温带莲与热带莲杂交F1代的等位基因特异性表达研究

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.

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。

遗传变异（特别是顺式调控变异）在植物表型多样化以及适应性进化中扮演重要角色。温带莲与热带莲是莲的两大生态型，它们的地下茎膨大程度有明显的差异，温带莲相对膨大的地下茎与其冬眠（过冬）相关。为了理解顺式调控分化在温带莲与热带莲适应性进化中所扮演的角色，我们对两种生态型莲的杂交F1代个体的花、叶和地下茎组织进行了等位基因异性表达分析。对于杂交F1代个体所有组织来说，全基因组约36%的基因表现出等位基因异性表达，并且约3%的基因在所有组织中都有一致的表达偏向性。绝大多数发生过等位基因特异性表达的基因在所有调查到的组织样本中都偏向于热带莲亲本，暗示着杂交个体中热带莲亲本的基因组相对于温带莲亲本基因组来说呈现出表达水平上的显性现象。我们进一步发现表达发生亲本偏向性的基因与两种生态型莲的表型分化有关，尤其体现在地下茎中代谢与植物激素等通路。总体来说，该研究揭示两种生态型莲的顺式调控分化的全景，突出了顺式调控在适应不同气候环境而发生地下茎膨大变异中所扮演的重要角色。