亚洲莲中的温带莲和热带莲在地下茎膨大和花期等表型上存在明显差异，比较转录组学研究也发现两种生态型间关于这两个性状的重要功能基因存在表达模式的差异。然而，造成这两种生态型莲基因表达模式分化背后的遗传变异基础尚不明确。申请人拟采用等位基因特异性表达（ASE）研究手段分析温带莲、热带莲及它们的杂交F1代的地下茎、花苞和直立叶的转录组，探索杂交F1代中发生的等位基因表达不平衡现象，以寻找顺式调控变异和反式调控变异的基因；进一步利用基因组重测序分析温带莲、热带莲两亲本间功能基因上下游调控区序列在SNP、InDel和转座子的插入移除这三个方面的遗传变异，从而揭示调控区序列分化与等位基因表达不平衡现象之间的因果关系。本项目的实施能从遗传变异角度揭示温带莲和热带莲之间基因表达、表型分化的分子机理，其中基因表达调控相关的遗传变异可有效地服务于今后莲的分子标记辅助育种。

The degree of rhizome enlargement and florescence are highly divergent between the temperate and tropical (Asian) lotus ecotypes, which is further reflected by large quantities of differentially expressed genes associated with these two traits between these two ecotypes by comparative transcriptomic studies. However, the genetic basis of these transcriptional divergence between temperate and tropical lotus remains unclear. I plan to apply allele-specific expression analysis on transcriptomes from rhizome, flower bud and young leaf of temperate lotus, tropical lotus and their F1 hybrids to explore allele expression imbalance in F1 for identification of genes with cis-regulatory variation and trans-regulatory variation; I will further investigate the upstream and downstream regulatory sequences of all genes in terms of SNP, InDel and insertion/deletion of transposable element between the two parental lotuses by genome resequencing analyses in order to elucidate the causal relationship between the regulatory region divergence and the degree of allele expression imbalance. Implementation of this project will uncover the molecular mechanisms behind the transcriptional and phenotypic divergence between temperate and tropical lotus in terms of genomic variation, and the gene-regulation-related genetic variations will serve to future marker assisted breeding of lotus.