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An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment.

Publication ,  Journal Article
Castano-Duque, L; Ghosal, S; Quilloy, FA; Mitchell-Olds, T; Dixit, S
Published in: Plant physiology
June 2021

Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages.

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Published In

Plant physiology

DOI

EISSN

1532-2548

ISSN

0032-0889

Publication Date

June 2021

Volume

186

Issue

2

Start / End Page

1042 / 1059

Related Subject Headings

  • Water
  • Seeds
  • Seedlings
  • Polymorphism, Single Nucleotide
  • Plant Growth Regulators
  • Plant Biology & Botany
  • Oryza
  • Germination
  • Genotype
  • Genome-Wide Association Study
 

Citation

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Castano-Duque, L., Ghosal, S., Quilloy, F. A., Mitchell-Olds, T., & Dixit, S. (2021). An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment. Plant Physiology, 186(2), 1042–1059. https://doi.org/10.1093/plphys/kiab100
Castano-Duque, Lina, Sharmistha Ghosal, Fergie A. Quilloy, Thomas Mitchell-Olds, and Shalabh Dixit. “An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment.Plant Physiology 186, no. 2 (June 2021): 1042–59. https://doi.org/10.1093/plphys/kiab100.
Castano-Duque L, Ghosal S, Quilloy FA, Mitchell-Olds T, Dixit S. An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment. Plant physiology. 2021 Jun;186(2):1042–59.
Castano-Duque, Lina, et al. “An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment.Plant Physiology, vol. 186, no. 2, June 2021, pp. 1042–59. Epmc, doi:10.1093/plphys/kiab100.
Castano-Duque L, Ghosal S, Quilloy FA, Mitchell-Olds T, Dixit S. An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment. Plant physiology. 2021 Jun;186(2):1042–1059.

Published In

Plant physiology

DOI

EISSN

1532-2548

ISSN

0032-0889

Publication Date

June 2021

Volume

186

Issue

2

Start / End Page

1042 / 1059

Related Subject Headings

  • Water
  • Seeds
  • Seedlings
  • Polymorphism, Single Nucleotide
  • Plant Growth Regulators
  • Plant Biology & Botany
  • Oryza
  • Germination
  • Genotype
  • Genome-Wide Association Study