Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Document Type

Article

Publication Title

Scientific reports

PubMed ID

33762605

MeSH Headings (Medical Subject Headings)

Computational Biology (methods); Edible Grain (genetics); Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genetic Association Studies; Genome-Wide Association Study (methods); Oryza (genetics); Phenotype; Stress, Physiological; Temperature

Abstract

High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

First Page

6747

DOI

10.1038/s41598-021-85921-z

Publication Date

3-24-2021

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