Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China.
PLoS One. 2013 Apr 24;8(4):e62317. doi: 10.1371/journal.pone.0062317. Print 2013.
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.
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.
RESULTS/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.
种间杂交可能会导致杂种基因组不稳定，这一观点已被广泛接受。然而，对于同源多倍体杂种和渐渗系的基因组分析研究较少。我们之前曾报道过，通过渐渗杂交，成功地产生了一组水稻（Oryza sativa L.）和野生稻（Zizania latifolia Griseb.）之间的渐渗系，这些渐渗系导致了几个品种的释放。
利用 96 个位于水稻核基因组和细胞器基因组中的微卫星标记，我们研究了三个典型渐渗系中的微卫星稳定性。还分析了一组错配修复（MMR）基因和含有微卫星的基因的表达。
结果/结论：与受体水稻品种（松前）相比，96 个微卫星标记中的 55 个在一个或多个渐渗系中发生了变异，其中 58.2%的变异等位基因至少在两条线中共享，这表明大多数变异发生在渐渗的早期阶段，然后才进一步分化。73.9%的非共享变异仅在一条渐渗系中检测到，即 RZ2。序列比对表明，变异包括在重复序列和侧翼区域内发生的替换和插入。有趣的是，渐渗系中一组 MMR 基因的表达与它们的水稻亲本相比发生了显著变化，这表明 MMR 系统参与了微卫星变异的产生。一些改变的微卫星位点与它们所携带的基因的表达改变一致，这表明它们可能在控制基因表达中具有顺式调控作用。由于这些基因与已知功能蛋白具有有意义的同源性，我们得出结论，渐渗引起的微卫星广泛变异可能导致了渐渗系的新表型。
