Genomic And Transcriptomic Comparisons Between Hybrid Rice Shanyou 63 And Its Parents And Development Of Visualization Application For Genomics Data

Rice is one of the most staple crops for people.With the increasing size of world population,decrease of cultivated area and severe environmental pollution,grain yield remains to be improved to meet the increasing demand.Heterosis is a widely natural phenomenon,and the molecular basis of heterosis is still vague.With the simple genome structure and the extensive studies of rice functional genomics,rice is a primary model for the study of heterosis.To increase productivity of crops,explanation of the molecular basis of heterosis is imperative.Based on the high-quality reference genome sequences for two parents of an elite rice hybrid Shanyou 63 and their expression profiles of 36 samples covering the entire life cycle,we explored the molecular basis of yield heterosis in rice.Comparing the genome sequences of two indica rice varieties,3,984 PAV genes from Zhenshan 97 genome and 4,308 PAV genes from Minghui 63 genome were found.Functional enrichment analysis for PAV genes indicated that these genes exhibited more diverse functions involved in yield,growth and development,stress resistance and disease resistance,which appeared functional complementarity.Further analysis found 15 PAV genes with vital functions.RAD23 involved in cell cycle,plant development and Pikp-2 associated with blast resistance were present only in the genome of Zhenshan 97.OsWOX3 A related to growth and development,GHD7 involved in yield and PSTOL1 associated with phosphorus starvation tolerance were present only in the genome of Minghui 63.In addition,the variations of functional characterized genes between the genome of Zhenshan 97 and Minghui 63 were exactly the same as the key variations associated with biological functions.These genes endowed the genome of the hybrid more genes and sequence diversity.Based on the expression profiles of 36 samples covering the entire life cycle,we found that 216 genes were expressed only in Zhenshan 97,and 230 genes were expressed only in Minghui 63.Most of these variety-specific expression genes were expressed in the hybrid,indicating that more genes worked in the hybrid.By analyzing the specific expressed genes with important functions,we found that stress responsive genes OsANS and blast resistant gene Pikm2-TS were expressed only in Zhenshan 97.OsHAL3 regulating cell division and photoperiod and OsDET1 modulating the ABA biosynthesis and ABA signaling pathways were expressed only in Minghui 63.Furthermore,based on the pathway data from Gramene database,we analyzed the biological pathways of PAV genes and specific expressed genes between Zhenshan 97 and Minghui 63.We found that two PAV genes were involved in the pathway of chorismate biosynthesis and chlorophyll biosynthesis respectively,and a gene related to the photorespiration pathway was expressed only in the genome of Minghui 63.To compare the genomes and expression profile between Zhenshan 97 and Minghui 63 more efficiently,we construct shinyCircos,a GUI software,for interactive creation of Circos plot.shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community.Users can create diverse plot types by mouse-click based on input,including scatter plot,line plot,bar plot,rectangle,heatmap,chromosome ideogram and connectors,which can be used to exhibit multiple omics data.For example,line plot or scatter plot can be used to show QTL or GWAS analysis.Heatmap is suitable for showing expression profile or transcriptome.Rectangle is used to exhibit genomic structure and connectors are appropriate for showing translocation variations of genome structure or two-locus interactions of genetic analysis.In this study,shinyCircos is used to show the sequence analysis between the two genomes,and we found a mass of translocations,the frequency of which was different between chromosomes.For example,frequency of translocations was high in chromosome 4,11 and 12.We identified non-additively expressed genes in young panicles of the hybrid at the secondary branch primordium stage(panicle 1)using h test,referring to the genes expressed differentially between the hybrid and mid-parent level.A total of 503 genes were nonadditively expressed in the panicle 1 sample,including 294 down-regulated genes and 209 up-regulated genes.In order to illuminate the potential contributions of non-additively expressed genes in the hybrid,we performed GO enrichment analysis for down-regulated genes and up-regulated genes,respectively.We found that 36 terms were enriched in down regulation focusing on basically functional processes,including “protein processing”,“protein maturation”,“transport”,“localization”,some metabolic processes and biosynthetic processes.A total of 23 GO terms(~68%)related to regulatory functions were enriched in up regulation,including “regulation of cellular process”,“regulation of metabolic process” and “regulation of gene expression”,etc.These results indicated that down regulation of basically biological processes and more complex regulation in the hybrid may be involved in efficient utilization of energy and further contribute to heterosis.We also found that functional characterized genes with key functions were non-additively expressed,which contributed to its growth and development,including OsDWARF4 and OsAt10 involved in yield and biomass,and OsPH1 regulating plant height,etc.The expression profiles of 36 samples were used to build the co-expression network of Zhenshan 97,Minghui 63 and the hybrid.We identified six hybrid specific modules by comparing the modules of the hybrid with that of the parents.One of the six modules was significantly correlated with the sample of palea/lemma.Another module was significantly correlated with the sample of panicle 1.In addition,three modules were identified as shared by the hybrid and Zhenshan 97 but not shared by Minghui 63 and one module was identified as shared by the hybrid and Minghui 63 but not shared by Zhenshan 97.These results revealed that gathering of co-expression networks in the hybrid may contribute to heterosis.In this study,we analyzed PAV genes and variety-specific expressed genes in two rice genomes,and we found that these genes were associated with various important functions,including growth and development,yield and resistance.Key variations of genes involved in yield,grain quality and seed dormancy were found in the genome of two parents.We also identified expression patterns of these genes in the hybrid,and we found that up regulation and down regulation of these genes were related to different biological pathways,resulting in down regulation of basically biological functions and more enhanced regulation in the hybrid.In addition,we explored the non-additively expressed genes that contributed to growth and development of the hybrid.These results suggested that PAV genes complemented the number and variety of genes and prepotent genes were expressed in the hybrid,which can contribute to generation of heterosis.These findings will provide new insight into further exploration of molecular mechanism of yield heterosis in rice.