Genome-Wide Analysis of Root Traits

根性状的全基因组分析

• 批准号: 0820624
• 负责人: Philip Benfey
• 金额: $ 429.9万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0820624&HistoricalAwards=false
• 关键词: Genome; Wide; Analysis; Root; Traits

PIs: Philip Benfey (Duke - Biology), John Harer (Duke - Mathematics), Jonathan Lynch (Penn State - Horticulture), Joshua Weitz (Georgia Tech - Biology); Senior Personnel: Herbert Edelsbrunner (Duke - Computer Science), Leon Kochian (Cornell-USDA-Boyce Thompson Institute), Daniel Williams (North Carolina Central University - Biology)The long-term goal of this project is to use genomic approaches to identify the genes that control the branching patterns of crop roots. How roots branch in soil is known as the plant's 'root system architecture' and it varies dramatically from plant to plant. These differences are known to impact the plant's ability to acquire water and nutrients. Since many plants have to deal with environments in which nutrients and water are limiting, the root system architecture is a central feature of how plants adapt to their environment. A better understanding of root system architecture addresses two of the major challenges confronting plant biology - how to feed a burgeoning world population in a sustainable manner and how to cope with global climate change. Poor soil fertility and environmental stress suppress crop yields in many parts of the world, and many models predict these stresses will increase in coming decades. Intensive irrigation and fertilization are not environmentally sustainable, nor economically viable in most developing countries. Thus, identifying the genes that underlie root system architecture could have a profound significance for agriculture and world food security. Surprisingly, little is known about the individual traits that comprise root system architecture. There are two principal issues that have restricted the understanding of the genetic basis of root system architecture: 1) the lack of cost-effective methods for non-invasively imaging growing roots and 2) the lack of adequate means of describing the complex spatial structure of root system architecture. Two non-invasive imaging technologies will be used in this project to acquire images of growing rice and maize roots under different environmental conditions. Response of root systems will be compared to responses when grown in soil under similar conditions. Mathematical approaches to describing growing root systems and simulations for comparing different root system architectures will be developed. Quantitative trait loci (QTL) for root architecture traits will be identified using special populations of rice and maize and efforts will be initiated toward isolating genes of significance to plant breeding.The broader impacts of this work stem, in part, from the nature of this research that it is inherently interdisciplinary, thus training at various levels (undergraduate, graduate, post-doctoral) will integrate quantitative approaches with applications to experimental biology. A course will be developed in collaboration with faculty at North Carolina Central University (NCCU) that focuses on understanding complex genetic traits. NCCU is a historically black university (HBCU) located 5 miles from the Duke campus. The course will use examples from plants as well as human disease to inform and educate undergraduates as to the issues involved in analyzing complex genetic traits and the cutting edge technologies and computational approaches now available for identifying the genes responsible for these traits. For qualified students who have taken this course, research internships will be provided. A website will be developed to disseminate the results from this project, as well as to describe methods and results of interest to researchers and breeders. The web site will be accessible at http://www.biology.duke.edu/benfeylab/.

PI：菲利普·本尼迪克特（杜克-生物学），约翰·哈雷尔（杜克-数学），乔纳森林奇（宾夕法尼亚州立大学-园艺），约书亚韦茨（格鲁吉亚理工-生物学）;高级人员：赫伯特·埃德尔斯布伦纳（杜克-计算机科学），莱昂·科钦（康奈尔-美国农业部-博伊斯汤普森研究所），丹尼尔威廉姆斯（北卡罗来纳州中央大学-生物学）该项目的长期目标是使用基因组方法来识别控制作物根系分枝模式的基因。根在土壤中的分支方式被称为植物的“根系结构”，不同植物的根系结构差异很大。已知这些差异会影响植物获取水分和养分的能力。由于许多植物必须应对营养和水分有限的环境，因此根系结构是植物如何适应环境的核心特征。更好地了解根系结构可以解决植物生物学面临的两个主要挑战-如何以可持续的方式养活迅速增长的世界人口以及如何科普全球气候变化。在世界许多地区，土壤肥力差和环境压力抑制了作物产量，许多模型预测这些压力将在未来几十年内增加。在大多数发展中国家，密集灌溉和施肥在环境上是不可持续的，在经济上也不可行。因此，确定根系结构的基因可能对农业和世界粮食安全具有深远的意义。令人惊讶的是，很少有人知道的个别性状，包括根系架构。有两个主要问题限制了对根系构型遗传基础的理解：1）缺乏用于非侵入性地成像生长的根的成本有效的方法，以及2）缺乏描述根系构型的复杂空间结构的适当手段。该项目将采用两种非侵入式成像技术，获取不同环境条件下水稻和玉米根系生长的图像。根系的反应将与在类似条件下生长在土壤中的反应进行比较。数学方法来描述生长的根系和模拟比较不同的根系结构将被开发。 将利用水稻和玉米的特殊群体鉴定根构型性状的数量性状位点（QTL），并将努力分离对植物育种有重要意义的基因。这项工作的更广泛影响部分源于这项研究的本质，即它本质上是跨学科的，因此需要在不同层次上进行培训（本科生，研究生，博士后）将定量方法与实验生物学应用相结合。将与北卡罗来纳州中央大学（NCCU）的教师合作开发一门课程，重点是了解复杂的遗传特征。NCCU是一所历史悠久的黑人大学（HBCU），距离杜克校园5英里。该课程将使用植物和人类疾病的例子来告知和教育本科生分析复杂遗传性状所涉及的问题，以及目前可用于识别这些性状的基因的尖端技术和计算方法。 对于谁采取了这门课程的合格的学生，将提供研究实习。 将开发一个网站，以传播该项目的结果，并介绍研究人员和育种者感兴趣的方法和结果。该网站的网址是http://www.biology.duke.edu/benfeylab/。