The Gene Expression And Regulation Studies On Backcross Introgression Lines (BILs) Of Oryza Longistaminata

Rice is an important food crop in the world and a model plant of monocotyledons.Many important agronomic traits of wild rice have potential value for the improvement of cultivated rice.Introduction of superior characteristics from wild rice into cultivated rice by building BILs is a method of using wild rice resources.In this study,three progeny lines(L1710,L1817 and L1730)of BILs and their parents(recurrent parent,O.sativa and donor parent,O.longistaminata)were used to study the expression of genes,and the regulated expression of noncoding RNAs(miRNAs and lncRNAs)using high-throughput sequencing in the three progeny lines,which provided the mechanisms of hybridization and backcrossing and the plant height variations of progeny lines.In this study,the internode of L1817 and L1730 are longer than that in their parents,and that of L1710 is shorter than that of O.sativa.The paraffin section of the internode showed that the cell length of the three progeny lines of BILs are longer than that of their parents.After calculating the cell number(internode length divided by the cell length of corresponding interrnode),we observed decreased cell number in L1710 and L1817,and increased cell number in L1730.These results indicated that the difference in plant height among the three progeny lines are the changes in internode cell number and cell length.The gene expression among the three progeny lines of BILs and their parents were obtained using RNA-seq technology,and a total of 32,084 expressed genes were identified,of which 21,050 were commonly expressed(co-expressed).Genes with fold change(FC)≥5 and P ≤0.01 were regarded as differentially expressed genes(DEGs),and more DEGs were identified in progeny/O.longistaminata comparisons than in progeny/O.sativa comparisons.Additionally,most genes were up-regulated in progeny lines compared with their parents.Approximately 80%of the genes showed expression level dominance to O.sativa(ELD-A),indicating that the gene expression in progeny lines were closer to the recurrent parent,which might be influenced by their parental genome dosage.After functional annotation analysis,we found some genes related to plant hormones and cell wall anabolism may play important roles in the different plant height of the three progeny lines of BILs.The above results could increase our understanding of the complex molecular mechanism of gene introgression that resulting in plant height variations in progeny lines.miRNA is an important regulator of gene expression in plants biological processes.A total of 513 miRNAs were identified using high-throughput sequencing,and of which 291 miRNAs were co-expressed in the three progeny lines of BILs and their parents.The miRNAs with FC>2 and FDR ≤0.001 were identified as differentially expressed miRNAs.More differentially expressed miRNAs were identified in progeny/O.longistaminata comparisons than in progeny/O.sativa comparisons,and 72%-87%of differential miRNAs showed ELD-A.In addition,approximately 16%to 64%of the differentially expressed miRNAs were predicted possessing coherent target genes(CTGs),and many of these miRNAs regulated multiple CTGs.Through functional annotation of CTGs,we speculated that ELD-A miRNAs may participate in the primary metabolism and cellular metabolism.In addition,we found CTGs of some miRNA were involved in plant hormone-related processes,and miRNAs may play roles in the internode cell splitting and elongation at the jointing stage by regulating the expression of CTGs,thereby affecting the plant height.lncRNA is a class of non-coding RNAs that exert their biological functions mainly though a variety of transcriptional regulatory mechanisms.In this study,1,254 lncRNAs were identified by high-throughput sequencing technology,of which more than two-thirds were co-expressed in the three progeny lines of BILs and their parents.The number and the fold change of differentially expressed lncRNA were positively correlated with the different degree of the plant height between each line,and more than 50%lncRNA showed parental ELD.The integrated analysis of lncRNAs,miRNAs and mRNAs showed that most lncRNAs and mRNAs were positively correlated,while most miRNAs and IncRNAs were negatively correlated.In addition,we found that several lncRNAs acted as miRNA precursor and served as decoys for miRNAs at the same time,which may regulate the expression of some genes related to growth and development through competitive binding to miRNAs.In the GO functional analysis,the potential target genes of lncRNAs were significantly enriched in primary metabolism and response to stimulus,suggesting that lncRNAs might participate in the basic metabolic processes and regulate the adaptability.In summary,the analysis of mRNAs,miRNAs and lncRNAs among the three progeny lines of BILs and their parents provided massive data,and we found that the expression of genes,miRNA and lncRNAs were both showed expression level domained to recurrent parent.Functional analysis revealed that the expression variations in genes related to plant hormones and cell walls may affect the plant height changes of three progeny lines.Through the expression regulatory network of genes,miRNAs and IncRNAs,we guessed several lncRNAs regulated the expression of miRNAs by sponge adsorption,thereby regulating the expression of genes related to growth and development.These results increase our understanding of the expression regulation of protein coding genes and non-coding RNAs during hybridization and backcrossing,provide a foundation for further study on the molecular mechanisms of the progeny different plant height and the introgression of wild rice on the gene regulation.