2020
Collection: LCC:Plant culture
Subject Terms: Rice, Blast disease, Genome-wide association study (GWAS), Marker-trait associations (MTAs), Blast resistance, Plant culture, SB1-1110
More Details: Abstract Background Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. Results The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11–2 and BRGC11–3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. Conclusions We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1939-8425
1939-8433
Relation: http://link.springer.com/article/10.1186/s12284-020-00431-2; https://doaj.org/toc/1939-8425; https://doaj.org/toc/1939-8433
DOI: 10.1186/s12284-020-00431-2
Access URL: https://doaj.org/article/811c07feed904eb0be17bd878bdd4a16
Accession Number: edsdoj.811c07feed904eb0be17bd878bdd4a16
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  Data: <searchLink fieldCode="AR" term="%22Andrea+Volante%22">Andrea Volante</searchLink><br /><searchLink fieldCode="AR" term="%22Alessandro+Tondelli%22">Alessandro Tondelli</searchLink><br /><searchLink fieldCode="AR" term="%22Francesca+Desiderio%22">Francesca Desiderio</searchLink><br /><searchLink fieldCode="AR" term="%22Pamela+Abbruscato%22">Pamela Abbruscato</searchLink><br /><searchLink fieldCode="AR" term="%22Barbara+Menin%22">Barbara Menin</searchLink><br /><searchLink fieldCode="AR" term="%22Chiara+Biselli%22">Chiara Biselli</searchLink><br /><searchLink fieldCode="AR" term="%22Laura+Casella%22">Laura Casella</searchLink><br /><searchLink fieldCode="AR" term="%22Namrata+Singh%22">Namrata Singh</searchLink><br /><searchLink fieldCode="AR" term="%22Susan+R%2E+McCouch%22">Susan R. McCouch</searchLink><br /><searchLink fieldCode="AR" term="%22Didier+Tharreau%22">Didier Tharreau</searchLink><br /><searchLink fieldCode="AR" term="%22Elisa+Zampieri%22">Elisa Zampieri</searchLink><br /><searchLink fieldCode="AR" term="%22Luigi+Cattivelli%22">Luigi Cattivelli</searchLink><br /><searchLink fieldCode="AR" term="%22Giampiero+Valè%22">Giampiero Valè</searchLink>
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  Data: Rice, Vol 13, Iss 1, Pp 1-17 (2020)
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  Data: Abstract Background Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. Results The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11–2 and BRGC11–3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. Conclusions We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
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        Value: 10.1186/s12284-020-00431-2
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      – Text: English
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        PageCount: 17
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      – SubjectFull: Rice
        Type: general
      – SubjectFull: Blast disease
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