Comparative Mammalian Genomics

犬类遗传学 犬科动物起源 我们的犬类研究分为驯化基因组学、形态变异和疾病基因定位。关于第一个，我们最近发表了高调的论文，描述了狗的驯化(vonHoldt等人，2013年)。这是在发表在《自然》杂志上的先前工作的基础上进行的，在那次工作中，我们对品种之间的关系进行了精炼的描述(vonHoldt等人，2010年)。最近，在加州大学洛杉矶分校的John Novembre博士领导的一项合作中，对野生犬类的测序揭示了有效种群数量可能在驯化瓶颈期间发生了30倍的严重减少，我们现在估计驯化瓶颈发生在大约15,000年前(Freedman，2014)。这些数据还表明，从假定的驯化中心而来的现存狼血统中，没有一种是狗的直接祖先，这意味着现在已经灭绝的狼种群可能是狗进化中缺失的一环。最后，这项研究证明了对影响大脑功能、新陈代谢和形态的基因的选择，支持了调节进化在驯化中的主要作用。 我们还展示了狗和狼之间杂交的证据，并提供了一个具有种群水平统计量化的工具包，该工具包可以使用一组具有不同等位基因频率分布的狗-狼祖先信息SNP来检测最近的狗-狼杂交(VonHoldt等人，2013年)。 形态学 在过去的四年里，我们的大部分犬类论文揭示了我们对犬类基因组组织及其与品种间形态差异的关系的日益加深的理解。我们最新的形态研究方法旨在了解头骨形状差异的遗传基础(舍内贝克，2014)，这种差异在不同品种之间差异很大(舍内贝克，2013；舍内贝克等人，2012年)。为了量化这种差异，我们使用微型数字记录仪从51个地标的533个博物馆头骨中收集了数据。由此产生的主成分分析(PCA)显示，前四个PC约占品种间头骨差异的77%。PC1描述了嘴的长度和角度、腭弓和颧弓的宽度以及脑颅的深度的深刻变化；本质上是介于短头(像斗牛犬的短头)和多头(像灰狗的长头)头骨之间的头面部特征的连续体。我们在PC1上发现了几个基因座。CFA32基因座显著降低了观察到的杂合度(HO)和升高了遗传分化(FST)，这是强选择的标志。我们确定了CFA32的致病变异，但来自12个头骨形状差异很大的狗品种的全基因组序列允许我们将其减少到一个，骨形态发生蛋白3(BMP3)基因(BMP3F452L)的F452L错义突变。 我们还扩大了我们的体型研究(Rimbault，2013)。在这篇文章中，我们分析了在先前的全基因组关联研究中发现的四个基因座，以确定包括候选基因GHR、HMGA2、Smad2和STC2的小区间。然后，我们在93个品种的500只家犬身上对每个标记以及之前报道的IGF1和IGF1R基因的大小相关变体进行了基因分型，并通过对30只野犬进行相同标记的基因分型来鉴定祖先的等位基因。我们观察到，所有标记上的衍生等位基因都与体型缩小相关。然而，品种并不是所有的标记都是固定的；在大多数品种中发现了多种基因型组合。我们发现，犬品种体型差异的46%-52.5%可以由特殊候选基因附近的七个标记来解释。在标准体重为41公斤(90磅)的品种中，基因类型至少能解释体重变异的64.3%。这项工作有助于增进我们对犬类体型和哺乳动物体型遗传的理解。 最后，我们对犬的毛色进行了研究，结果表明，马鞍色斑纹的表达需要涉及ASIP、RALY、MC1R、DEFB103和一个未知修饰基因的多基因交互作用(Dreger等人，2013)。 犬癌 现代犬种的巨大表型多样性代表着长达15,000年的人工和自然选择实验的终点。每个品种都经过了严格的人工选择，在这种选择中，养狗的人根据许多特征进行选择，包括身体大小、皮毛类型、颜色、头骨形状，甚至行为，以创造出新的品种。通过品种障碍规则，任何狗都不能成为一个品种的注册成员，除非它的母犬和公犬都是注册成员，这确保了每个品种内相对封闭的基因库。因此，包括与品种相关的遗传病在内的被识别的品种内有很强的表型同质性。 我们最近对犬病的基因研究几乎完全集中在癌症上，我们认为这是人类癌症遗传学的一个强有力的模型。指端鳞状细胞癌(SCCD)是一种局部侵袭性癌症，以骨溶解、复发和偶尔因转移而死亡为特征。标准贵宾犬是患SCCD风险最高的品种之一，但只有深色标准贵宾犬容易患上SCCD。我们在黑色标准贵宾犬上进行了GWAS实验，并证明Kit Ligand(KITLG)基因座与SCCD有很强的相关性。包含预测的增强子元件的拷贝数变体(CNV)被发现与STPO中的SCCD密切相关(P=1.72 10(-8))(Karyadi 2013)。在顺式基因中没有至少一个等位基因和四个拷贝的狗不会有任何疾病风险(Karyadi，2013)。这个基因座在狗身上承受着很大的选择压力，可能是对毛色偏好的反应，因为KITLG已经被发现与人类、老鼠和鱼的色素沉着有关。

Canine Genetics Canine Origins Our canine studies are divided into genomics of domestication, morphologic variation, and disease gene mapping. With regard to the first we have published recent, high-profile papers that describe the domestication of dogs (vonHoldt et al., 2013). This builds on previous work, published in Nature, where we presented a refined description of how breeds are related to each other (vonHoldt et al., 2010). Very recently, in a collaboration led by Dr. John Novembre at UCLA, sequencing of wild canids revealed a severe 30-fold reduction in effective population size that likely occurred during the domestication bottleneck, which we now estimate occurred about 15,000 years ago (Freedman, 2014). These data also show that none of the extant wolf lineages from putative domestication centers are directly ancestral to dogs, implying that a now extinct population of wolves may be the missing link in dog evolution. Finally, the study demonstrates selection on genes affecting brain function, metabolism, and morphology, supporting a major role for regulatory evolution in domestication. We also show evidence for hybridization between dogs and wolves, and provide a tool kit with population-level statistical quantification that can detect recent dog-wolf hybridization using a panel of dog-wolf ancestry-informative SNPs with divergent allele frequency distributions (VonHoldt et al., 2013). Morphology A majority of our dog papers over the past four years reveal our growing understanding of canine genome organization and its relationship to morphologic variation between breeds. Our newest avenue of morphologic study is aimed at understanding the genetic underpinning of skull shape variation (Schoenebeck, 2014) which varies dramatically across breeds (Schoenebeck, 2013; Schoenebeck et al., 2012). To quantify the variation, we collected data from 533 museum skulls at 51 landmarks using a microscribe digitizer. The resulting principal components analysis (PCA) showed that the top four PCs account for about 77% of skull variance across breeds. PC1 describes profound changes in rostrum length and angle, palate and zygomatic arch width, and depth of the neurocranium; essentially the continuum of craniofacial features that extend between brachycephalic (short head like a bulldog) and dolichocephalic (long head like a greyhound) skulls. Our GWAS on PC1 revealed several loci. The CFA32 locus demonstrated a marked reduction in observed heterozygosity (Ho) and elevated genetic differentiation (FST), which are hallmarks of strong selection. We identified causative variants on CFA32 but whole genome sequence from 12 dog breeds of widely varying skull shapes allowed us to reduce it to one, an F452L missense mutation in the bone morphogenesis protein 3 (BMP3) gene (BMP3F452L). We also expanded our body size studies (Rimbault, 2013). In this paper we analyzed four loci discovered in a previous genome-wide association study to define small intervals that included the candidate genes GHR, HMGA2, SMAD2, and STC2. We then genotyped each marker, together with previously reported size-associated variants in the IGF1 and IGF1R genes, on a panel of 500 domestic dogs from 93 breeds, and identified the ancestral allele by genotyping the same markers on 30 wild canids. We observed that the derived alleles at all markers correlated with reduced body size. However, breeds are not generally fixed at all markers; multiple combinations of genotypes are found within most breeds. We show that 46%-52.5% of the variance in body size of dog breeds can be explained by seven markers in proximity to exceptional candidate genes. Among breeds with standard weights <41 kg (90 lb), the genotypes accounted for at least 64.3% of variance in weight. This work helps to advance our understanding of canine body size and body size genetics for mammals in general. Finally we did work on canine coat color, showing that a multi-gene interaction involving ASIP, RALY, MC1R, DEFB103, and a yet-unidentified modifier gene is required for expression of saddle tan color pattern (Dreger et al, 2013). Canine Cancer The tremendous phenotypic diversity of modern dog breeds represents the end point of a >15,000-year experiment in artificial and natural selection. Each breed has undergone strong artificial selection, in which dog fanciers selected for many traits including body size, fur type, color, skull shape, and even behavior, to create novel breeds. The adoption of the breed barrier rule that no dog may become a registered member of a breed unless both its dam and sire are registered members ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within the breeds recognized including breed-associated genetic disease. Our recent genetic studies of dog disease have focused almost exclusively on cancer, which we argue is a strong model for human cancer genetics. Squamous cell carcinoma of the digit (SCCD) is a locally aggressive cancer typified by lytic bone lesions, recurrence, and occasional death from metastasis. Standard Poodles are among the breeds with the highest risk of SCCD, however only the dark pigmented standard poodles are susceptible. We conducted a GWAS using on black Standard Poodles, and demonstrated that the Kit Ligand (KITLG) locus is strongly associated with SCCD. A copy number variant (CNV) containing predicted enhancer elements was found to be strongly associated with SCCD in STPOs (P = 1.72 10(-8)) (Karyadi 2013). Dogs without at least one allele with four copies in cis are not at any risk for disease (Karyadi, 2013). This locus is under strong selective pressure in dogs, likely in response to coat color preferences, as KITLG has been linked to pigmentation in humans, mice and fish.