Extensive Microsatellite Variation in Rice Induced by Introgression from Wild Rice (<i>Zizania latifolia</i> Griseb.)

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. Methodology 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.研究背景 学界普遍认为，种间杂交可诱导杂交后代产生基因组不稳定性。然而，针对同倍体杂种（homoploid hybrids）与渐渗系（introgression lines）的基因组分析研究仍较为匮乏。本团队此前已通过渐渗杂交技术，成功构建了栽培稻（Oryza sativa L.）与菰（Zizania latifolia Griseb.）的一套渐渗系材料，并依托该材料育成了多个栽培品种。 研究方法 本研究选取分布于水稻核基因组与细胞器基因组的96个微卫星标记（microsatellite markers），对3株典型渐渗系的微卫星稳定性进行检测；同时分析了一组错配修复（MMR）基因以及含微卫星序列的基因的表达情况。 结果与结论 与受体水稻品种松前（Matsumae）相比，96个微卫星位点中有55个在至少1株渐渗系中出现了等位基因变异；其中58.2%的变异等位基因可在至少2个渐渗系中被检测到，表明多数变异事件发生于渐渗过程早期，在后续分化之前即已产生。73.9%的非共享变异仅在单株渐渗系RZ2中被检出。序列比对结果显示，变异类型涵盖重复序列区域及侧翼区域内的碱基替换与插入缺失（indels）。值得注意的是，相较于亲本水稻，渐渗系中一组错配修复基因的表达发生了显著改变，提示错配修复系统参与了微卫星变异的产生过程。部分发生变异的微卫星位点所在基因的表达也随之改变，表明这些微卫星可能通过顺式调控作用参与基因表达的调控。由于这些基因与已知功能蛋白具有显著同源性，因此本研究认为，渐渗杂交诱导产生的大范围微卫星变异，可能是导致渐渗系出现新颖表型的重要原因。