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

利用遗传和表观遗传变异调控番茄果实品质性状

基本信息

批准号：
1564366
负责人：
Esther Van der Knaap
金额：
$ 499.35万
依托单位：
University of Georgia Research Foundation Inc
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2015
资助国家：
美国
起止时间：
2015-09-16 至 2022-04-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1564366&HistoricalAwards=false
关键词：
Exploitation Genetic Epigenetic Variation Regulation

项目摘要

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/).

PI：Esther van der Knaap（佐治亚大学）COPIS：ANA CAICEDO（马萨诸塞大学）；丹妮丝·蒂曼（佛罗里达大学）；卢卡斯·穆勒（Boyce Thompson Institute）合作者：JoaquinCañizares，Maria Jose Diez，Jose Blanca（政治上的瓦伦西亚大学）；索非亚签证，迪恩·弗拉加（Dean Fraga），西蒙·格雷（Simon Gray）（伍斯特（Wooster of Wooster））高质量的番茄有望具有良好的风味，尺寸，颜色和牢固性。多年的选择性育种产生了现代番茄，但是农作物的质量和生产效率仍然需要提高。尽管需要这种需要，但通常很难找到可以提高水果质量的理想特征，部分原因是指定水果特征的基本因素尚不完全了解。另一个障碍是在繁殖过程中消除了或隐藏了一些有益的特征，从而降低了现代番茄基因组的可用遗传多样性。项目科学家发现了一种未开发的资源，可以从野生番茄亲戚和在不同地理位置的祖先种群中找到新的特征。这些植物的小小的，柔软的或不可生的果实可能看起来不太明确。但是，这些亲戚实际上是遗传金矿：它们保持在番茄驯化过程中丢失的DNA有用和未开发的特征。现在可以使用新的技术和遗传方法来挖掘这些野生番茄基因组的新繁殖特征。该项目使用选定的野生种群来探索和捕获与水果重量，坚硬，风味和颜色相关的优质特征。该项目将确定这些水果特征的分子基础，并将提供新的特征，以提高现代番茄的繁殖潜力。该项目为包括博士后研究人员和研究生在内的所有人提供了基因组学，计算数据分析和育种的跨学科培训。通过夏季研讨会，将接受番茄基因组学和育种培训，将直接与科学家互动，并获得研究技能。这些受过训练的学生将是通过科学发现来推动农业发展的劳动力的关键补充。栽培植物的野生亲戚和半动植物的种质为农艺性状的关键调节剂提供了重要的遗传和表观遗传学多样性。未来的作物改善依赖于利用这种多样性。但是，针对农业重要特征的有益特征的有益等位基因的采矿半动植物种质并不直接，因为水果质量是定量遗传的。因此，对未选择的种质的目视检查不会很容易地鉴定出具有理想特征以改善现代种质的加入。特征与控制水果质量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，应提供一个模型，用于研究如何有效地挖掘壁橱野生亲戚的种质，以实现定量性状基因座，从而导致切实的作物改善。为了确定控制复杂番茄水果质量特征的基因和途径，该项目将（1）组装和表型A番茄种群（Solanum spp。）构成野生，半静药和祖先地面的连续性；（2）通过全基因组关联研究（GWAS）鉴定局部基本的水果质量特征，并以不同的方式表达了小的RNA；（3）从遗传上确认与基因候选区域相关的特征，（4）分析控制水果质量的发育和生化途径。该项目将产生150个番茄加入的基因组序列数据，其中包括耕种番茄的最接近但完全相对的20个，来自野生和半驯化的驯养番茄的直接祖先，还有20个来自最早的培养番茄的地面。此外，该项目将从该人群的一个子集中从番茄水果开发的不同阶段产生小的RNA序列数据，并将为150个加入中的每一个提供有关风味，牢固性，重量和可口的详细水果质量信息。 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/).