Studies On The Role Of Imprinted Genes In Rice Seed Development

Rice cultivation promoted human civilization,and rice is one of the most important food crops in the world.Seed size is directly related to crop yield and production.Rice seed consists of seed coat,endosperm,and embryo.The endosperm is the nutrient source for embryonic and seed development,which accounts for the majority of seed volume and determines the seed size.The expression of imprinted genes is dependent on the parent-of-origin effect and is regulated by epigenetic mechanisms.Imprinting occurs primarily in the placenta of mammals and the endosperm of flowering plants.It is thought that imprinted genes as well as many other factors control the endosperm development in rice.Now there are two hypotheses to explain the biological significance of genetic imprinting.A prevailing hypothesis for imprinting is known as the "parental-conflict model",which suggests that imprinting is a strategy for mother and father to resolve maternal resource distribution to the offspring.However,this model does not apply to self-fertilizing organisms like rice.An alternative model is the "parental-offspring coadaptation model" proposes that genomic imprinting is a consequence of natural selection for increased offspring fitness,by enhancing the genetic integration of co-adapted traits such as seed size between offspring and parents.However,genetic and functional evidence for the coadaptation model is very limited in plants and animals.This research aims to explain the regulatory mechanism of imprinted genes control the rice seed size.To understand the function of imprinted genes,we selected five candidate imprinted genes that are highly expressed in endosperm using the bioinformatics analysis of existing genome-wide gene expression datatsets developed in our laboratory.MEG2(Os07g20110)and MEG3(Os06g30280)are maternally expressed genes;FBD(Os01g41370),FBX365(Osl0g04980)and FBDUF48(Os10g37540)are paternally expressed genes.The results were as follows:Using CRISPR/Cas9 technology,we produced locus-specific mutations for each candidate gene and made homozygous lines.The seed length and width were reduced by?10%in meg2-1 and meg2-2 homozygous mutants,but glumes(maternal tissue)remained unchanged,ruling out a possibility of the maternal effect on seed development.In addition,the 1000-grain weight of two frame-shift mutations(meg2-1 and meg2-2)was significantly reduced compared to the transgenic control.In the meg3 mutant,1000-grain weight was reduced,but seed size and glumes were unchanged relative to the transgenic control.Interestingly,in the reciprocal crosses involving a homozygous mutation(meg2-1),when the meg2-1 was used as the female parent,F1 seeds were smaller than those in the reciprocal cross.The seed size of meg2-1 X Nipponbare but not Nipponbare X meg2-1 resembled that of meg2-1 mutant.These data confirmed the maternal transmission of MEG2 that contributed to the seed size in rice.Moreover,the grain length and the 1000-grain weight were reduced in fbx365,but the glumes remained unchanged.In the fbduf48 mutant,the seed width was reduced by?10%,and the 1000-grain weight was significantly reduced compared to the transgenic control.The results indicated that the paternally imprinted genes FBX365 and FBDUF48 affected the seed size in rice.The "parent-conflict model" predicts that paternally imprinted genes promote seed development,while maternally imprinted genes suppress seed growth.In contract to this prediction,the mutation of both maternally and paternally imprinted genes reduced seed size.The results supported the "parental-offspring coadaptation model",which selectively maintains parental and offspring traits to achieve the optimal offspring size.The candidate imprinted genes identified from this study can be used to improve grain yield of rice and other cereal crops.In conclusion,this study provided genetic and molecular evidence that the maternally imprinted genes MEG2(Os07g20110)and MEG3(Os06g30280),the paternally imprinted genes FBX365(Os10g04980)and FBDUF48(Os10g37540)regulate the endosperm development and grain size in rice.