Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing

Abstract

BackgroundHybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies.Methodology/Principal FindingsIn this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizania latifolia Griseb. in general, 131 millions 90 base pair (bp) paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs) and 17,839 homozygous insertions/deletions (indels) were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs) was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q) RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35.Conclusions/SignificanceOur results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a sexually incompatible species may represent a potent means to generate novel genetic diversities, and which may have played relevant roles in plant evolution and can be manipulated for crop improvements.

Analysis of specific sequences in mutant rice generated by introduction of exogenous corn DNA

“…Moreover, the mutations were not only present in the 14 specific bands, but also in the remaining genome. Wang et al (2013) hybridized Zizania with rice and obtained a stability variant line (RZ35). Using whole genome sequencing, they found that there were a large number of nucleotide mutations in RZ35 (Wang et al, 2013).…”

“…Wang et al (2013) hybridized Zizania with rice and obtained a stability variant line (RZ35). Using whole genome sequencing, they found that there were a large number of nucleotide mutations in RZ35 (Wang et al, 2013). These results are consistent with our experiments and demonstrate that wide crosses and exogenous DNA can induce biological mutation.…”

“…Using analysis of base replacement, Wang et al (2013) found that the rate of base transition was significantly higher than that of transversion in RZ35. Using RAPD analysis of whole genomes, Deng et al (2011) compared six mutants found in lotus with a control lotus and found the rate of base transition was 2.7 times higher than that of transversion in mutant lotus induced by ion implantation, indicating that direct introduction of exogenous DNA was similar to distant hybridization and ion implantation in biological mutation.…”

“…Using whole genome sequencing, they found 27 genes corresponding to relevant variant traits and some mutations arising in these genes in the V20B rice (Sun et al, 2013). Wang et al (2013) hybridized Zizania with rice and obtained a stability variant line (RZ35). Using whole genome sequencing, they discovered a high number of SNPs, insertions, and deletions in RZ35 (Wang et al, 2013).…”

“…Wang et al (2013) hybridized Zizania with rice and obtained a stability variant line (RZ35). Using whole genome sequencing, they discovered a high number of SNPs, insertions, and deletions in RZ35 (Wang et al, 2013). However, in all of the above studies, little was reported regarding the types of mutations occurring and the mutation sites.…”