Integrative genomic and transcriptomic approaches decipher pre-harvest sprouting resistance in rice

Area of Science:

• Agricultural Science
• Genetics
• Plant Biology

Background:

• Pre-harvest sprouting (PHS) significantly reduces rice yield and quality.
• Genetic resistance is crucial for mitigating PHS, necessitating advanced breeding strategies.

Purpose of the Study:

• To construct high-resolution genetic variation maps for indica rice.
• To identify causal genes conferring resistance to PHS using multi-omics approaches.

Main Methods:

• Whole-genome re-sequencing of 165 diverse indica rice accessions.
• Genome-wide association studies (GWAS) and transcriptomic analysis.
• Identification and prioritization of candidate genes, including haplotype analysis.

Main Results:

• A high-density genetic variation map with 1,584,905 SNPs was created.
• GWAS identified 21 candidate loci and multiple PHS-associated genes.
• Integration of GWAS and transcriptomics highlighted UGT74J1, with UGT74J1-Hap3 showing superior PHS resistance.

Conclusions:

• The study provides valuable multi-omics data and identified key genes for PHS resistance.
• UGT74J1 is a promising candidate gene for developing PHS-resistant rice.
• These findings support molecular breeding for enhanced PHS resistance in rice.