异源杂交多倍化鲫鲤特有性状的转录组及后转录组水平变化规律研究

Aquaculture provides higher and higher proportion of protein nutritions for human world widely. There is the same trend in Yunnan Province as well. Thus, theories related to aquaculture provide basis for its long-term aquaculture progress. In Yunnan and related regions, there are several dozens of polyploidy species, and some of these fish are important fishery resources, including high-backed type hexaploid of goldfish. Meanwhile, investigation on genomic changes at the initial stage is still under survey. The occurrence of allopolyploidy can result in instantaneous speciation. Because new allopolyploids are immediately reproductively isolated from their congeners, it is thought that allopolyploidization is likely to play an important role in the diversification of flowering plants and some vertebrates. Newly formed allopolyploids with redundant two alien genomes must respond to the instantaneous changes at different levels, which resembles "genome shock" syndrome to survive and reproduce successfully. Thus, genomic change in the initial stages of an allopolyploid is often thought as important stage for young allopolyploid. Recent investigations suggest that those changes in the initial stage after allopolyploidization can be at transcriptomic and post-transcriptomic level for phenotypical traits; yet which level is dominant is still poorly understood. The allopolyploidy line by goldfish (♀4n = 100) × common carp (♂4n = 100) can be very useful model for the related investigation in polyploidization, since the allopolyploidy line with its gynogenetic offspring with obvious trait discrimination and clear genetic background. We plan to find the specific-expressed transcripts in epithelial tissue and muscular tissue, and to analyze the transcriptomic data in the allopolyploid offsprings comparing to their progenitors with different pigmentation characters. afterwards, we will identify possible microRNA (miRNA) and the 3' UTRs of their target genes. Finally we expect to find clues that which is more functionally important in considering transcriptomic and post-transcriptomic level to a specific phenotypical trait.The results will provide evidence that how changes at transciptomic and post-transcriptomic level in the initial stage after polyploidization contribute to the phenotypic changes, the acquired knowledge also provides theoretic basis for fishery industry to use the feature, polyploidization.

研究异源多倍化初期基因组变化与性状改变的关系不但是国际上研究的热点，而且在云南省鱼类遗传育种上也有重要的应用前景，因为本区及相关地区分布有数十种多倍化鱼类。本项目拟从世界上首例远源属间杂交获得的、家系背景清晰且具有明显性状差异的多倍化杂交鲫鲤（红鲫♀n=100×普通鲤♂n=100）入手，研究与性状相关的转录组水平及可能的转录后水平的变化，比较二者在性状控制上的贡献大小。申请者拟借助高通量测序技术,利用鲫鲤多倍化体系,筛选在上皮、肌肉组织中特异表达转录本，比较体色不同的个体间存在的差异；筛选候选miRNA和特异靶基因3'非编码区(3'UTR)，以期从转录和转录后水平获得与性状改变相关的信息；比较基因表达的改变和非编码区的转录后调控作用对性状改变所做的贡献，进一步阐明多倍化物种在多倍化发生初期其转录、转录后水平的调控变化如何贡献于脊椎动物的多倍化演化，也为渔业生产更好地利用多倍化提供理论基础。

本项目以世界上首例远源属间杂交获得的、家系背景清晰且具有明显性状差异的多倍化杂交鲫鲤（红鲫♀n=100×普通鲤♂n=100）为研究系统，研究与性状相关的转录组水平及可能的转录后水平的变化，以期阐明多倍化物种在多倍化发生初期其转录、转录后水平的调控变化如何贡献于脊椎动物的多倍化演化，比较转录及转录后调控的影响效应。目前获得的研究进展如下：.首先，在DNA水平对杂交鲫鲤体系亲本和子代比较获得的遗传变化的研究提示，子代核基因与亲本相比，存在广泛的镶嵌现象、插入、缺失以及基因转换，可能是由于串联重复序列和转座元件造成的；其次，基于三种组织的DNA甲基化数据分析提示，不同世代之间可能发生了剧烈的DNA甲基化模式改变，且在子代精巢中，DNA甲基化水平的降低尤为突出，这可能与F1代育性降低、胚胎个体极低的出苗率相关，F1代精子中剧烈变化的甲基化水平可能是基因组休克的结果，或可能为克服基因组休克的表现；第三，不同倍性世代在不同组织中呈现多样的转录模式，提示基因组休克效应下转录水平休克效应的发生，此外，发现二倍体与四倍体杂交形成的三倍体其精子发生的基因低表达，同样提示基因组休克效应可能是精子育性降低的原因；最后，基于miRNA表达模式以及RNA编辑模式与基因表达相关性的分析，提示复杂和多层次的转录后调控变化模式的存在。以上从遗传、表观遗传以及转录和调控机制的研究执行，为未来多层次揭示杂交鲫鲤表型变化的复杂机制提供研究基础和依据，也提示目前无法评估转录和转录后调控何为更显著的效应。本研究结果也为渔业生产更好地利用多倍化提供理论基础，同时对了解天然水体中存在的数十种多倍化鱼类发生初期基因组各个层次的变化提供了线索。.项目执行过程中，由于肌肉组织难以提取RNA，且考虑到复杂表型变化机制可能是由遗传、表观遗传以及调控网路等多水平复杂网络共同决定，故本项目的执行的过程中，对与肌肉相关的少量研究内容作了相应调整，但不影响整体对转录和转录后相关的总体研究结果。

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