Exploitation of Genetic and Epigenetic Variation in the Regulation of Tomato Fruit Quality Traits

PI: Esther van der Knaap（佐治亚大学）；PI: Ana Caicedo（马萨诸塞大学）；丹尼斯·蒂曼（佛罗里达大学）；合作伙伴：Joaquin Cañizares， Maria Jose Diez, Jose Blanca (Universitat Politecnica De Valencia)；索菲亚·维萨，迪恩·弗拉加，西蒙·格雷（伍斯特学院）：高质量的番茄应该具有良好的风味、大小、颜色和硬度。经过多年的选育，现代番茄已经诞生，但其品质和生产效率仍有待提高。尽管有这种需求，但改善水果品质的理想性状往往很难找到，部分原因是确定水果性状的潜在因素还不完全清楚。另一个障碍是一些有益的性状在育种过程中被消除或隐藏，从而减少了现代番茄基因组中可用的遗传多样性。项目科学家发现了一种尚未开发的资源，可以从野生番茄亲缘种和生长在不同地理位置的祖先种群中发现新的性状。这些植物可能看起来不受欢迎，因为它们有小的、有籽的、软的或难吃的果实。然而，这些近亲实际上是基因金矿：它们的DNA中含有在番茄驯化过程中丢失的有用且未开发的特征。现在有新的技术和遗传方法可以从这些野生番茄基因组中挖掘出新的育种性状。该项目使用选定的野生种群来探索和捕捉与果实重量、硬度、风味和颜色相关的品质性状。该项目将确定这些果实性状的分子基础，并将提供新的性状，以提高现代番茄的育种潜力。该项目为所有相关人员提供基因组学、计算数据分析和育种方面的跨学科培训，包括博士后研究人员和研究生。通过暑期讲习班，高中生和大学生将接受番茄基因组学和育种方面的培训，将直接与科学家互动，并将获得研究方面的实际技能。这些训练有素的学生将成为通过科学发现推动农业发展的劳动力的重要补充。栽培植物的野生近缘种和半驯化种质资源为农艺性状的关键调控因子提供了重要的遗传和表观遗传多样性。未来的作物改良依赖于利用这种多样性。然而，由于果实质量是定量遗传的，因此挖掘半驯化和野生种质的有益等位基因并不是一件简单的事情。因此，对未选择的种质的目视检查不容易导致鉴定具有理想特性的材料，以改善现代种质。性状与控制果实品质的基因的关联，以及驯化过程中可能丢失的有益等位基因的鉴定，为研究如何有效地从野生近缘种质中挖掘数量性状位点，从而实现作物的切实改良提供了一种模式。为了确定控制复杂番茄果实品质性状的基因和途径，本项目将(1)组装一个由野生、半驯化和祖先地品种组成的番茄群体（Solanum spp.）并进行表型分析；(2)通过全基因组关联研究（GWAS）和差异表达的小rna鉴定果实品质性状的基因座；(3)确定候选区域与基因相关的性状；(4)分析控制果实品质的发育和生化途径。该项目将获得150个番茄品种的基因组序列数据，其中20个来自栽培番茄最近但完全野生的近亲，110个来自驯化番茄的野生和半驯化直系祖先，20个来自栽培番茄最早的地方品种。此外，该项目将从这一群体的一个子集中生成番茄果实发育不同阶段的小RNA序列数据，并将提供150个品种中每个品种的风味、硬度、重量和适口性等详细的水果质量信息。这些信息将通过Sol基因组网络（SGN, http://www.sgn.cornell.edu/）这一公共资源提供，而种质资源库网站（TGRC, http://tgrc.ucdavis.edu/；和COMAV， http://www.comav.upv.es/）将提供所获材料的种子。

PI: Esther van der Knaap (University of Georgia) CoPIs: Ana Caicedo (University of Massachusetts); Denise Tieman (University of Florida); Lukas Mueller (Boyce Thompson Institute) Collaborators: Joaquin Cañizares, Maria Jose Diez, Jose Blanca (Universitat Politecnica De Valencia); Sofia Visa, Dean Fraga, Simon Gray (College of Wooster)A high quality tomato is expected to have good flavor, size, color and firmness. Years of selective breeding have produced the modern tomato, and yet the quality and production efficiency of the crop still needs improvement. Despite this need, desirable traits that will improve fruit quality are often hard to find, partly because the underlying factors that specify fruit traits are not fully known. Another impediment is that some beneficial traits were eliminated or hidden during breeding, thus reducing the available genetic diversity in modern tomato genomes. Project scientists have discovered an untapped resource to find new traits from wild tomato relatives and from ancestral populations growing in diverse geographic locations. These plants may appear undesirable by having small, seedy, soft or unpalatable fruits. However, these relatives are actually genetic gold mines: they hold within their DNA useful and untapped traits that were lost during tomato domestication. New technologies and genetic methods are now available to mine these wild tomato genomes for new suites of breeding traits. This project uses the selected wild populations to explore and capture quality traits associated with fruit weight, firmness, flavor and color. The project will identify the molecular basis of these fruit traits and will deliver new traits to improve the breeding potential of the modern tomato. The project provides interdisciplinary training in genomics, computational data analysis and breeding to all involved, including post-doctoral researchers and graduate students. Through summer workshops, high school and college students will be trained in tomato genomics and breeding, will interact directly with scientists, and will gain hands-on skills in research. These trained students will be critical additions to a workforce that advances agriculture through scientific discovery. Wild relatives and semi-domesticated germplasm of cultivated plants provide a significant reservoir of genetic and epigenetic diversity for key regulators of agronomic traits. Future crop improvement relies on harnessing this diversity. However, mining semi-domesticated and wild germplasm for beneficial alleles of agriculturally important traits is not straightforward because fruit quality is quantitatively inherited. Consequently, visual inspection of unselected germplasm does not readily lead to the identification of accessions that have desirable characteristics to improve modern germplasm. The association of traits with genes controlling fruit quality and the identification of beneficial alleles that may have been lost during domestication should provide a model for studying how to efficiently mine germplasm of the closest wild relatives for quantitative trait loci leading to tangible crop improvement. To identify genes and pathways that control complex tomato fruit quality traits, this project will (1) assemble and phenotype a tomato population (Solanum spp.) constituting the continuum of wild, semi-domesticated and ancestral landraces; (2) identify loci underlying fruit quality traits through genome-wide association studies (GWAS) and differentially expressed small RNAs; (3) confirm genetically the traits associated with candidate regions to genes, and (4) analyze the developmental and biochemical pathways that control fruit quality. The project will result in genome sequence data for 150 tomato accessions, including 20 from the closest but fully wild relative of cultivated tomato, 110 from wild and semi-domesticated direct ancestors of domesticated tomatoes and 20 from the earliest landraces of cultivated tomatoes. In addition, the project will generate small RNA sequence data from different stages of tomato fruit development from a subset of this population, and will provide detailed fruit quality information about flavor, firmness, weight and palatability for each of the 150 accessions. The information will be available through a public resource, the Sol Genomic Network (SGN, http://www.sgn.cornell.edu/), and seeds of the accessions will be available from germplasm repository sites (TGRC, http://tgrc.ucdavis.edu/; and COMAV, http://www.comav.upv.es/).