Transcriptome-wide analysis of rice temperature memory and heat responses

• Grant number: 19/13158-8
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: June 01, 2021
• End date: May 31, 2026
• Field of knowledge: Biological Sciences - Botany - Pant Physiology
• Principal Investigator: Cristiane Paula Gomes Calixto
• Grantee: Cristiane Paula Gomes Calixto
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Abdellah Barakate ; Marcia Maria Auxiliadora Naschenveng Pinheiro Margis ; Maria Helena de Souza Goldman ; John W S Brown ; Runxuan Zhang ; Silvana Aparecida Creste Dias de Souza ; Wenbin Guo
• Associated research grant(s): 21/00394-5 - Multi-user Equipment approved in grant 2019/13158-8: camara growth house for plant, AP.EMU
• Associated scholarship(s): 24/03165-5 - Evaluation of antioxidant defense in response to heat in rice cultivars contrasting for thermotolerance., BP.IC; 23/16278-0 - RICE GENETIC TRANSFORMATION, BP.TT; 22/02633-0 - In silico functional analysis and construction of CRISPR/Cas9 knockout-allowing plasmid for rice (Oryza sativa L.) heat stress-responsive gene Telomere Repeat-Binding Factor 1, BP.IC; + associated scholarships 22/03433-4 - Establishment and maintenance of rice germplasm and transformation protocols, BP.TT; 21/12014-2 - Establishment of the CRISPR-Cas9 methodology and obtaining knockout plants in candidate genes for regulators of alternative RNA processing in heat stress in rice, BP.MS; 21/00795-0 - Two putative heat-sensitive splicing regulators: expression analysis and cloning in plant overexpression vectors, BP.IC - associated scholarships

Abstract

The future of food security is being threatened by climate change. Rice is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of thermotolerance must be understood. The mechanisms underlying the formation, extent, and resetting of thermotolerance and HS memories in plants is largely unknown. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses and recent evidence suggest they may play an important role in temperature memory. To investigate this hypothesis, our project aims to explore the transcriptome of rice cultivars contrasting for thermotolerance to investigate both basal and acquired thermotolerance responses, which will be examined with state-of-the-art analysis methods established by our team. Additionally, we will investigate the sensitivity and speed of expression and alternative splicing (AS) behaviour of key heat-sensitive genes in different heat stress conditions, as well as its regulation in rice cultivars with contrasting heat tolerance/sensitivity. Lastly, we will investigate putative heat-affected regulators of AS, selected by our preliminary analysis, by generating over-expression and loss-of-function (non-transgenic CRISPR-Cas9) lines in candidate genes, which will be monitored for heat stress phenotypes. The resulting knowledge will provide insight and strategies to rapidly advance rice breeding in response to changing environments. (AU)

Scientific publications

(4)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BOULANGER, HADRIEN GEORGES; GUO, WENBIN; REBOCHO MONTEIRO, LUCCA DE FILIPE; CALIXTO, CRISTIANE PAULA GOMES. Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance. FRONTIERS IN MOLECULAR BIOSCIENCES, v. 10, p. 10-pg., 2023-02-02. (19/13158-8, 22/02633-0)

CALIXTO, CRISTIANE PAULA GOMES. Molecular aspects of heat stress sensing in land plants. Plant Journal, v. 121, n. 6, p. 16-pg., 2025-03-01. (19/13158-8)

VITORIANO, CHARLES BARROS; CALIXTO, CRISTIANE PAULA GOMES. Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress. PLANTS-BASEL, v. 10, n. 8, AUG 2021. (19/13158-8)

PONTE, LUCAS ROANI; ALVES, JOVER DA SILVA; LIMA-MELO, YUGO; MENGUER, PALOMA KOPROVSKI; BOULANGER, HADRIEN GEORGES; GIEHL, RICARDO FABIANO HETTWER; CALIXTO, CRISTIANE PAULA GOMES; MARGIS-PINHEIRO, MARCIA; RICACHENEVSKY, FELIPE KLEIN. Abscisic acid, stress andripening (ASR) proteins play a role in iron homeostasis in rice (Oryza sativa L.). Plant Physiology and Biochemistry, v. 223, p. 14-pg., 2025-06-01. (19/13158-8)