Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.
Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.
复制标题
DOI：
10.1371/journal.pgen.1003100
复制
发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Groenen MA
中科院分区：
文献类型：
--
作者：
Bosse M;Megens HJ;Madsen O;Paudel Y;Frantz LA;Schook LB;Crooijmans RP;Groenen MA
近亲交配一直被认为是野生种群和驯化种群适合度降低的主要原因。近亲交配导致血统完全相同的单倍型遗传(IBD)，并导致后代基因组上的纯合子延伸。纯合区(RoHS)的大小和位置预计与GC含量和重组率等基因组特征相关，但也与选择方向相关。因此，RoHS应该在基因组中非随机分布。因此，人口历史可能不能完全预测近亲交配的影响。猪基因组重组率的分布具有相对异质性，这使得Sus scrofa成为研究重组地形和人口统计学对基因组变异影响的一个很好的模型。这项研究利用下一代测序数据来分析基因组ROH模式，使用比较滑动窗口方法。我们基于三个不同的参数对基因组变异进行了深入的研究：RoHS外的核苷酸多样性、基因组中RoHS的数量和平均ROH大小。我们在欧亚大陆商业猪品种和野生猪的所有基因组中都发现了丰富的RoHS。RoHS的规模和数量与已知的人口统计学相一致，人口瓶颈极大地增加了ROH的发生。RoHS外的核苷酸多样性在源自大量古代种群的种群中很高，无论当前种群规模如何。此外，我们还发现基因组ROH的分布是不均匀的，ROH的大小和丰度与重组率和GC含量有很强的相关性。全球基因含量与ROH频率无关，但在商业品系和野生种群中，某些ROH热点确实包含阳性选择基因。这项研究强调了人口统计学和重组对基因组纯合性的影响对理解近亲繁殖的影响的重要性。由于有害等位基因的较高表达，较小的种群患近亲繁殖衰退的风险增加。这可能会对这些人口的生存能力产生重大影响。在人工选择的繁殖种群中的驯养物种中，以及在经历栖息地衰退的野生种群中，保持遗传多样性是至关重要的。序列技术的最新进展使我们能够确定单个基因组中核苷酸变异的模式。我们筛选了欧亚大陆野猪和商品猪的全基因组，寻找纯合区域。我们发现这些纯合子区域是由猪的人口历史和有效种群大小造成的。欧洲野猪的变异最小，但欧洲野猪的基因组中也包含大量纯合子延伸。此外，一个区域枯竭的可能性取决于它在基因组中的位置，因为变异与重组率有很高的相关性。端粒区域的变化要大得多，染色体的中心区域有更高的机会包含纯合子的长区域。这些发现增加了对基因组变异的精细结构的了解，它们对种群遗传管理特别重要。
Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding. Small populations have an increased risk of inbreeding depression due to a higher expression of deleterious alleles. This can have major consequences for the viability of these populations. In domesticated species like the pig that are artificially selected in breeding populations, but also in wild populations that experience habitat decline, maintaining genetic diversity is essential. Recent advances in sequence technology enabled us to identify patterns of nucleotide variation in individual genomes. We screened the full genome of wild boars and commercial pigs from Eurasia for regions of homozygosity. We found these regions of homozygosity were caused by the demographic history and effective population size of the pigs. European wild boars are least variable, but also European breeds contain large homozygous stretches in their genome. Moreover, the likelihood of a region becoming depleted depends on its position in the genome, because variation has a high correlation with recombination rate. The telomeric regions are much more variable, and the central region of chromosomes has a higher chance of containing long regions of homozygosity. These findings increase knowledge on the fine-scaled architecture of genomic variation, and they are particularly important for population genetic management.
登录
查看更多内容
影响因子：
3.7
作者：
Kirin M;McQuillan R;Franklin CS;Campbell H;McKeigue PM;Wilson JF
通讯作者：
Wilson JF
影响因子：
64.8
作者：
Li, Heng;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
4.5
作者：
Lohmueller KE;Albrechtsen A;Li Y;Kim SY;Korneliussen T;Vinckenbosch N;Tian G;Huerta-Sanchez E;Feder AF;Grarup N;Jørgensen T;Jiang T;Witte DR;Sandbæk A;Hellmann I;Lauritzen T;Hansen T;Pedersen O;Wang J;Nielsen R
通讯作者：
Nielsen R
影响因子：
7
作者：
Auton, Adam;Bryc, Katarzyna;Bustamante, Carlos D.
通讯作者：
Bustamante, Carlos D.
影响因子：
14.9
作者：
Haider S;Ballester B;Smedley D;Zhang J;Rice P;Kasprzyk A
通讯作者：
Kasprzyk A