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

合著者：崔月华和David Douches（密歇根州立大学），蒋继明（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）马铃薯是继水稻和小麦之后世界上第三重要的粮食作物，因其薯类而种植，薯类是一种地下储存器官。马铃薯不同于许多其他主要作物，因为它是无性繁殖的，有四组染色体（四倍体），所有品种都是高度杂合的。因此，马铃薯比水稻、玉米和大豆等有性繁殖的二倍体保留有害基因突变的可能性更大。由于缺乏对复杂背景下遗传要素相互作用的认识，这三个特点使得马铃薯的遗传改良缓慢且不可预测。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它们如何与表型相关的知识有限。本项目的目的是了解基因/等位基因、转录本、拷贝数变异和表观基因组特征对马铃薯适应度相关表型性状复合物的贡献。该项目产生的数据将包括基因组、转录组和表观基因组的特征分析，这些数据来自多个染色体数量和杂合度不同的马铃薯群体，并进行统计分析，以确定与活力相关的一组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。许多与马铃薯有关的遗传和基因组问题不能轻易地用二倍体模式植物来解决。探索马铃薯遗传复杂性的项目努力将作为其他具有类似难育种系统的无性繁殖、高度杂合作物的基因组学系统的模型，包括苜蓿、香蕉、木薯、葡萄、草莓、甘蔗、甘薯、山药和许多小型园艺作物，从而提高对表型多样性背后的遗传机制的理解。通过该项目的推广活动，公众将获得植物生物学的知识，特别是马铃薯的用途及其独特的生物学，通过与密歇根州立大学儿童和园艺园的一系列活动，涉及所有年龄段。通过高中和代表性不足的群体的参与，该项目将为学生提供机会，使他们将科学视为一种可行的职业机会，并增加女性在计算机相关科学/技术学科中的代表性。本项目所采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等相关新兴学科的研究生和博士后提供丰富的培训环境。通过在公共数据库中发表和存储该项目所产生的数据，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张高分辨率图谱。序列数据将通过项目网站（可通过http://buell-lab.plantbiology.msu.edu/访问）、SOL Genomics Network （http://solgenomics.net/）以及NCBI Sequence Read Archive和NCBI Gene Expression Omnibus进行永久存档。本项目开发和/或使用的种质资源将根据要求通过NRSP-6美国马铃薯基因库（http://www.ars-grin.gov/nr6/）长期提供。

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/).