CAFRI-Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

Area of Science:

• Plant Genomics
• Functional Genomics
• Bioinformatics

Background:

• Rice (Oryza sativa L.) is a vital staple crop, but functional genomic research is challenged by gene redundancy, masking knockout phenotypes.
• Existing multi-omics data and mutant populations have not fully overcome the bottleneck of functional compensation in rice.

Purpose of the Study:

• To develop an intuitive tool, CRISPR Applicable Functional Redundancy Inspector to accelerate functional genomics in rice (CAFRI-Rice).
• To systematically identify genes exhibiting functional redundancy in the rice genome.

Main Methods:

• Generated a phylogenetic heatmap estimating protein sequence and expression pattern similarity using 2,617 phylogenetic trees and 8 tissue RNA-sequencing datasets.
• Analyzed 33,483 genes, sorting them into 2,617 families, and tested ~24,980 genes for functional redundancy.
• Validated the threshold for functional redundancy using 111 known genes and 5,170 duplicated genes.

Main Results:

• Predicted 7,075 genes with functional redundancy based on the validated threshold.
• Identified anther/pollen-preferred gene clusters as having higher functional redundancy compared to other clusters.
• Demonstrated CAFRI-Rice's utility by overcoming functional redundancy in two root-preferred genes via loss-of-function analyses.

Conclusions:

• CAFRI-Rice provides an effective approach to identify functionally redundant genes in rice, accelerating functional genomics.
• The CAFRI-Rice tool and methodology can be readily adapted for functional genomics studies in other plant species.
• CAFRI-Rice facilitates target selection for CRISPR/Cas9-mediated mutagenesis, advancing rice research and crop improvement.