Molecular Studies Of Super Hybrid Rice Heterosis LYP9

Cross-breeding has been explored to agriculture for over 100 years.While,the genetic basis and molecular mechanisms for the phenomenon that hybrid offspring exhibit phenotypic performance that is superior to that of their parents are still elusive.Currently,there are two hypotheses to explain genetic basis of heterosis,dominance hypothesis and overdominance hypothesis.But the evidences supporting these two hypothesis are insufficient.This study is intended to find molecular mechanisms for heterosis using hybrid rice and its parents.First,we chose the super hybrid rice LYP9,which displayed great advantage in yield and vigor than both parents 9311 and PA64S.Moreover,we used the Affymetrix probe to acquire gene expression dataset.And then,we used Bioconductor package in R language to calculate the differentially expressed genes(DEGs).We compared gene expression between two different organs,two different treatment among three varieties.Interestingly,we found that most differentially expressed genes were present in both parents(86.17%),only few DEGs exists solely between parents and offspring.Compared with maternal PA64S,there are more DEG between LYP9 and paternal 9311.Further,we evaluated the gene expression pattern of the offspring,demonstrating that the predominance pattern was additive(84.5%-95.5%).On the other hand,only small proportion of DEGs are overdominant and underdominant.Besides,We identified Present/Absent gene(PAe).Consistent with DEGs,number of PAe between 9311 and LYP9 is larger than that of PA64S and LYP9,indicating that,there were more PAe between 9311 and LYP9,while more non-PAe existed between PA64S and LYP9.At the same time,we located DEGs to QTLs.Our in-depth analysis revealed that DEGs were enriched in QTLs related to yield and growth vigor.27.9%DEGs could be mapped to QTLs less than 1M,most of which were correlated with biomass,plant height and thousand seed weight.In order to analyze the function of DEGs,we used the GO enrichment analysis.Among the 1233 DEGs between hybrid and parental lines,583 have a corresponding GOID.And taking the 111,54 genes having a corresponding GO ID as control,We eventually got a total of 40 enriched GO classification,out of which 10 were in Biological Process,2 were in Cellular component and 28 were in Molecular Function.