Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing.
BACKGROUND
Hybridization 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.


RESULTS
In 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 Zizanialatifolia 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
Our 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.
Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China ; Faculty of Agronomy, Jilin Agricultural University, Changchun, China.
Zhen-Hui
ZH
Wang
Di
D
Zhang
Yan
Y
Bai
Yun-Hong
YH
Zhang
Ying
Y
Liu
Ying
Y
Wu
Xiu-Yun
XY
Lin
Jia-Wei
JW
Wen
Chun-Ming
CM
Xu
Lin-Feng
LF
Li
Bao
B
Liu
D020029:Base Pairing / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D003198:Computer Simulation; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics / Q000276:immunology; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D006720:Homozygote; D007178:Inbreeding; D009154:Mutation / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*
D004251:DNA Transposable Elements; D018744:DNA, Plant; D009711:Nucleotides