Nature Genetics Advance Online Publication Population Genomics of Populus Trichocarpa Identifies Signatures of Selection and Adaptive Trait Associations
Nature Genetics Advance Online Publication Population Genomics of Populus Trichocarpa Identifies Signatures of Selection and Adaptive Trait Associations
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L. Evans;G. Slavov;Eli Rodgers-Melnick;Joel A. Martin;P. Ranjan;W. Muchero;A. Brunner;Wendy S. Schackwitz;L. Gunter;Jin‐Gui Chen;G. Tuskan;Stephen;P. Difazio
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作者：
L. Evans;G. Slavov;Eli Rodgers-Melnick;Joel A. Martin;P. Ranjan;W. Muchero;A. Brunner;Wendy S. Schackwitz;L. Gunter;Jin‐Gui Chen;G. Tuskan;Stephen;P. Difazio
一系列的力量和因素，包括突变、重组、选择、种群历史和基因复制，影响种内遗传变异的模式。区分哪些因素影响了基因组中的序列变异，需要对多个个体进行广泛的全基因组测序，这直到最近才变得容易处理1。大多数大规模的全基因组重测序研究集中在模式物种和驯化物种1-5上。然而，对自然种群的广泛测序对于促进对进化生物学的理解大有裨益，包括识别功能变异和适应的分子基础。最近在一些物种中的工作已经确定了显示正选择特征的基因组区域，这表明这些区域包含控制适应性状4、6-8的基因座。然而，将全基因组扫描和表型数据相结合的研究相对较少，以确定通过计算识别的选定区域是否影响可适应的表型变异5、9-13。对大型自然群体的全基因组研究结合表型测量是必要的，以确定哪些因素影响物种内遗传变异的模式，从而加强对适应的理解。林木的地理范围大，环境梯度大，研究历史悠久，表明当地适应14，是研究自然种群遗传变异形成过程的理想选择。林木覆盖陆地面积的约30%15，对全球气候提供直接反馈，通常是组织整个生物群落和生物地球化学系统的基础物种16，17。显然，生物和非生物的相互作用影响了种群的大小和林木的分布，在当今种群14，18，19的基因组中留下了诊断特征。深入了解形成这些模式的进化和生态力量将为生态系统管理、应用树木改良和加速驯化工作提供洞察和选择20。&Gray，是一种占主导地位的河岸树，已成为推进林木基因组水平洞察的典范21。对16个毛果树基因组的测序揭示了广泛存在的连锁不平衡(LD)和种群结构22，广泛的基因组生态学研究揭示了生长、营养物候和水分利用效率和光合作用等生理性状的高度适应性表型变异，表明局部适应是普遍存在的。到目前为止，候选基因关联分析已经揭示了对表型性状26、27有显著影响的基因座。然而，到目前为止，还没有文献描述毛果青杨适应性状的全基因组关联，或者它们与…中选择特征的关系
A suite of forces and factors, including mutation, recombination, selection, population history and gene duplication influence patterns of intraspecific genetic variation. Distinguishing which factors have shaped sequence variation across a genome requires extensive whole-genome sequencing of multiple individuals, which has only recently become tractable 1. Most large-scale whole-genome resequencing studies have focused on model and domesticated species 1–5. However, extensive sequencing of natural populations holds great promise for advancing understanding of evolutionary biology, including identifying functional variation and the molecular bases of adaptation. Recent work in a number of species has identified genomic regions that show signatures of positive selection, suggesting that such regions contain loci that control adaptive traits 4,6–8. Relatively few studies, however, have combined genome-wide scans with phenotypic data to determine whether computationally identified selected regions influence adap-tive phenotypic variation 5,9–13. Genome-wide studies of large natural populations combined with phenotypic measurements are necessary to determine which factors shape patterns of genetic variation within species and, therefore, enhance understanding of adaptation. With large geographic ranges spanning wide environmental gradients and a long history of research showing local adaptation 14 , forest trees are ideal for examining the processes shaping genetic variation in natural populations. Forest trees cover approximately 30% of terrestrial land area 15 , provide direct feedback to global climate 15 and are often foundation species that organize entire biotic communities and biogeochemical systems 16,17. Clearly, biotic and abiotic interactions have influenced population sizes and distributions of forest trees, leaving diagnostic signatures in the genomes of present-day populations 14,18,19. A deeper understanding of the evolutionary and ecological forces that shaped these patterns will offer insights and options for ecosystem management, applied tree improvement and accelerated domestication efforts 20. Black cottonwood, Populus trichocarpa Torr. & Gray, is a dominant riparian tree that has become a model for the advancement of genome-level insights in forest trees 21. The sequencing of 16 P. trichocarpa genomes revealed widespread patterns of linkage disequilibrium (LD) and population structure 22 and extensive genecological studies have revealed a high degree of adaptive phenotypic variation in growth, vegetative phenology and physiological traits such as water-use efficiency and photosynthesis 23–25 , suggesting that local adaptation is prevalent. To date, candidate gene–association analyses have revealed loci with significant effects on phenotypic traits 26,27. However, thus far there have been no publications describing whole-genome associations for adaptive traits in P. trichocarpa, or their relationship to signatures of selection in …