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，这引起了人们的担忧，即过度依赖现有育种库存可能会限制小麦生产的未来收益。在被现代农业取代之前，欧洲、北方和亚洲数千年来传统上养殖的地方品种中存在着显著的遗传多样性。该项目通过生成八个地方品种的基因组序列来解决保护，发现和动员这些遗传资源的关键需求，这些地方品种是早期区域种植中心的基础，并涵盖了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，是小麦遗传学，进化，育种和生物技术研究进步的跳板。关于培训和公共外联，该项目将继续开展既定的教育、外联和培训活动，包括本科生暑期研究实习、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。该项目将进一步增加科学、技术、工程和数学（STEM）教育者培训，公众科学素养，并为多元化的劳动力做出贡献。八个战略选择的地方品种的基因组序列的生成和注释，沿着更新的国际小麦基因组测序联盟中国春参考基因组序列，将提供一个关键的一步，在世界范围内的努力，以改善小麦通过确定程度的基因组多样性，适应性性状的基础。地方品种是一个特别重要的表型性状库，经过许多代适应当地环境和农艺系统。这九个基因组组装体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，这些进展已被证明可以提供低成本、铂质量的组装体，即使是大而复杂的基因组，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，以告知多样性小组的基因模型。中国春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策划的基因模型，将保留在新的RefSeq版本中，并在8个地方品种基因组中识别出syntelog。为了使这一资源适用于遗传和育种研究的先进方法，该项目将开发一个实用的单倍型图表示这些和其他公共参考基因组序列开发的社区。这些产品将超越以往的小麦泛基因组努力，并使小麦社区能够战略性地整合未充分利用的种质资源，以应对作物研究和改良中当前和未来的挑战。所有项目成果将通过NCBI等长期资料库向公众提供（适用于源自美国的数据）或EMBL-EBI（对于源自欧洲的数据），并通过IWGSC数据库、GrainGenes、Ensembl Plants、该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准。

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.