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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）CoPI：Ana Caicedo（马萨诸塞大学）；丹尼斯·蒂曼（佛罗里达大学）； Lukas Mueller（博伊斯汤普森研究所）合作者：Joaquin Cañizares、Maria Jose Diez、Jose Blanca（瓦伦西亚理工大学）； Sofia Visa、Dean Fraga、Simon Gray（伍斯特学院）高质量的番茄应具有良好的风味、大小、颜色和硬度。经过多年的选育，现代番茄诞生了，但其品质和生产效率仍需提高。尽管有这种需求，但通常很难找到能够提高果实品质的理想性状，部分原因是指定果实性状的潜在因素尚不完全清楚。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未开发的资源，可以从野生番茄近缘种和生长在不同地理位置的祖先群体中寻找新特征。这些植物可能因果实小、多籽、软或难吃而显得不受欢迎。然而，这些亲戚实际上是遗传金矿：它们的 DNA 中保留着番茄驯化过程中丢失的有用且未开发的特征。现在可以使用新技术和遗传方法来挖掘这些野生番茄基因组，以获得新的育种性状。该项目利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特征。该项目将确定这些水果性状的分子基础，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，与科学家直接互动，并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推动农业发展的劳动力队伍的重要补充。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节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，从半驯化和野生种质中挖掘农业重要性状的有益等位基因并不容易，因为果实品质是数量遗传的。因此，对未选择的种质进行目视检查并不容易识别出具有改进现代种质所需特征的种质。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应该为研究如何有效地挖掘最接近的野生近缘种的种质以获得数量性状基因座提供一个模型，从而导致切实的作物改良。为了确定控制复杂番茄果实品质性状的基因和途径，该项目将 (1) 组装构成野生、半驯化和祖先地方品种连续体的番茄种群 (Solanum spp.) 并对其进行表型分析；（2）通过全基因组关联研究（GWAS）和差异表达的小RNA识别水果品质性状的基因座；（3）从遗传学上确认与候选基因区域相关的性状，以及（4）分析控制果实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接近但完全野生的近缘种，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，并且种质的种子可从种质资源库网站（TGRC，http://tgrc.ucdavis.edu/；和 COMAV，http://www.comav.upv.es/）获得。