Genomewide Variation In An Introgression Line Of Rice-Zizania Revealed By Whole-genome Re-sequencing

Hybridization between genetically diverged organisms is an important avenuethat drives plant genome evolution. The possible outcomes of hybridization would bethe occurring of genomic shock‘‘which could evoke the genetic variation in thederived hybrids. The new induced variations may result in phenotypic noveltiesdirectly or indirectly, and eventually increase the fitness of the resulted hybrids.To address the molecular mechanism of how the inter-specific hybridizationcauses the genetic variation and to what extent it leads to the phenotypical novelties atwhole genome level, we re-sequenced the genomes of Oryza sativa ssp. japonica cv.Matsumae and one of its derived introgressant RZ35that was obtained from anintrogressive hybridization between Matsumae and Zizania latifolia Griseb.According to the results, our study generated a total of131millions90base pair (bp)paired-end reads which covered13.2and21.9folds of the Matsumae and RZ35genomes, respectively. In addition, a total of41,724homozygous single nucleotidepolymorphisms (SNPs) and17,839homozygous insertions/deletions (INDELs) wereidentified in RZ35. Notably, we found that these SNPs tended to occur in thechromosome as clusters and thus a number of high mutation regions (HMRs) wereidentified in our study. Interestingly, we found that11HMRs were located within thedomesticated related regions, implying that the HMRs may fragile and hence labile tomutations as a result of introgressive hybridization.In addition, our results revealed that3,797SNPs were nonsynonymous mutationswhich randomly distributed in2,250genes. To further investigate how these mutatedgenes contributed to phenotypic novelties of RZ35, we submitted these genes intoKEGG and identified that some of these mutated genes were concentrated in severalphysiologically important pathways including glycolysis/gluconeogenesis, fatty acidbiosynthesis and phenylpropanoid biosynthesis pathways. The results yield theconclusion that inter-specific hybridization has indeed resulted in the phenotypicnovelties that enhance the abilities of plant to tolerance the stresses.In addition to the observed genetic variation, rampant mobilization oftransposable elements (TEs) was also identified in the RZ35genome. Notably, a totalof63mobilization events representing11TE families were found including mPing,Osr29, Tos17and so on. To further examine how the mobilization of TEs affects thefunctions of genes, we analyzed the locations of each TE insertions. For example, we found that a member of mPing family was inserted in the intron regions ofLOC_Os05g11130. It indicates that inter-specific hybridization can cause theactivation of TEs and some of which may result the alterations in gene function andeventually lead to phenotypic novelties of resulted hybrids.To examine how the phenotypic novelties contributed to the fitness of hybrids,we performed the inoculation experiment between Matsumae and RZ35usingMagnaporthe grisea. Results from pathogen inoculation revealed that RZ35exhibitedenhanced resistance to blast relative to cv. Matsumae. Notably, one nonsynonymousmutation was identified in Pid3/Pi25. This finding coupled with the results ofreal-time quantitative (q) RT-PCR illustrated that it may be responsible for theenhanced resistance to rice blast in RZ35.Our results demonstrated that introgressive hybridization by alien pollens of evena sexually incompatible species may represent a potent means to generate novelgenetic diversities, and which may have played relevant roles in plant evolution andcan be manipulated for crop improvements.