Both maternally and paternally imprinted genes regulate seed development in rice

Area of Science:

• Plant genetics
• Epigenetics
• Molecular biology

Background:

• Genetic imprinting, unequal parental allele expression, is known in plants but functions are understudied.
• Identifying and characterizing imprinted genes in rice is crucial for understanding seed development.

Purpose of the Study:

• To perform a genome-wide analysis of imprinted genes in rice endosperm.
• To investigate the functions of imprinted genes in seed development using CRISPR/Cas9 technology.

Main Methods:

• Genome-wide analysis of gene expression, DNA methylation, and small RNAs in rice endosperm.
• Functional testing of five imprinted genes using CRISPR/Cas9 gene editing.
• Association analysis with quantitative trait loci (QTLs) for grain yield.

Main Results:

• Identified 162 maternally expressed genes (MEGs) and 95 paternally expressed genes (PEGs) in rice endosperm.
• MEGs and PEGs are linked to transposable elements, differentially methylated loci, and small RNAs.
• Significant overlap found between imprinted genes and grain yield QTLs; gene disruption impacts starch content, grain size, and fertility.

Conclusions:

• Both MEGs and PEGs in rice are vital for nutrient metabolism and endosperm development.
• Imprinted genes optimize seed development and offspring fitness, facilitating parental-offspring coadaptation.
• These findings provide targets for improving grain yield in rice and other crops.