六倍体小麦微进化过程中小分子RNA及其调控网络演变模式研究

Bread wheat or common wheat (Triticum aestivum) is an alloehexalpoid (AABBDD, 2n=6x=42) which was formed by two rounds of polyploidization from three homoeologous genomes. Due to the presence of the Pairing homoeologous 1 or Ph1 gene, homoeologous chromosomes in common wheat are rarely recombined and thus gene dosage regulations are considered to be achieved mostly by chromatin epigenetic modification. Small RNAs have been shown to play important roles in many biological processes of plants, such as disease resistance, flowering, and endosperm development, as well as chromatin remodeling; but their expression patterns and regulatory networks in the context of wheat microevolution are poorly investigated. This project studies the microevolution of wheat varieties from four major wheat growing regions in China with different photoperiod, disease, and spike morphology using RNA-seq and small RNA sequencing. Taking advantage of recently available wheat DD and AA genomes as well as the hexaploid wheat (Chinese Spring) draft genome which help distinguish the three homoeologs in the hexaploid wheat, we propose to study the expressions of small RNAs and their regulatory networks under the above breeding pressures. Newly synthesized hexaploid wheat lines are to be used as controls because their genomes are in the process of stabilization and may show contrasting regulatory plasticity under different selection pressures. This project is expected to find key genes and their regulatory networks for regional adaptation under combinatory pressures of both natural and domestic selections. The results will also provide novel evidences for gene dosage effect hypothesis in polyploid plants and contribute novel rules to the body of plant microevolution theory.

普通小麦(Triticum aestivum, AABBDD, 2n=6x=42)是由三个不同二倍体物种经过两次多倍化过程形成的异源六倍体。普通小麦中Ph1基因阻止部分同源染色体配对，使得等位基因间鲜有重组，基因表达调控多在表观遗传学水平进行。小分子RNA参与植物抗病、开花、产量等重要生物学过程的调控。但与其调控网络在小麦表型变异微进化中的模式和机制尚未有研究。本课题选取驯化关系清晰的不同麦区农家和育成品种，利用现有的小麦野生近缘种DD和AA基因组信息，采用小分子RNA和转录组分析技术，以前期发现的多倍化早期小分子RNA和重要基因调控路径为参照，研究人工选择过程中光周期、抗病、籽粒发育等重要性状变化驱动下的小麦小分子RNA及其调控网络的演变规律，揭示其在自然选择和人工驯化等压力下部分同源基因剂量效应（Gene dosage effect）的平衡法则，推进多倍体植物微进化理论的发展和完善。

普通小麦是全球最重要的谷类作物之一。中国被视为小麦多样性中心之一。我国262份小麦微核心种质是对我国小麦遗传资源进行深入评价和有效利用的不可多得的材料。262份微核心种质中，包括来自于十大麦区的农家种164份，育成种81份，国外品种17份。首先，在已有的11个产量和发育相关的农艺性状的基础上，进一步完善了开花期、穗粒数、植株高度和籽粒大小等农艺性状。采取外显子捕获重测序方法，对中国262份小麦微核心种质进行外显子捕获测序，测序区域涵盖了小麦基因组107X3 M非重复、低拷贝区域。采用GATK和samtools方法，结果取交集，经VQSR校正，共检测到115,814,718个SNP。SNP过滤参数选用单个样品测序深度>=10X，基因型质量控制>=5,群体缺失率控制在<=0.25，共获得1,054,097 个SNPs。这些SNP的获得为进一步进行进化分析、关联分析奠定了良好的基础。