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

主要研究者：Esther货车der Knaap（格鲁吉亚大学）CoPI：Ana Caicedo（马萨诸塞州大学）; Denise Tieman（佛罗里达大学）; Lukas Mueller（博伊斯Thompson研究所）合作者：Joaquin Cañizares，Maria Jose Diez，Jose Blanca（瓦伦西亚理工大学）;索菲亚Visa，Dean Fraga，Simon Gray（伍斯特学院）一个高品质的番茄应该具有良好的风味，大小，颜色和硬度。经过多年的选择性育种，已经培育出了现代番茄，但这种作物的质量和生产效率仍然需要改进。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，部分原因是指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植物和生长在不同地理位置的祖先种群中发现新的性状。这些植物可能因具有小的、有籽的、软的或不好吃的果实而显得不受欢迎。然而，这些亲戚实际上是基因金矿：它们在DNA中保留了在番茄驯化过程中丢失的有用和未开发的特性。新的技术和遗传方法现在可以用来挖掘这些野生番茄基因组，以获得新的育种性状。该项目使用选定的野生种群来探索和捕获与果实重量，硬度，风味和颜色相关的质量性状。该项目将确定这些水果性状的分子基础，并提供新的性状，以提高现代番茄的育种潜力。该项目为所有参与者，包括博士后研究人员和研究生，提供基因组学、计算数据分析和育种方面的跨学科培训。通过夏季研讨会，高中生和大学生将接受番茄基因组学和育种方面的培训，将与科学家直接互动，并将获得研究方面的实践技能。这些训练有素的学生将成为通过科学发现促进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库。未来的作物改良依赖于利用这种多样性。然而，挖掘半驯化和野生种质的有益等位基因的农业上重要的性状是不简单的，因为水果品质是定量遗传的。因此，目视检查的种质不容易导致鉴定的加入，具有理想的特性，以改善现代种质。性状与控制果实品质的基因的关联以及在驯化过程中可能丢失的有益等位基因的鉴定，应该为研究如何有效地挖掘最接近的野生亲缘种质以获得导致有形作物改良的数量性状基因座提供一个模型。为了鉴定控制复杂番茄果实品质性状的基因和途径，本项目将（1）组装和表型番茄种群（Solanum spp.）这些研究包括：（1）通过全基因组关联研究（GWAS）和差异表达的小分子RNA鉴定水果品质性状的基因座;（2）通过基因组关联研究（GWAS）和差异表达的小分子RNA鉴定水果品质性状的基因座;（3）从遗传学上确认与基因候选区域相关的性状;（4）分析控制水果品质的发育和生化途径。该项目将产生150个番茄品种的基因组序列数据，其中20个来自栽培番茄的最近但完全野生的亲戚，110个来自野生和半驯化的驯化番茄的直接祖先，20个来自栽培番茄的最早地方品种。此外，该项目还将从该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，并将为150个品种中的每一个品种提供有关风味、硬度、重量和适口性的详细果实质量信息。这些信息将通过公共资源Sol基因组网络（SGN，http：//www.sgn.cornell.edu/）提供，而种质的种子将从种质库网站（TGRC，http：//tgrc.ucdavis.edu/;和COMAV，http：//www.comav.upv.es/）提供。

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/).