Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice

Area of Science:

• Agricultural Science
• Genetics
• Plant Biology

Background:

• Seed dormancy is crucial for rice production, but its genetic mechanisms remain largely unknown.
• Previous studies have identified only a limited number of genes controlling rice seed dormancy.

Purpose of the Study:

• To identify quantitative trait loci (QTLs) associated with rice seed dormancy.
• To uncover novel genetic factors influencing seed germination and dormancy in rice.

Main Methods:

• Evaluated seed germination rate (GR) in 195 diverse rice accessions under control and dormancy-breaking conditions (dry heating and gibberellic acid).
• Conducted genome-wide association study (GWAS) using 1,120,223 single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM).

Main Results:

• Identified 30 QTLs across 10 chromosomes, explaining 7.3-20.4% of phenotypic variance in GR.
• Discovered 20 novel QTLs, with 10 overlapping previously reported regions.
• Predicted 13 high-confidence candidate genes for key QTLs, showing high expression during seed development and hormone regulation.

Conclusions:

• This study enhances understanding of the genetic and molecular basis of rice seed dormancy and germination.
• Identified accessions and molecular markers for manipulating seed dormancy levels in rice breeding programs.