Molecular Mechanism For Heterosis In Super Hybrid Rice During Early Vegetative Growth Phase Based On Negative Control

Heterosis has long been exploited for crop breeding,but the genetic mechanisms,especially the initial establishment of heterosis in early vegetative growth phase,are still elusive.In order to interpret the genetic basis of heterosis from the perspective of gene expression,many researches concentrated on the genome-wide transcriptome analysis between hybrid and parents.However,results varied from diffent hybridization to different tissue or even different development stages.The reason for this controversy probably lies in that there are many differentially expressed genes between hybrid and parents,even that hybrid did not exhibit any visible heterosis.Therefore,the most challenge in identifying heterosis related genes is to exclude the background differentially expressed genes.Herein,we carried out a well-designed experiment:all seedlings of hybrid and parents were planted evenly in raw soil under the same condition except that one group was well-fertilized with compound fertilizer and the other group was applied with nothing but water.Interestingly,seedling of hybrid in fertilized group exhibit obviously enhanced growth heterosis,whereas,did not exhibit any visible growth heterosis in nutrition starved environment.Therefore,using nutrition starved hybrid with no visible growth heterosis as control,it could be convenient to filter these background differentially expressed genes.Intriguingly,if negative control was not used,1605 DEGs were identified,which is not significantly different from previous reports.However,if negative control was used,only 336 DEGs were identified as heterosis related genes,which is much less than previously reported,and could ensure the reliability for subsequent analysis.Among these 336 DEGs,approximately 35.4%DEGs were exclusively up or down-regulated between hybrid and either parents.Interestingly,function analysis revealled that up-regulated genes in hybrid mainly encoded various enzymes,which is consistent with our expectations;Whereas,down-regulated genes in hybrid were enriched in responses to stress,indicating that hybrid may benefit from alleviating fitness cost through allelic interactions.For the first time we observed the phenomenon that down-regulation of genes responsible for stress might contribute to heterosis.Moreover,when background noise genes were taken into consideration,significantly larger number of DEGs were inherited from maternal line than that from paternal line(498 versus 358),which is in accord with previous observations in Arabidopsis and mice.However,if we excluded background noise genes,significantly larger number of DEGs were inherited from paternal line than that of maternal line(148 versus 110).That is to say,more differentially expressed genes in hybrid were inherited from paternal line,rather than maternal line,suggesting a more importantly anticipated role for parental effect in early vegetative growth phase of hybrid.Furthermore,significantly high proportion of asymmetric genes(?23.4%)and genes with high non-synonymous substitutions rates could be detected in these DEGs,suggesting a potential contribution to establishment of heterosis in early vegetative growth phase of super hybrid rice.