TRTech-PGR: Unlocking Bread Wheat Genome Diversity: Foundational Genome Sequences and Resources to Advance Breeding and Biotechnological Improvement of a Global Food Security Crop

普通面包小麦(Triticum aestivum L.)是一种主要的粮食安全作物，提供了全球约20%的人类膳食卡路里和蛋白质。遗传多样性是农业生产力和适应能力的基础；然而，今天的高产小麦品种只包含可用基因库的一小部分，这引发了人们的担忧，即过度依赖现有育种种群可能会限制小麦产量未来的增长。在被现代农业取代之前，欧洲、北非和亚洲传统上耕种了数千年的地方品种中保存着显著的遗传多样性。该项目解决了保存、发现和调动这些遗传资源的迫切需要，通过产生八个地方品种的基因组序列来保护、发现和调动这些遗传资源，这些地方品种是早期区域生长中心的基础，包括面包小麦的全球多样性。此外，该项目还将更新国际小麦基因组测序联盟(IWGSC)中国春参考基因组序列，这是一个重要的社区资源，一直是小麦遗传、进化、育种和生物技术研究进展的跳板。在培训和公众宣传方面，该项目将继续开展既定的教育、宣传和培训活动，包括暑期本科生研究实习、年度国际讲习班、早期职业演讲者奖和每月网络研讨会系列。该项目将进一步加强科学、技术、工程和数学(STEM)教育人员的培训，提高公众的科学素养，并为多样化的劳动力做出贡献。8个战略选择的地方品种的基因组序列的生成和注释，以及更新的国际小麦基因组测序联盟中国春季参考基因组序列，将通过确定构成适应性状的基因组多样性的程度，在全球范围内的小麦改良努力中向前迈出关键的一步。地方品种是一个特别重要的表型性状储存库，经过许多世代的适应，适应了当地的环境和农艺系统。这9个基因组组合将通过应用长读测序、光学图谱和染色体构象捕获测序的最新进展来产生，这些技术已被证明提供了低成本、白金质量的甚至大型和复杂基因组的组合，例如六倍体小麦(Triticum aestivum L.2n=6x=42，AABBDD)。所有基因组都将使用已建立的管道和登录衍生的转录组数据进行注释，以向多样性小组的基因模型提供信息。中国春天参考基因组序列中的现有注释，包括数千个社区贡献和手动管理的基因模型，将被保留在新的RefSeq版本中，并在八个地方种基因组中确定Syntelog。为了使这一资源适用于遗传和育种研究的先进方法，该项目将开发这些和社区开发的额外公共参考基因组序列的实用单倍型图表示法。这些产品将超过以前的小麦泛基因组努力，并使小麦社区能够战略性地整合未得到充分利用的种质，以应对当前和未来在作物研究和改良方面的挑战。所有项目成果的公众访问将通过NCBI(数据来自美国)或EMBL-EBI(数据来自欧洲)等长期存储库提供，并通过IWGSC数据存储库、GrainGenes、EnSembl Plants和数据发布进一步向社区发布。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Common bread wheat (Triticum aestivum L.) is a major food security crop, providing ~20% of human dietary calories and proteins worldwide. Genetic diversity underlies the productivity and adaptive capacity of agriculture; yet, today’s high-yielding wheat varieties contain only a small fraction of the available gene pool, raising concerns that overreliance on existing breeding stocks could limit future gains in wheat production. Significant genetic diversity is held within landraces that were traditionally farmed across Europe, Northern Africa, and Asia for thousands of years prior to their displacement by modern agriculture. This project addresses a critical need to preserve, discover, and mobilize these genetic resources by generating genome sequences of eight landraces that are foundational to early regional growing centers and encompass the worldwide diversity of bread wheat. In addition, this project will update the International Wheat Genome Sequencing Consortium (IWGSC) Chinese Spring reference genome sequence, an important community-resource that has served as a springboard for advancements in wheat genetics, evolution, breeding and biotechnology research. With respect to training and public outreach, this project will continue established education, outreach and training activities, including summer undergraduate research internships, annual international workshops, early career speaker awards, and monthly webinar series. The project will further increase Science, Technology, Engineering and Mathematics (STEM) educator training, public scientific literacy, and contribute to a diversified workforce.Generation of genome sequence and annotation of eight strategically selected landraces, along with the updated International Wheat Genome Sequencing Consortium Chinese Spring reference genome sequence, will provide a crucial step forward in world-wide efforts to improve wheat by identifying the extent of genomic diversity that underlies adaptive traits. Landraces are a particularly important reservoir of phenotypic traits, having adapted over many generations to localized environments and agronomic systems. The nine genome assemblies will be generated by applying recent advances in long-read sequencing, optical maps, and chromosome conformation capture sequencing, which have been demonstrated to provide low-cost, platinum-quality assemblies of even large and complex genomes such as hexaploid wheat (Triticum aestivum L. 2n = 6x = 42, AABBDD). All genomes will be annotated using established pipelines and accession-derived transcriptome data to inform gene models across the diversity panel. Existing annotations in the Chinese Spring reference genome sequence, including thousands of community-contributed and manually curated gene models, will be preserved in the new RefSeq version, with syntelogs identified in the eight landrace genomes. To make this resource applicable to advanced methods of genetic and breeding research, the project will develop a practical haplotype graph representation of these and additional public reference genome sequences developed by the community at large. These products will exceed previous wheat pan-genome efforts and empower the wheat community to strategically incorporate underutilized germplasms to meet current and future challenges in crop research and improvement. Public access to all project outcomes will be provided through long-term repositories such as NCBI (for data originating in the United States) or EMBL-EBI (for data originating in Europe) and further released to the community via the IWGSC Data Repository, GrainGenes, Ensembl Plants, and through data publication.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.