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ARS Home » Southeast Area » Raleigh, North Carolina » Soybean and Nitrogen Fixation Research » Research » Publications at this Location » Publication #376686

Research Project: Exploiting Genetic Diversity through Genomics, Plant Physiology, and Plant Breeding to Increase Competitiveness of U.S. Soybeans in Global Markets

Location: Soybean and Nitrogen Fixation Research

Title: Rice flooding resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater

item ALAM, REJBANA - University Of California
item HUMMEL, MAUREEN - University Of California
item YEUNG, ELAINE - University Of California
item Locke, Anna
item IGNACIO, JOHN CARLOS - International Rice Research Institute
item BALTAZAR, MIRIAM - Cavite State University
item JIA, ZHENYU - University Of California
item ISMAIL, ABDELBAGI - International Rice Research Institute
item SEPTININGSIH, ENDANG - University Of California
item BAILEY-SERRES, JULIA - University Of California

Submitted to: Plant Direct
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/17/2020
Publication Date: 7/22/2020
Publication URL:
Citation: Alam,R., Hummel, M., Yeung, E., Locke, A.M., Ignacio, J.I., Baltazar, M.D., Jia, Z., Ismail, A.M., Septiningsih, E.M., Bailey-Serres, J. 2020. Rice flooding resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct. 4(7): 1-19.

Interpretive Summary: Two key genes conferring flood tolerance in rice are AG1 and SUB1. AG1 allows seeds to germinate under floodwaters, and SUB1 allows plants in the vegetative growth stage to survive long, deep floods. When both genes are present, seeds can still germinate under water, but seedling growth and development underwater can be delayed. Transcriptome analyses showed that the impacts of AG1 and SUB1 change over 14 days of seedling development, and carbohydrate metabolism and growth-related transcripts are especially impacted by AG1-SUB1 interactions.

Technical Abstract: Genetic pyramiding of abiotic stress tolerance loci is important for crop improvement. In rice (Oryza sativa L.), ANAEROBIC GERMINATION 1 (AG1) encoding TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 (TPP7) promotes mobilization of endosperm reserves to enhance elongation growth of a hollow coleoptile in seeds sown into shallow paddies. This trait can reduce planting labor costs and herbicide use. Tolerance of established seedlings to complete submergence is conferred by SUBMERGENCE 1 (SUB1), encoding ethylene-responsive transcription factor SUB1A-1 that dampens elongation of shoots and enhances regrowth upon desubmergence. We evaluated interactions between these two stress resilience genes under three flooding scenarios. Analysis of growth, carbohydrate content, and embryo plus shoot transcriptome of near-isogenic genotypes in seedlings established underwater for 14 d revealed, (a) TPP7 enhances early coleoptile elongation; (b) SUB1A-1 promotes precocious upregulation of mRNAs associated with photoautotrophy followed by restricted underwater elongation; and (c) interaction between AG1 and SUB1 results in delayed growth, including the delayed transition to photoautotrophy. mRNA-sequencing highlighted complex time-dependent and genotype-specific regulation of mRNAs associated with plastid biogenesis, starch catabolism, carbohydrate transport, elongation growth, chromatin modifications, and defense responses. The interaction between AG1 and SUB1 could impact seedling establishment if paddy depth is not effectively managed after seeding.