Gene Expression and miRNA Regulation Changes in Leaves of Rice Backcross Introgression Lines

Abstract

High-throughput sequencing was used to distinguish the gene and miRNA expression profiles in the leaves of three progenies from a rice backcross introgression line (BC2F12) and their parents (Oryza sativa and wild rice, O. longistaminata). A total of 33,419 genes and 513 miRNAs were identified in two parents and three lines, and the majority of the genes and miRNAs were commonly expressed. The results show that 10.23% to 17.94% of the genes were differentially expressed genes (DEGs) in the progenies compared with those of the two parents, and the majority of them were up-regulated. Of the miRNAs, 12.56% to15.43% were differentially expressed in the progeny/O. sativa comparisons and the majority of which were up-regulated, while 42.02% to 45.21% of miRNAs were differentially expressed in the progeny/O. longistaminata comparisons, of which nearly half were down-regulated. Most of the DEGs and differentially expressed miRNAs showed expression levels close to that of O. sativa, indicating that the expression of genes and miRNAs in progenies was closely related to their chromosome complements and that the miRNAs were more susceptible than the genes to the effects of genomic composition. Furthermore, a larger number of target genes were predicted in the progeny/O. longistaminata comparisons. Finally, we found that the expression of some genes and miRNAs might increase the possibility for abiotic stress responses and adaptation in progenies. Together, our findings increase the understanding of the molecular mechanisms of hybridization and backcrossing on the expression levels of genes and miRNAs in rice leaves.

Significance of introgression hybridization for extension of genetic variability in recipient genome

“…longistaminata, which differed from the recipient rice variety in terms of plant height, gene and miRNA expression profiles were studied using high-throughput RNA sequencing technology. It was established that compared to the rice variety, high lines are characterized by a decrease in the expression of genes, some of which are related to the formation of the cell wall and the synthesis of hormones, and such a decrease is associated with an increase in the expression of miRNAs, for which the mentioned genes are the target [64,65]. Introgression lines of the same origin were investigated by the same method for lncRNAs.…”