title: Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).
abstract: BACKGROUND
  It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars.
  
  
  METHODS
  Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed.
  
  
  CONCLUSIONS
  Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the introgression lines.
authors: Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China. zhydong@genetics.ac.cn
authors: Zhenying
authors: Z
authors: Dong
authors: Hongyan
authors: H
authors: Wang
authors: Yuzhu
authors: Y
authors: Dong
authors: Yongming
authors: Y
authors: Wang
authors: Wei
authors: W
authors: Liu
authors: Gaojian
authors: G
authors: Miao
authors: Xiuyun
authors: X
authors: Lin
authors: Daqing
authors: D
authors: Wang
authors: Bao
authors: B
authors: Liu
mesh_terms: D001483:Base Sequence; D053843:DNA Mismatch Repair / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D042822:Genomic Instability; D006824:Hybridization, Genetic; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D020161:Physical Chromosome Mapping; D006109:Poaceae / Q000235:genetics*; D016415:Sequence Alignment
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