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doi:10.1534/genetics.105.040964
A more recent version of this article appeared on August 1, 2005.
REGULAR RESEARCH PAPERS |
Extensive de novo Genomic Variation in Rice Induced by Introgression from Wild Rice (Zizania latifolia Griseb.)
Yong-ming Wang 1, Zhen-Ying Dong 1, Zhong-juan Zhang 1, Xiu-yun Lin 1, Ye Shen 1, Dao-wei Zhou 1 and Bao Liu 1*
1 Northeast Normal University
* To whom correspondence should be addressed. E-mail: baoliu6677{at}yahoo.com.cn.
Submitted on January 27, 2005
Revised on February 28, 2005
Accepted on 14 April 2005
To study the possible impact of alien introgression on a recipient plant genome, we examined over 6,000 unbiased genomic loci of three stable rice recombinant inbred lines (RILs) derived from intergeneric hybridization between rice (cv. Matsumae) and a wild relative (Zizania latifolia Griseb.) followed by successive selfing. Results from amplified fragment length polymorphism (AFLP) analysis showed that, whereas the introgressed Zizania DNA comprised less than 0.1% of genome content in the RILs, extensive and genome-wide de novo variations occurred in up to 30% of the analyzed loci for all three lines studied. The AFLP-detected changes were validated by DNA gel blot hybridization and/or sequence analysis of genomic loci corresponding to a subset of the differentiating AFLP fragments. A BLAST analysis revealed that the genomic variations occurred in diverse sequences including protein-coding genes, transposable elements and sequences of unknown functions. Pairwise sequence comparison of selected loci between a RIL and its rice parent showed that the variations represented either base substitutions or small insertion/deletions. Genome variations were detected in all 12 rice chromosomes, although their distribution was uneven both among and within chromosomes. Taken together, our results implicate that even cryptic alien introgression can be highly mutagenic to a recipient plant genome.
Key Words: AFLP, Introgression, Zizania, genomic variation, rice
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