Unraveling the Heterozygosity, Allelic Composition, and Copy Number Variation of Potato

揭示马铃薯的杂合性、等位基因组成和拷贝数变异

基本信息

  • 批准号:
    1237969
  • 负责人:
  • 金额:
    $ 436.17万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2012
  • 资助国家:
    美国
  • 起止时间:
    2012-10-01 至 2017-09-30
  • 项目状态:
    已结题

项目摘要

PI: C. Robin Buell (Michigan State University) Co-PIs: Yuehua Cui and David Douches (Michigan State University), Jiming Jiang (University of Wisconsin-Madison), and Richard Veilleux (Virginia Polytechnic Institute and State University)Potato is the third most important food crop in the world following rice and wheat and is cultivated for its tuber, a below-ground storage organ. Potato is distinct from many other major crops in that it is asexually propagated, has four sets of chromosomes (tetraploid), and all cultivars are highly heterozygous. As a consequence, potato has a greater probability of retaining deleterious gene mutations than sexually propagated diploids such as rice, maize, and soybean. These three characteristics make genetic improvement of potato slow and unpredictable due to a lack of understanding of the interaction of genetic elements in a complex background. Furthermore, there is limited knowledge regarding the molecular nature of heterozygosity and allelic composition in the potato genome and how these correlate with phenotype. The objectives of this project are to understand the contribution of genes/alleles, transcripts, copy number variation and epigenomic features to a complex of phenotypic traits associated with fitness in potato. Data to be generated from this project will include characterization of the genome, transcriptome and epigenome from multiple potato populations with differential degrees of chromosome number and heterozygosity and statistical analyses to identify genes and alleles associated with a set of phenotypes associated with vigor. These data will also facilitate modeling genomic features into phenotype. Many of the genetic and genomic questions associated with potato cannot be readily addressed by using diploid model plants. Project efforts to probe the genetic complexities of potato will serve as a model genomics system for other vegetatively propagated, highly heterozygous crops with similarly intractable breeding systems, including alfalfa, banana, cassava, grape, strawberry, sugarcane, sweet potato, yam and scores of minor horticultural crops, thereby improving the understanding of the genetic machinery underlying phenotypic diversity. Through outreach activities in this project, the public will gain knowledge of plant biology, specifically in the uses of potato and its unique biology, through a suite of activities with the Michigan State University Children's and Horticulture Garden involving all age groups. Through engagement of high school and under-represented groups, this project will provide opportunities for students to see science as a viable career opportunity and increase the representation of women in computer-related science/technology disciplines. The techniques and approaches used in this project will provide a rich training environment for graduate students and postdoctoral fellows in relevant and emerging disciplines of bioinformatics, genomics, and epigenomics. The data to be generated in this project through publication and deposition in public databases will provide the first high-resolution map of genome variation and its association with gene expression, epigenetic modifications, and phenotypic traits in potato. Sequence data will be made public through the project website (to be accessible via http://buell-lab.plantbiology.msu.edu/), the SOL Genomics Network (http://solgenomics.net/) and through the NCBI Sequence Read Archive and the NCBI Gene Expression Omnibus for permanent archiving. Germplasm developed and/or used in this project will be available on request and long-term through the NRSP-6 U.S. Potato Genebank (http://www.ars-grin.gov/nr6/).
PI:C。Robin Buell(密歇根州立大学)共同项目研究员:Yuehua Cui和大卫Douches(密歇根州立大学),Jiming Jiang(威斯康星大学麦迪逊分校)和Richard Veilleux(弗吉尼亚理工学院和州立大学)马铃薯是世界上仅次于水稻和小麦的第三大粮食作物,种植它的块茎是一种地下储存器官。马铃薯与许多其他主要作物的不同之处在于它是无性繁殖的,有四套染色体(四倍体),并且所有的栽培品种都是高度杂合的。因此,马铃薯比有性繁殖的二倍体如水稻、玉米和大豆更有可能保留有害的基因突变。这三个特征使得马铃薯的遗传改良缓慢且不可预测,这是由于缺乏对复杂背景下遗传元件相互作用的理解。此外,关于马铃薯基因组中杂合性和等位基因组成的分子性质以及这些如何与表型相关的知识有限。该项目的目标是了解基因/等位基因,转录本,拷贝数变异和表观基因组特征的复杂的表型性状与马铃薯的健身的贡献。该项目产生的数据将包括来自多个马铃薯群体的基因组、转录组和表观基因组的表征,这些马铃薯群体具有不同程度的染色体数目和杂合性,以及统计分析,以鉴定与一组与活力相关的表型相关的基因和等位基因。这些数据也将有助于将基因组特征建模为表型。与马铃薯相关的许多遗传和基因组问题不能通过使用二倍体模式植物容易地解决。探索马铃薯遗传复杂性的项目努力将作为其他植物繁殖的高度杂合作物的基因组学系统模型,这些作物具有类似的难以处理的育种系统,包括苜蓿、香蕉、木薯、葡萄、草莓、甘蔗、甘薯、山药和许多次要园艺作物,从而提高对表型多样性背后的遗传机制的理解。通过这一项目的推广活动,公众将获得植物生物学知识,特别是马铃薯的用途及其独特的生物学知识,这是通过与密歇根州立大学儿童和园艺园举办的涉及所有年龄组的一系列活动实现的。通过高中和代表性不足群体的参与,该项目将为学生提供机会,使他们将科学视为一个可行的职业机会,并增加妇女在计算机相关科学/技术学科中的代表性。本项目中使用的技术和方法将为生物信息学、基因组学和表观基因组学的相关和新兴学科的研究生和博士后研究员提供丰富的培训环境。 该项目通过在公共数据库中发表和存储而产生的数据将提供马铃薯基因组变异及其与基因表达、表观遗传修饰和表型性状的关联的第一个高分辨率图谱。 序列数据将通过项目网站(可通过http://buell-lab.plantbiology.msu.edu/访问)、SOL基因组学网络(http://solgenomics.net/)以及NCBI序列读取档案和NCBI基因表达综合数据库公开,以永久存档。 本项目开发和/或使用的种质将通过NRSP-6美国马铃薯基因库(http://www.ars-grin.gov/nr6/)按要求长期提供。

项目成果

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Carol Buell其他文献

Carol Buell的其他文献

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{{ truncateString('Carol Buell', 18)}}的其他基金

PlantSynBio: Construction of a plant chassis as a platform for biological discoveries and innovations
PlantSynBio:构建植物底盘作为生物发现和创新的平台
  • 批准号:
    2308873
  • 财政年份:
    2023
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Standard Grant
EAGER: Comparative single cell transcriptomics and regulomics: A proof-of-concept application of cutting-edge -omics techniques with non-model systems
EAGER:比较单细胞转录组学和调节组学:尖端组学技术与非模型系统的概念验证应用
  • 批准号:
    2309665
  • 财政年份:
    2023
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Standard Grant
RESEARCH-PGR: Multiple origins of tuber formation: Evolution of a unique storage organ
研究-PGR:块茎形成的多重起源:独特储存器官的进化
  • 批准号:
    2140176
  • 财政年份:
    2021
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Standard Grant
PlantSynBio: Chassis design for sustainable production of high value terpenoids in the crop species tomato
PlantSynBio:用于在番茄作物中可持续生产高价值萜类化合物的底盘设计
  • 批准号:
    2126592
  • 财政年份:
    2021
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Standard Grant
RESEARCH-PGR: Multiple origins of tuber formation: Evolution of a unique storage organ
研究-PGR:块茎形成的多重起源:独特储存器官的进化
  • 批准号:
    1929982
  • 财政年份:
    2019
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Standard Grant
Evolution of Specialized Metabolite Biosynthetic Pathways in the Lamiaceae: Sources of Chemical Diversity for Molecules Essential for Human Use and Plant Defense
唇形科专门代谢物生物合成途径的进化:人类使用和植物防御所必需的分子化学多样性的来源
  • 批准号:
    1444499
  • 财政年份:
    2015
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Continuing Grant
U.S.-Peru Workshop: International Collaborations in Cyberinfrastructure-enabled Genomics Workshop
美国-秘鲁研讨会:网络基础设施支持的基因组学研讨会的国际合作
  • 批准号:
    0742699
  • 财政年份:
    2008
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Standard Grant
Generation of Potato Sequence and Annotation Resources
马铃薯序列和注释资源的生成
  • 批准号:
    0834044
  • 财政年份:
    2007
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Continuing Grant
An Annotation Resource for the Rice Genome
水稻基因组注释资源
  • 批准号:
    0834043
  • 财政年份:
    2007
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Continuing Grant
Generation of Potato Sequence and Annotation Resources
马铃薯序列和注释资源的生成
  • 批准号:
    0604907
  • 财政年份:
    2006
  • 资助金额:
    $ 436.17万
  • 项目类别:
    Continuing Grant

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Investigating the protective effect of maternal Thm1 heterozygosity against cleft palate
母体 Thm1 杂合性对腭裂的保护作用研究
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