Genome-wide association study identifies a gene responsible for temperature-dependent rice germination

Area of Science:

• Plant genetics and molecular biology
• Agricultural science
• Environmental adaptation in crops

Background:

• Agricultural productivity is significantly influenced by environmental factors, leading to crop breeding for environmental adaptation.
• Seed germination physiology is assumed to be optimized for diverse climatic conditions.

Purpose of the Study:

• To investigate the genetic basis of seed germination in rice.
• To analyze genotype-by-environment interactions affecting rice germination rates under varying temperatures.

Main Methods:

• Conducted a genome-wide association study (GWAS) on Japanese rice cultivars.
• Examined germination rates under different temperature conditions.
• Identified a specific genetic variant (4 bp InDel) in the GF14h gene.

Main Results:

• A 4 bp insertion/deletion (InDel) in the GF14h gene significantly impacts rice germination rates, especially at optimal temperatures.
• The GF14h protein interacts with OREB1 and MOTHER OF FT AND TFL 2 to regulate abscisic acid (ABA)-responsive genes controlling germination.
• A loss-of-function allele in GF14h enhances ABA signaling, reducing germination rate.

Conclusions:

• The GF14h gene plays a crucial role in temperature-dependent seed germination regulation in rice.
• The identified GF14h allele is prevalent in rice varieties from northern regions and modern East Asian cultivars, indicating its role in geographical adaptation.
• This study elucidates a complex molecular system enabling rice cultivation across diverse geographical locations.