Genomic analysis of inbreeding depression in the wild.

野生近交衰退的基因组分析。

• 批准号: 423718723
• 负责人: Martin Stoffel
• 金额: --
• 依托单位: School of Biological Sciences
• 依托单位国家: 德国
• 项目类别: Research Fellowships
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 无数据
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/423718723?language=en
• 关键词: Genomic; analysis; inbreeding; depression; wild.

The detrimental consequences of inbreeding have fascinated scientists since Darwin. One and a half centuries later, we know that inbreeding depression is ubiquitous in diploid organisms and evidence for its critical impacts on a broad range of traits, individual fitness and population viability comes from all over the animal and plant kingdoms. Despite the enormous significance of inbreeding depression, little is known about its most fundamental features: How many regions of the genome contribute to inbreeding depression? What are the underlying genes and alleles and how strong are their deleterious effects? How strongly is inbreeding depression selected against over the generations? Is inbreeding depression stronger in earlier or in later life-stages? These questions can only be addressed in wild populations, where fitness can be measured under the pressures of natural environments, but until recently we lacked the genomic tools to answer them. Here, I propose the most in-depth genomic investigation of inbreeding depression in a wild population to date. In one of the best-phenotyped free-living study populations in the world, the Soay sheep of St Kilda, I will use high density SNP data for selected pedigree members in combination with population-wide 50k SNP chip data to impute more than 450,000 SNP genotypes throughout the genomes of thousands of study individuals. Using this dataset, I will quantify regions in the genome which are identical-by-descent (IBD) to (1) investigate whether most inbreeding depression resides in long stretches of IBD derived from recent inbreeding, (2) quantify the abundance of embryonic lethal alleles in the population, (3) locate the genetic variants causing inbreeding depression across the genome and quantify their effect sizes using a combination of established and novel methods and (4) follow-up large effect loci using whole-genome-sequencing data for a deeper investigation of the underlying genes and the mode of selection involved.

自达尔文以来，近亲繁殖的有害后果一直让科学家们着迷。一个半世纪后，我们知道近亲繁殖抑制在二倍体生物中普遍存在，它对广泛的性状、个体适应性和种群生存能力产生重要影响的证据来自所有动植物王国。尽管近亲繁殖抑郁症具有巨大的意义，但人们对其最基本的特征知之甚少：基因组中有多少区域与近亲繁殖抑郁症有关？潜在的基因和等位基因是什么？它们的有害影响有多强？在几代人中，近亲繁殖的抑制有多强？近亲繁殖抑郁症是在生命早期还是后期更严重？这些问题只能在野生种群中解决，在自然环境的压力下可以测量适应性，但直到最近我们还缺乏基因组工具来回答这些问题。在这里，我提出了最深入的基因组研究近交抑郁症的野生种群到目前为止。在世界上表型最好的自由生活研究群体之一，St Kilda的Soay羊中，我将使用高密度的SNP数据来选择系谱成员，结合种群范围内的50k SNP芯片数据，在数千个研究个体的基因组中计算超过450,000个SNP基因型。利用这个数据集，我将量化基因组中相同血统（IBD）的区域，以：(1)调查大多数近交抑郁是否存在于最近近交产生的IBD的长段中，(2)量化种群中胚胎致死等位基因的丰度，(3)在整个基因组中定位导致近交抑制的遗传变异，并使用现有的和新的方法相结合的方法量化它们的效应大小；(4)使用全基因组测序数据跟踪大型效应位点，以深入研究潜在基因和所涉及的选择模式。