CAREER: Integrating Whole-Genome Association Mapping and Landscape Genomics to Understand Climatic Adaptation in Populus

职业：整合全基因组关联图谱和景观基因组学以了解杨树的气候适应

• 批准号: 1054444
• 负责人: Jason Holliday
• 金额: $ 120.58万
• 依托单位: Virginia Polytechnic Institute and State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-02-01 至 2017-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1054444&HistoricalAwards=false
• 关键词: CAREER; Integrating; Whole; Genome; Association

Endodormancy is a hallmark of woody perennial plants of the temperate and boreal regions that enables above ground meristems to survive the freezing and dehydration stresses of winter. This project takes a population genomics approach to dissect the genomic basis for endodormancy transitions and cold hardiness in Populus. A recently developed technology for genome complexity reduction will be used to pursue this goal on a genome-wide scale, and collaboration with groups working in related poplar species will facilitate comparative analysis of adaptation. Sequence capture technology will be employed to retrieve exons and upstream regulatory sequences for all expressed genes in Populus trichocarpa (black cottonwood), and captured targets will be sequenced in a large black cottonwood mapping population that spans most of the species range. Genotype-phenotype associations will be sought with three phenotypic traits, namely, timing of budset, timing of budflush, and cold hardiness. Associations will also be sought with climate variables that represent the principle selective constraint related to these traits. Positive associations will be validated in a separate cohort of poplar clones, and using data provided by collaborators, the extent of overlap in adaptive loci in both Populus tremuloides (trembling aspen) and Populus deltoides (eastern cottonwood) will be determined. A web-based bioinformatic resource will be developed to disseminate sequence data, SNP data, and SNP associations. This work will provide by far the most comprehensive picture to date of the genomic basis for local adaptation to climate in a tree species. In addition to answering long standing questions in evolutionary ecology about the genomic architecture of adaptation, this work will provide a link to practical breeding applications that can exploit naturally occurring ecologically-relevant genetic variation for tree improvement in a changing climate. Forest tree populations are well adapted to their local environments at present, but climate change is substantially altering adaptive landscapes, and is expected to lead to widespread maladaptation of tree populations to their seasonal temperature regimes. Adapting management strategies to account for these changes depends crucially on an understanding of the genomic architecture of adaptive traits. By integrating molecular biology, bioinformatics, and population genomics, this project will substantially advance this goal, while providing interdisciplinary education and training at various levels (undergraduate, graduate and postdoctoral). Research personnel associated with this project will develop investigative field workshops for students and landowners in collaboration with Virginia's Link to Education about Forestry (LEAF) program. Field trials will be used to host these outdoor LEAF learning workshops, through which landowners, practitioners, and local students will explore the relationship between climatic adaptation and seed sources, as well as the potential impacts of climate change on forest productivity. In addition, publicaly available web-based modules complimentary to the field experiences workshop will be developed. Sequence data will be deposited at GenBank, dbSNP at NCBI, and genotype-phenotype data at Data Dryad (www.datadryad.org).

内休眠是温带和北方地区多年生木本植物的一个标志，它使地上分生组织能够在冬季的冷冻和脱水胁迫下存活。 本项目采用群体基因组学方法，对杨树内休眠转变和抗寒性的基因组学基础进行了剖析。最近开发的降低基因组复杂性的技术将用于在全基因组范围内实现这一目标，与相关白杨物种工作组的合作将有助于对适应进行比较分析。将采用序列捕获技术来检索杨树（黑棉白杨）中所有表达基因的外显子和上游调控序列，并将在跨越大部分物种范围的大型黑棉白杨作图群体中对捕获的靶标进行测序。基因型-表型的关联将寻求与三个表型性状，即，时间的萌芽，时间的萌芽，抗寒性。协会也将寻求与气候变量代表的原则选择性约束有关的这些特征。正相关性将在一个单独的杨树克隆群中进行验证，并使用合作者提供的数据，确定美洲山杨（颤白杨）和美洲黑杨（东部棉白杨）适应性基因座的重叠程度。一个基于网络的生物信息资源将被开发来传播序列数据、SNP数据和SNP关联。 这项工作将提供迄今为止最全面的图片的基因组基础上，当地适应气候的树种。除了回答进化生态学中长期存在的关于适应基因组结构的问题外，这项工作还将提供一个与实际育种应用的联系，这些应用可以利用自然发生的生态相关遗传变异来改善气候变化中的树木。目前，森林树木种群很好地适应了当地环境，但气候变化正在大大改变适应性景观，预计将导致树木种群对季节性温度制度的普遍适应不良。调整管理策略来应对这些变化，关键取决于对适应性性状基因组结构的理解。通过整合分子生物学，生物信息学和人口基因组学，该项目将大大推进这一目标，同时提供各级（本科，研究生和博士后）的跨学科教育和培训。与该项目相关的研究人员将与弗吉尼亚州的林业教育链接（LEAF）计划合作，为学生和土地所有者开发调查现场研讨会。实地试验将用于举办这些户外LEAF学习研讨会，通过这些研讨会，土地所有者，从业者和当地学生将探索气候适应和种子来源之间的关系，以及气候变化对森林生产力的潜在影响。此外，还将开发可供公众使用的网上模块，作为实地经验讲习班的补充。序列数据将保存在GenBank，dbSNP保存在NCBI，基因型-表型数据保存在Data Dryad（www.datadryad.org）。