Sequence Resources for Cotton, a Model System for Allopolyploid Crops

棉花是美国主要农作物中遗传多样性最低的植物之一。自最初的创始种群以来，在数千年的繁殖过程中，野生环境中包含的大部分自然遗传多样性已经丧失。DNA测序技术的发展使量化和描述这种缺失的遗传多样性的新策略成为可能。本项目将对506份棉花（及其野生二倍体近缘种）材料进行筛选和重测序。这些DNA序列将用于鉴定含有独特遗传多样性的单个植物。对棉花遗传多样性的认识将有助于阐明棉花的基本生物学过程，并为我国棉花作物的改良提供基因组资源。该项目还将为杨百翰大学和爱荷华州立大学的教师（7-12年级）提供暑期研究培训实习。该计划将介绍基因组分析策略的概念和实验基础。届时，教师将能够与他们的高中生和中学生分享他们的基因组测序知识。驯化植物及其野生近缘种遗传多样性的数量和分配是作物改良的关键问题。该项目将对506个棉花品种进行重测序，其中包括具有广泛代表性的具有重要商业价值的异源多倍体（ad基因组）物种G. hirsutum和G. barbadense，以及代表其他异源多倍体和祖先二倍体（a， D）基因组的相关野生物种。通过对每个加入的DNA文库进行高覆盖率测序产生的序列读数将使用各种计算工具映射到参考棉花基因组，以开始识别和量化不同加入的染色体上的核苷酸变异。群体基因组学分析将揭示公共棉花种质资源中独特的等位基因、单核苷酸多态性（SNPs）和拷贝数变异（CNVs）。利用这些信息，将合成棉花的泛基因组，以更好地了解在物种形成、群体分化、驯化和育种过程中出现的基因组变异的范围、速度和模式。所有项目成果将通过项目网站向公众公布。序列数据将通过GenBank、NCBI的SRA和Phytozome等长期存储库访问。数据也将通过棉花基因组学、遗传和育种社区数据库CottonGen （http://www.cottongen.org/）长期提供。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Cotton has one of the lowest amounts of genetic diversity of any of the major crop plants in the U.S. Much of the natural genetic diversity contained in the wild was lost during the thousands of years of breeding since the original founding population. Developments in DNA sequencing technology have enabled new strategies to quantify and characterize this missing genetic diversity. This project will select and re-sequence 506 accessions of cotton (and its wild, diploid relatives). These DNA sequences will be used to identify individual plants that contain unique genetic diversity. The understanding of genetic diversity will illuminate basic biological processes in cotton and will provide genomic resources for improvement of the domestic cotton crop. This project will also provide summer research training internships for teachers (grades 7-12) at both Brigham Young University and Iowa State University. The program will introduce the conceptual and experimental foundations of genome analysis strategies. Teachers will then be able to share their knowledge of genome sequencing with their high school and middle school students.The amount and apportionment of genetic diversity in domesticated plants and their wild relatives are key concerns for crop improvement. This project will re-sequence 506 accessions of cotton that include a broad representation of the commercially important allopolyploid (AD-genome) species G. hirsutum and G. barbadense as well as related wild species representing other allopolyploids and progenitor diploid (A, D) genomes. Sequence reads generated through high-coverage sequencing of DNA libraries for each accession will be mapped to the reference cotton genome using a variety of computational tools to begin to identify and quantify nucleotide variation along chromosomes of various accessions. Population genomics analyses will reveal unique alleles, single nucleotide polymorphisms (SNPs), copy number variants (CNVs) in accessions within the public cotton germplasm collection. Using this information, a pan-genome of cotton will be synthesized to better understand the scope, pace, and pattern of genomic variations that arise during speciation, population differentiation, and domestication and breeding. All project outcomes will be made available to the public through a project website. Sequence data will be accessible through long-term repositories such as GenBank, the NCBI's SRA, and Phytozome. Data will also be available long-term through CottonGen (http://www.cottongen.org/), a community genomics, genetics and breeding database for cotton.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.