大豆驯化改良中不同功能单元微进化规律

Domestication was one of the most important events during the development of agriculture. In the concept of biology, domestication is a process of genetic modification of wild species into cultivated species by increasing adaptations to meet human needs. During the domestication, only limited numbers of the best lines are used for breeding of the next generation. Therefore, artificial selection played important role in driving the micro-evolution during crop domestication and improvement. Several of these domestication-relevant genes have been isolated through quantitative trait locus fine-mapping. With the rapid development of next-generation sequencing technology, powerful genomic approaches have been used to screen for selective sweeps or genes at a genome-wide level. Thus far, large numbers of genes undergoing selection during plant domestication have been identified from different species. However, except for the protein coding genes, non-coding genes also have also been demonstrated to play important roles in regulating agronomically important traits in crops. Nevertheless, a genome-wide dissection of the selection of non-coding genes during crop domestication has not been achieved. In this study, we will investigate single-nucleotide polymorphisms (SNPs) in protein coding genes and in non-coding genes, such as miRNA and LncRNA using our previously reported 302 re-sequenced soybean accessions. At the same time, we will investigate the selection of these functional elements at transcriptional level through RNA-seq, miRNA-seq, LncRNA-seq and methylation-seq. By comprehensive comparison the differential evolution patterns of different functional elements and the factors that influencing their evolution, we will reveal the micro-evolution mechanism of polyploidy soybean genome during domestication and improvement.

对于野生动植物的驯化和改良是农业发展中最为重要的活动，人工选择在驯化和改良中起到关键作用。全基因组水平研究驯化和改良中的遗传变异，对于揭示人工选择下家养动植物适应人工环境的遗传机制具有重要意义。在生物体内，根据遗传物质功能的不同，可以将其分为基因、miRNA、长非编码RNA等不同功能单元。并且根据表达模式、表达水平、重复状态等，各个功能单元还可进一步具体分为不同类型。然而，目前对于驯化和改良中遗传变异的研究主要停留在功能基因层面，并且集中在对重要农艺性状的解析。关于miRNA和LncRNA，以及不同类型功能单元在驯化改良过程中的进化规律还未见报道。本研究拟以大豆为研究材料，系统开展大豆驯化改良中不同功能单元微进化规律的研究，解析不同类型的基因、miRNA和LncRNA在驯化和改良中受到的人工选择及其影响因素，以期为阐明多倍化基因组在驯化改良中的微进化规律奠定重要理论基础。

驯化是农业发展中最为重要的活动，人工选择在驯化中起到关键作用。驯化中的遗传变异研究对于揭示人工选择下家养动植物适应人工环境的遗传机制具有重要意义。目前，对于驯化中遗传变异的研究主要集中在功能基因，关于不同类型功能单元在驯化过程中的进化规律还未见报道。本项目结合单分子实时测序、单分子光学图谱和高通量染色体构象捕获技术，从头组装了国审大豆品种“中黄13”的基因组，得到1.025 Gb的基因组序列，contig N50为3.46 Mb，scaffold N50 为51.87 Mb，是目前连续性最好的植物基因组之一，为大豆基础研究提供了重要的资源。.为了探索表观变异在作物驯化改良过程中的作用，对9个野生大豆、12个农家种和24个栽培品种进行了全基因组甲基化测序。通过亚群之间的甲基化水平比较，在驯化中鉴定到4248个DNA甲基化变异区间。进一步分析发现，DNA甲基化在作物驯化过程中是独立于DNA变异受到选择的，且DNA甲基化受选择基因在碳水化合物通路中显著富集。该研究首次在群体水平证明表观遗传变异确实可以作为一种遗传资源在驯化中被选择，为作物驯化研究提供新的思路。.通过对大豆驯化和改良过程中全基因组范围内MIRNA和靶基因的进化研究发现，miRNA和靶基因在驯化中展现出几个相似的进化模式：高表达、重复、有更多互作成员的MIRNA基因或者靶基因核苷酸多样性低，暗示表达水平、重复基因状态、miRNA-靶基因互作对MIRNA基因和靶基因的进化非常重要；但总体MIRNA基因比miRNA靶基因的进化速率快。本研究为大豆驯化过程中miRNA和靶基因的共进化关系提供了线索。.通过全基因组关联分析，鉴定到一个控制大豆种子休眠基因，进一步研究发现该基因在大豆、水稻和番茄中的驯化中受到平行选择。生化分析表明，G蛋白可能通过调控植物脱落酸代谢发挥作用。该基因是首个被发现在多个科作物驯化中受到平行选择的基因，这对于新物种的驯化具有重要指导意义。.总之，通过对不同类型功能单元在大豆驯化过程中的进化分析，发现不同功能单元在驯化中受到选择方式不同，这为更好理解驯化机制奠定了坚实基础。