RESEARCH-PGR: Dissecting the dynamic evolution of paralogs in shaping trait variation across the Solanum Pan-Genome

不断增长的人口和极端气候正在威胁粮食安全。农业在很大程度上以几种主要作物为基础，基因组测序和CRISPR基因组工程的革命性技术正在加速它们的改进。这些技术还可以改善“孤儿”作物，这些作物没有被广泛种植或研究，但有可能增加粮食生产的多样性和抗灾能力。孤种作物与主要作物相关，允许它们之间的知识转换。然而，孤儿作物缺乏研究工具，一个更大的挑战是确定是否可以通过改造使主要作物受益的特定基因突变来改善孤儿作物的类似性状。这是因为随着物种的进化，基因序列和功能会发生变化，尤其是在复制的基因中，这在植物中很常见。该项目将利用茄科植物（茄子、胡椒和番茄等许多主要和孤立作物的来源）研究重复基因如何进化并影响相关物种的农业性状。基因组测序和CRISPR的结合将揭示数千个重复基因的序列多样性，并提高跨物种基因工程和性状的可预测性。该项目将培养注重多样性和包容性的年轻科学家，并通过一个关于孤种作物的社区科学项目促进公众对植物生物学中基因组工程的理解。最后，为一所小型文理学院的本科生提供的新课程和研究机会将扩大在植物科学中代表性不足的群体的参与和培训。该项目将利用大规模参考基因组测序、基因共表达分析和CRISPR基因组编辑方面的进展，剖析平行多样化如何影响一个属中具有基础和应用重要性的物种特异性表型。将对50种茄属植物（包括16种孤儿作物）进行测序，建立具有端粒-端粒参考序列的茄属泛基因组，为全属比较基因组学和功能遗传学奠定基础。将开发基于基因组学数据的计算方法，用于复杂基因组的精确组装和比较，以及基于其变体和表达模式的相似物及其关系的识别和分类。同时，将为一系列茄属植物开发和部署转化协议和基因组编辑，以测试相似物如何影响物种内部和物种之间的基因型-表型关系。通过关注主要驯化基因家族及其控制的适应性和生产力性状，这项协同工作将提供对进化平行多样化的新理解，并更有力地将农业相关的基因型-表型关系转化为孤儿作物。除了为植物研究人员和育种人员提供宝贵的茄属植物参考基因组、表达数据和CRISPR系的社区资源外，这个多学科项目还将产生新的工具、资源和原理，使其他分类群和性状的研究和工程对植物生物学和作物改良都有重要意义。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The growing population and climate extremes are threatening food security. Agriculture is largely based on a few major crops, and revolutionary technologies in genome sequencing and CRISPR genome engineering are accelerating their improvement. These technologies can also improve “orphan” crops, which are not widely cultivated or studied but have the potential to increase the diversity and resilience of food production. Orphan crops are related to major crops, allowing translation of knowledge between them. However, orphan crops lack research tools, and an even greater challenge is determining whether specific genetic mutations that benefitted major crops can be engineered to improve traits similarly in orphan crops. This is because gene sequence and function change as species evolve, especially among genes that become duplicated, which is common in plants. This project will take advantage of the nightshade family – a source of many major and orphan crops, such as eggplant, pepino, and tomato – to study how duplicated genes evolve and affect agricultural traits in related species. Combining genome sequencing and CRISPR will reveal sequence diversity among thousands of duplicated genes and enable improved predictability in engineering genes and traits across species. This project will train young scientists with a focus on diversity and inclusion, as well as promote public understanding of genome engineering in plant biology through a community science program on orphan crops. Finally, new curricula and research opportunities for undergraduate students at a small liberal arts college will broaden participation and training of underrepresented groups in the plant sciences.This project will exploit advances in large-scale reference genome sequencing, gene co-expression analyses, and CRISPR genome editing to dissect how paralog diversification impacts species-specific phenotypes in a genus of both fundamental and applied importance. Fifty Solanum species, including 16 orphan crops, will be sequenced to establish a Solanum Pan-Genome with telomere-to-telomere reference assemblies, providing a foundation for genus-wide comparative genomics and functional genetics. Computational approaches based on genomics data will be developed for precise assembly and comparison of complex genomes, and identification and classification of paralogs and their relationships based on their variants and expression patterns. Simultaneously, transformation protocols and genome editing will be developed and deployed for an array of Solanum to test how paralogs impact genotype-to-phenotype relationships within and between species. By focusing on major domestication gene families and the adaptation and productivity traits they control, this synergistic work will provide both a new understanding of paralog diversification in evolution and a more robust translation of agriculturally relevant genotype-to-phenotype relationships to orphan crops. Beyond a valuable community resource of Solanum reference genomes, expression data, and CRISPR lines for plant researchers and breeders, this multidisciplinary project will result in new tools, resources, and principles that will enable the study and engineering of other taxa and traits of significance to both plant biology and crop improvement.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.