Animal Breeding and Genomics Center, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands.
BMC Genomics. 2011 Feb 3;12:94. doi: 10.1186/1471-2164-12-94.
Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken.
We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome.
We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.
个体基因组内的变异范围从单核苷酸多态性（SNPs）到千碱基甚至兆碱基大小的结构变异（SVs），如缺失、插入、倒位和更复杂的重排。尽管人们对人类和小鼠中 SVs 的程度有了很多了解，在这些物种中，SVs 对表型有显著影响，但对于鸡的 2.5 倍小且重复序列更少的基因组中 SVs 的程度却知之甚少。
我们在四个商业鸡系中相对于参考鸡基因组鉴定出数百个共享和分化的 SVs。大多数 SVs 位于内含子和基因间区，我们还在编码区发现了 SVs。为了鉴定 SVs，我们结合了来自 25 个个体的混合样本的高通量短读对端测序和参考基因组的 DNA 序列的计算映射。
我们首次揭示了鸡中大量小结构基因组变异的存在。根据我们的结果推断，鸡基因组中存在数千个重排，其中大多数位于非编码区。我们观察到结构变异导致了当前家养鸡品种和红原鸡之间的遗传分化。我们预计，由于其丰富的存在，SVs 可能解释表型差异，并在鸡基因组的进化中发挥作用。最后，我们的研究为在测序基因组中鉴定结构变异提供了一种高效且具有成本效益的方法。
