Sequence Resources for Cotton, a Model System for Allopolyploid Crops

棉花是美国主要作物中遗传多样性最低的植物之一，野生植物中的大部分天然遗传多样性在最初的建立种群以来的数千年育种过程中丢失了。DNA测序技术的发展使新的策略能够量化和描述这种缺失的遗传多样性。该项目将选择506份棉花（及其野生二倍体近缘种）并重新测序。这些DNA序列将用于识别含有独特遗传多样性的植物个体。对棉花遗传多样性的了解将有助于阐明棉花的基本生物学过程，并为国内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州立大学的教师（7-12年级）提供暑期研究培训实习机会。 该计划将介绍基因组分析策略的概念和实验基础。教师将能够与高中和初中学生分享他们的基因组测序知识。驯化植物及其野生亲缘植物的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份棉花种质进行重新测序，其中包括具有广泛代表性的具有重要商业意义的异源多倍体（AD基因组）物种G。棉和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。将使用各种计算工具将通过每个登记的DNA文库的高覆盖度测序产生的序列读段映射到参考棉花基因组，以开始鉴定和量化沿着各种登记的染色体的核苷酸变异沿着。 群体基因组学分析将揭示公共棉花种质资源中的独特等位基因、单核苷酸多态性（SNPs）、拷贝数变异（CNVs）。利用这些信息，将合成棉花的泛基因组，以更好地了解物种形成、种群分化、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等长期储存库访问。数据也将通过CottonGen（http：//www.cottongen.org/）长期提供，CottonGen是一个社区棉花基因组学、遗传学和育种数据库。该奖项反映了NSF的法定使命，并被认为值得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来支持。

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.