Data from: The ‘heritability’ of domestication and its functional partitioning in the pig

We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to subsets of single nucleotide polymorphisms (SNPs) defined in terms of their annotation, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genetic variance as the whole set of 25 million SNPs. This suggests that domestication may have affected protein sequence to a larger extent than regulatory or other kinds of mutations. A pathway-guided analysis revealed ovarian steroidogenesis and leptin signaling as highly relevant in domestication. The genomic regression approach proposed in this study revealed molecular processes not apparent through typical differentiation statistics. We propose that at least some of these processes are likely new discoveries because domestication is a dynamic process of genetic selection, which may not be completely characterized by a static metric like Fst. Nevertheless, and despite some particularly influential mutation types or pathways, our analyses tend to rule out a simplistic genetic basis for the domestication process: neither a single pathway nor a unique set of SNPs can explain the process as a whole.本研究提出，当以野生/家养状态作为目标表型时，可通过全基因组标记回归分析估算其解释的方差比例（即基因组遗传力（genomic heritability））。该方法与标准群体分化指数Fst不同，可通过通用形式考量个体间的遗传相似性。我们将此策略应用于来自亚洲与欧洲的47头野生和家养猪的全基因组完整数据。当我们将总基因组方差按照单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）的注释信息划分为不同子集关联的组分后，发现9566个潜在有害的非同义突变位点所解释的遗传方差，与全部2500万个SNP位点的总遗传方差相当。这表明相较于调控突变或其他类型突变，驯化过程对蛋白质序列的影响程度更强。通路导向分析显示，卵巢类固醇生成通路与瘦素信号通路在猪驯化过程中具有高度相关性。本研究提出的基因组回归分析方法，揭示了通过常规分化统计方法无法发现的分子进程。我们认为其中至少部分进程属于全新发现，原因在于驯化是一个动态的遗传选择过程，而类似Fst这样的静态统计指标无法完全刻画该过程的特征。尽管存在部分影响显著的突变类型或通路，但我们的分析结果并不支持驯化过程存在单一简单的遗传基础：无论是单条通路还是特定的SNP集合，均无法完整解释整个驯化过程。