Recombinational landscape and population genomics of Caenorhabditis elegans.
Recombinational landscape and population genomics of Caenorhabditis elegans.
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DOI：
10.1371/journal.pgen.1000419
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发表时间：
2009-03
期刊：
影响因子：
4.5
通讯作者：
Kruglyak L
中科院分区：
文献类型：
--
作者：
Rockman MV;Kruglyak L
遗传速率和连锁不平衡，后者是人口基因组过程的函数，是通过连锁和关联作图的关键参数，它们在秀丽隐杆线虫中的模式知之甚少。我们对一大批重组自交高级互交系（RIAILs）进行了高密度SNP基因分型。在一组野生菌株上，描述种群基因组模式。我们证实C.线虫的常染色体表现出离散的区域，重组率几乎是恒定的，我们第一次表明，这种模式也适用于X染色体。每条染色体的末端结构域，跨越约7%的基因组，有效地表现出没有重组。RIAIL显示出遗传图谱的5.3倍扩展。标记间距中位数为61 kb，是定位柑橘数量性状基因座的有力资源。优雅的。在125个野生菌株中，我们只确定了41个不同的单倍型。基因型相似性的模式表明，一些假定的野生菌株是实验室污染物。夏威夷株CB 4856与全球种群的其余部分表现出遗传隔离，其成员表现出充分的交叉和重组证据。从连锁不平衡模式估计的群体有效重组率与估计的减数分裂重组率相关，但其幅度意味着异交的有效率极低，证实了针对重组基因型的选择报告。尽管群体低，有效的重组率和染色体之间广泛的连锁不平衡，这是技术，占背景水平的基因组相似性，允许关联映射在野生C。elegans菌株。 C.线虫是生物学不同领域的模型系统，但其作为数量性状基因作图模型的能力取决于其在实验室和自然界中的重组率。后者是蠕虫如何在野外交配和迁移的函数。我们在实验室中进行了数千次减数分裂，并在从自然界分离的菌株中进行了重组。这些数据表明，减数分裂重组率是非常有规律的蠕虫，与离散域的边界，我们确定。天然菌株的模式表明，群体结构，群体大小，异交率，和选择联合收割机结合，以抑制重组的整体效果。此外，一些“野生”菌株似乎是实验室污染物。然而，野生蠕虫的重组历史足以使基因型和表型之间的相关性，以查明负责表型变异的基因座。
Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolation from the remainder of the global population, whose members exhibit ample evidence of intercrossing and recombining. The population effective recombination rate, estimated from the pattern of linkage disequilibrium, is correlated with the estimated meiotic recombination rate, but its magnitude implies that the effective rate of outcrossing is extremely low, corroborating reports of selection against recombinant genotypes. Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains. C. elegans is a model system for diverse fields of biology, but its ability to serve as a model for quantitative trait gene mapping depends on its recombination rate in the laboratory and in nature. The latter is a function of how worms mate and migrate in the wild. We examined the patterns of recombination in a population that we put through thousands of meioses in the laboratory and in a collection of strains isolated from nature. The data suggest that meiotic recombination rate is highly regular in worms, with discrete domains whose boundaries we identify. The pattern in natural strains suggests that population structure, population size, outcrossing rate, and selection combine to suppress the overall effects of recombination. Moreover, some “wild” strains appear to be laboratory contaminants. Nevertheless, the history of recombination in wild worms is sufficient to permit correlations between genotype and phenotype to pinpoint the loci responsible for phenotypic variation.
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