Comprehensive Analysis of Ghd7 Variations Using Pan-Genomics and Prime Editing in Rice

Area of Science:

• Plant genetics
• Crop science
• Molecular biology

Background:

• The Ghd7 gene is vital for rice heading date, plant height, and grain yield.
• Understanding Ghd7 variations is key for rice improvement, but remains incomplete.

Purpose of the Study:

• To investigate structural variations (SVs) in the Ghd7 locus across diverse rice accessions.
• To develop a method for identifying Ghd7 SVs using next-generation sequencing (NGS) data.
• To explore the functional impact of Ghd7 variations and apply gene editing for crop enhancement.

Main Methods:

• Pan-genome analysis of 372 rice varieties to identify Ghd7 structural variations.
• Development of an NGS and Polymerase Chain Reaction (PCR)-based method for SV identification.
• Identification of single-nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) in the Ghd7 coding region.
• Application of prime editing (PE) technology to correct Ghd7 mutations.

Main Results:

• Identified structural variations in the Ghd7 locus across 372 rice varieties.
• Developed and validated an NGS/PCR method to detect Ghd7 SVs in 977 accessions.
• Characterized 46 SNPs and one InDel in the Ghd7 coding region, forming 49 haplotypes.
• Demonstrated that a splice-site mutation in haplotype H6 causes aberrant mRNA splicing.
• Successfully restored Ghd7 function using PE in Yixiang 1B (YX1B), delaying heading by ~16 days.

Conclusions:

• Integrating pan-genomics and precision gene editing accelerates crop improvement.
• Targeted modification of Ghd7 can enhance agronomic traits like heading date.
• This approach improves hybrid rice seed production efficiency by synchronizing heading dates.