The epigenetic fate of introgressed DNA in the wheat genome

面包小麦（Triticum aestivum）是全世界20%的卡路里消耗的来源。了解其生物学和遗传学对于发展可持续和生产性的农业景观至关重要。现代面包小麦起源于大约10，000年前两种谷物物种（粗山羊草和小麦）的杂交。参与这种杂交和随后的近亲繁殖的个体数量有限，这意味着面包小麦的遗传多样性水平降低。这种多样性的缺乏降低了育种者创造能够应对当前和未来环境挑战的品种的能力。渐渗，相关物种之间的遗传物质的转移，已被成功地利用在育种计划中，以克服这一瓶颈，扩大面包小麦基因组的多样性，并引入农艺学上有益的性状。但是，渗入的遗传元件是如何适应宿主基因组的，为什么有些渗入被保留下来，而另一些则从基因组中删除？这些是这个博士项目的核心问题，该项目将功能小麦基因组学与染色质遗传学和生物信息学相结合，为下一代植物科学家提供尖端的培训经验。作为项目的一部分，学生将首先通过RNA测序来确定已建立和新创建的小麦种质中渐渗的转录活性。接下来，将通过亚硫酸氢盐测序和染色质免疫沉淀分析DNA甲基化和组蛋白H3 K27 me 3标记。这两种表观遗传修饰都是控制外源遗传因子的重要介质。这些分析将伴随Hi-C实验，以研究渗入片段整合到宿主的3D基因组中。总之，这些分析将使学生能够定义渗入片段的遗传适应中的共享模式。为了分析和评估生成的大规模数据集，学生接受了高通量数据的高级生物信息学分析管道和基本编码技能的应用培训。这位博士研究员在巴斯大学新成立的米尔纳进化中心工作，并被纳入布里斯托的小麦基因组学小组和BBSCR战略计划“设计未来小麦”。与诺丁汉大学的合作将使学生能够参观朱莉·金的实验室，并获得小麦遗传操作的实践经验。

Bread wheat (Triticum aestivum) is the source of 20% of all calories consumed worldwide. Understanding its biology and genetics is essential in developing a sustainable and productive agricultural landscape. Modern bread wheat derived from the hybridisation of the two cereal species (Aegilops tauschii and Triticum turgidum) approximately 10,000 years ago. The limited number of individuals involved in this hybridization, and subsequent inbreeding, mean that bread wheat has reduced levels of genetic diversity. This lack of diversity diminishes the ability of breeders to create cultivars able to respond to present and future environmental challenges. Introgression, the transfer of genetic material between related species, has been successfully exploited in breeding programs to overcome this bottleneck and expand the diversity of the bread wheat genome and to introduce agronomically beneficial traits. But how are introgressed genetic elements adapting to the host genome and why are some introgressions retained and others removed from the genome? These are the questions at the heart of this PhD project that combines functional wheat genomics with chromatin genetics and bioinformatics to provide a cutting- edge training experience for the next generation plant scientists.As part of the project, the student will initially characterise the transcriptional activity of introgressions in established and newly created wheat accessions by RNAsequencing. Next, DNA methylation and histone H3K27me3 markings will be analysed by bisulfite sequencing and chromatin immunoprecipitation. Both epigenetic modifications are important mediators in the control of foreign genetic elements. These analyses will be accompanied by Hi-C experiments to study the integration of the introgressed segment into the 3D genome of the host. Together, these analyses will enable the student to define shared pattern in the genetic adaptation of introgressed segments. To analyse and evaluate the generated large-scale datasets the student has been trained in the application of advanced bioinformatic analysis pipelines of high-throughput data and essential coding skills. The doctoral researcher is based at the newly established Milner Centre for Evolution at the University of Bath and integrated into the wheat genomics group in Bristol and the BBSCR strategic programme 'Designing Future Wheat'. A collaboration with the University of Nottingham will enable the student to visit the lab of Julie King and gain hands-on experience on wheat genetic manipulation.