Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

Area of Science:

• Plant Science
• Genetics
• Agricultural Science

Background:

• Seed germination is vital for crop production, with radicle protrusion being a critical early stage.
• Understanding the genetic basis of seed protrusion is essential for improving rice cultivation and yield.

Purpose of the Study:

• To identify genetic loci and candidate genes controlling seed protrusion percentage (PP) in rice.
• To analyze the association between specific alleles and improved germination and protrusion phenotypes.

Main Methods:

• Genome-Wide Association Study (GWAS) on 302 rice microcore germplasm populations for protrusion percentage (PP).
• Candidate gene analysis and haplotype analysis of identified quantitative trait loci (QTLs).
• Phenotypic validation of candidate genes' effects on germination percentage and vigor index.

Main Results:

• Six PP-associated QTLs were detected, with qPP2 identified repeatedly.
• Three candidate genes (LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1), LOC_Os04g0425 (CTB2)) were identified for major QTLs.
• Specific haplotypes of ETR3, GH3.1, and CTB2 were found to be elite alleles, significantly enhancing PP, germination, and vigor.

Conclusions:

• Identified three key candidate genes (ETR3, GH3.1, CTB2) involved in the genetic control of rice seed protrusion.
• Demonstrated the potential of specific elite alleles for marker-assisted selection to improve rice seed germination and crop establishment.
• Provided valuable genetic insights for breeding superior rice varieties with enhanced germination traits.