Phenotypic Diversity And Homeologous Expression In Newly Synthesized Rice Tetraploids Between Japonica And Indica Subspecies

Polyploidization(whole genome doubling)is believed as a driving force to angiosperm evolution and can prompt speciation.Series of evidences indicate that a large number of flowering plants have been through polyploidization or,at least,have undergone one round of polyploidization.Thus far,the polyploidy has been considered to have better adaptability from the broad scope of environmental conditions than the diploid.In this study,by taking advantage of newly synthetic tetraploid rice,99 NN and NN9 derived from F1 hybrids of diploid parents Nipponbare(O.sativa ssp.japonica)and 93-11(O.sativa ssp.indica)9N and N9,we tried to dissect how polyploidization affects the plant physiology in the scope of evolution.MassArray genotyping,pyro-sequencing and real-time qPCR technology were also employed to examine the impact on hybridization and polyploidization in terms of comparing different phenotypic and genetic effects.Furthermore,the response to low nitrogen stress of tetraploid rice has also been investigated.By measuring different phenotypic parameters including plant height,flag leaf width and seed length to width ratio,we observed clear phenotypic diversities existed in tetraploid population compared to diploid parents and F1 hybrids.Based on genotyping results from 52 loci-specific MassArray analysis,tetraploid rice populations exhibited wide range of variation in terms of relative homeologous gene expression among different individual plant.Meanwhile,relative homeologous gene expression in F1 hybrids was mostly centralized as 1:1 ratio,meaning that two subgenomes contribute equally in hybrid.This observation was mainly due to variation of trans-regulation effect exhibiting the major contribution.Comparison between F1 hybrid and in virto “hybrid” displayed a large number of genes showed inherited relative gene expression patterns of parents,which phenomenon is so-called “parental legacy”.In tetraploid population,less than 50% analyzed genes from each individual showed parental legacy expression,however,most individuals displayed novel expression patterns compared to orthologous expression in vitro “hybrid”.The data showing strong correlation from DNA and RNA genotyping result revealed that the extensive homeologous gene expressional variation occurred due to DNA copy number alteration caused by unknown chromosome rearrangement mechanism during meiosis of polyploidy formation,which can be speculated as rearrangement,trans-location and so forth.Also,we discovered one or both parental homeologs were silenced in certain tissues together with the existence of chromosome fragment,indicating that instant genetic and epigenetic regulation could occur during the onset of polyploidization.Real-time qPCR result on randomly selected 10 genes revealed that unlike the case of homeologous relative gene expression in tetraploid,total gene expression patterns varied at population level in a relatively narrow range.The canalization of gene expression may be due to low divergence between genome of Nipponbare and 93-11.Consequently,total gene expression patterns displayed similar patterns among different individuals regardless of having different homeologous proportion.This results could be explained using gene balance hypothesis.When exposing rice materials under low nitrogen stress,no obvious difference homeologous constitution could be observed between the control and stressed groups.This result indicated that low nitrogen stress was not strong enough to make tetraploids adjust the subgenome content.This result also implies that tetraploid rice harbor higher tolerance to low nitrogen stress.According to real-time qPCR results,gene expressional level of F1 hybrid were not apparently decreased under low nitrogen environment.In contrast,although gene expression levels of tetraploids were not upregulated compared to diploid parents in the control group,the numbers of up-regulated and non-additive genes were increased in stressed group.The decreased fresh weight variation in stressed group compared to the control group indicated that low nitrogen restricted the rice growth and development.Compared to diploid parents,fresh weight of tetraploids only slightly decreased,especially in NN99,but no statistical difference was found between control and stressed groups.These results indicate that polyploids are less sensitive to low nitrate stress compared to diploid parents to low nitrogen.In conclusion,hybridization and polyploidization possesses displayed different effects on plant growth and development.Hybridization attenuated the inherent homolog divergences in diploids.On the contrary,genome doubling generated colorful unexpected homeologous gene expression patterns and divergences due to DNA copy number alteration and variation.Thus,we propose polyploidization conferred better adaptation to low nitrogen environment in rice.