Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance
Abstract Background Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2023-05-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-023-00641-4 |
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| author | Beatriz Andreo-Jimenez Dennis E. te Beest Willem Kruijer Nathan Vannier Niteen N. Kadam Giovanni Melandri S. V. Krishna Jagadish Gerard van der Linden Carolien Ruyter-Spira Philippe Vandenkoornhuyse Harro J. Bouwmeester |
| author_facet | Beatriz Andreo-Jimenez Dennis E. te Beest Willem Kruijer Nathan Vannier Niteen N. Kadam Giovanni Melandri S. V. Krishna Jagadish Gerard van der Linden Carolien Ruyter-Spira Philippe Vandenkoornhuyse Harro J. Bouwmeester |
| author_sort | Beatriz Andreo-Jimenez |
| collection | DOAJ |
| description | Abstract Background Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance. |
| first_indexed | 2024-03-13T08:58:52Z |
| format | Article |
| id | doaj.art-e2695fa189834e6da672f73d0cb1dbf7 |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-03-13T08:58:52Z |
| publishDate | 2023-05-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-e2695fa189834e6da672f73d0cb1dbf72023-05-28T11:27:44ZengSpringerOpenRice1939-84251939-84332023-05-0116111610.1186/s12284-023-00641-4Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought ToleranceBeatriz Andreo-Jimenez0Dennis E. te Beest1Willem Kruijer2Nathan Vannier3Niteen N. Kadam4Giovanni Melandri5S. V. Krishna Jagadish6Gerard van der Linden7Carolien Ruyter-Spira8Philippe Vandenkoornhuyse9Harro J. Bouwmeester10Laboratory of Plant Physiology, Wageningen University and ResearchBiometris, Wageningen University and ResearchBiometris, Wageningen University and ResearchEcoBio, CNRS, Université de Rennes IInternational Rice Research InstituteLaboratory of Plant Physiology, Wageningen University and ResearchInternational Rice Research InstitutePlant Breeding, Wageningen University and ResearchLaboratory of Plant Physiology, Wageningen University and ResearchEcoBio, CNRS, Université de Rennes ILaboratory of Plant Physiology, Wageningen University and ResearchAbstract Background Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.https://doi.org/10.1186/s12284-023-00641-4DroughtFungiRoot mycobiotaGWASOryza sativa (rice)Roots |
| spellingShingle | Beatriz Andreo-Jimenez Dennis E. te Beest Willem Kruijer Nathan Vannier Niteen N. Kadam Giovanni Melandri S. V. Krishna Jagadish Gerard van der Linden Carolien Ruyter-Spira Philippe Vandenkoornhuyse Harro J. Bouwmeester Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance Rice Drought Fungi Root mycobiota GWAS Oryza sativa (rice) Roots |
| title | Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance |
| title_full | Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance |
| title_fullStr | Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance |
| title_full_unstemmed | Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance |
| title_short | Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance |
| title_sort | genetic mapping of the root mycobiota in rice and its role in drought tolerance |
| topic | Drought Fungi Root mycobiota GWAS Oryza sativa (rice) Roots |
| url | https://doi.org/10.1186/s12284-023-00641-4 |
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