A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny
A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny
复制标题
DOI：
10.1016/j.ympev.2008.08.026
复制
发表时间：
2008-11-01
影响因子：
4.1
通讯作者：
Amorim, Antonio
中科院分区：
文献类型：
--
作者：
Pereira, Filipe;Carneiro, Joao;Amorim, Antonio
哺乳动物Y染色体上的遗传变异对于理解群体多样性的全球模式和性别特异性群体参数如雄性介导的扩散或基因渗入是极其有用的（Hurles和Jobling，2001; Petit等人，2002年）。它的单亲遗传模式和完全没有减数分裂重组在几乎所有的程度意味着每个人都有一个单一的单倍型和系统发育分析是相对简单的解释。这些特征可能有助于解开动物驯化的复杂性，并补充线粒体DNA（mtDNA）调查中出现的画面（Hanotte et al.，2000; Bruford等人，2003; Pidancier等人，2006; Meadows等人，2006年）。对Y染色体的研究在驯化物种中特别感兴趣，因为常见的育种策略迫使只有少数雄性对下一代有遗传贡献，导致驯化过程中的强烈性别偏见（Lindgren et al.，2004年）。第一个在近东肥沃新月地区被驯化的牲畜物种是山羊（Capra hircus），至少在10，000年前驯化了野生牛黄山羊（Capra aegagrus）（Mason，1984; Zeder，2006）。最近一系列基于线粒体DNA序列变异的遗传研究揭示了山羊驯化的复杂模式（Luikart等人，2001; Naderi等人，2007年）。在世界范围内的山羊种群中发现了6个不同的mtDNA单倍型群，这表明许多遗传谱系被整合到山羊基因库中，很可能来自不同的牛黄山羊种群。Y染色体单倍型的一致性遗传学的发展将是特别有用的，以了解父系的贡献，山羊畜牧业的起源和随后的运动在世界范围内。在这里，我们提出了一个快速和强大的多重PCR/引物延伸检测基因型的山羊Y染色体单核苷酸多态性（SNPs）的一组先前描述（Lenstra，2005）。选择位于SRY基因两个侧翼结构域（启动子区和30个非翻译区）的4个诊断性SNPs来区分迄今为止在国内山羊群体中鉴定的4种Y染色体单倍型Y1 A、Y1 B、Y1 C和Y2。SNP变体的检测是基于SNaP-shot单碱基测序（也称为minisequencing），其包括使用双脱氧核苷酸（ddNTPs）对未标记引物进行单碱基延伸，所述未标记引物退火相关SNP上游的一个碱基。然后可以通过自动化毛细管电泳（用于分离已知长度的延伸产物）和多色荧光1055 -7903/$鉴定单倍型-参见前题2008 Elsevier Inc. All rights reserved. doi：10.1016/j. ympev. 2008.08. 026
Genetic variation on the mammalian Y chromosome is extremely useful for understanding global patterns of population diversity and sex-specific population parameters such as male-mediated dispersals or introgressions (Hurles and Jobling, 2001; Petit et al., 2002). Its uniparental mode of inheritance and the complete absence of meiotic recombination in almost all its extent imply that each individual has a single haplotype and that phylogenetic analyses are relatively straightforward to interpret. These features may help to unravel the complexity of animal domestication and complement the picture emerged from mitochondrial DNA (mtDNA) surveys (Hanotte et al., 2000; Bruford et al., 2003; Pidancier et al., 2006; Meadows et al., 2006). Studies on the Y chromosome are of particular interest in domesticated species because common breeding strategies impose that only a few males contribute genetically to the next generation leading to a strong sex-bias in the domestication process (Lindgren et al., 2004). The first livestock species to be domesticated in the Fertile Crescent of the Near East was the goat (Capra hircus) by taming of the wild bezoar goat (Capra aegagrus) at least 10,000 years ago (Mason, 1984; Zeder, 2006). A series of recent genetic studies based on mtDNA sequence variation has revealed a complex pattern of caprine domestication (Luikart et al., 2001; Naderi et al., 2007). Six divergent mtDNA haplogroups have been found in domestic goat populations worldwide, suggesting the incorporation of numerous genetic lineages into the domestic goat gene pool, most likely from different populations of the bezoar goat. The development of a coherent phylogeny of Y-chromosomal haplotypes will be particularly useful to understand patrilineal contributions to the origin and subsequent movements of goat pastoralism worldwide. Here we present a rapid and robust multiplex PCR/primer extension assay to genotype a set of goat Y chromosome single nucleotide polymorphisms (SNPs) previously described (Lenstra, 2005). Four diagnostic SNPs located in two flanking domains of the SRY gene (promoter region and 30 untranslated region) were selected to allow the discrimination of the four Y-chromosomal haplotypes Y1A, Y1B, Y1C and Y2 identified so far in domestic goat populations. The detection of SNP variants is based on the SNaP-shot single-base sequencing (also known as minisequencing), which consists in using dideoxynucleotides (ddNTPs) for singlebase extension of an unlabeled primer that anneals one base upstream to the relevant SNP. Identification of haplotypes is then possible by automated capillary electrophoresis (for separation of extended products of known lengths) and multicolour fluorescence1055-7903/$-see front matter Ó 2008 Elsevier Inc. All rights reserved. doi: 10.1016/j. ympev. 2008.08. 026