Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.
Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.
复制标题
连锁不平衡的估计和根据果蝇醇脱氢酶区域中的分离核苷酸位点确定的重组参数。
DOI：
10.1093/genetics/135.2.541
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发表时间：
1993
期刊：
影响因子：
3.3
通讯作者：
Miller,EL
中科院分区：
文献类型：
--
作者：
Schaeffer,SW;Miller,EL
用果蝇的乙醇脱氢酶（Adh）区域（包括Adh和Adh-Dup两个基因）研究了分离核苷酸位点对之间的连锁不平衡模式和组织。本文收集了99个来自D.用聚合酶链反应介导的技术对假暗细胞进行核苷酸序列测定。在3.5 kb的Adh区域的359个多态性位点的所有对进行了测试显着的连锁不平衡与Fisher的精确检验。在74，278个分离位点的成对比较中，有127个在5%水平上处于显著连锁不平衡。将5个连锁不平衡估计量D（ij）、D2、r（ij）、r2和D（ij）的分布与理论分布进行了比较。D（ij）、D2、r（ij）和r2的观测分布与无限位点模型下的理论分布一致。观察到的D（ij）分布与理论分布不同，因为-1和1处的值过多。在Adh区域的连锁不平衡模式中没有观察到空间模式，除了在Adh的成人内含子和内含子2中非随机关联的两个位点簇。连锁不平衡的大小随着核苷酸距离的增加而显著降低，或者说是距离效应。Adh-Dup对重组参数4 Nc的估计值大于Adh，其中N是有效群体大小，c是重组率。突变和重组参数的比较显示，每个突变事件发生7-17个重组事件。重组参数的异质性估计和连锁不平衡和核苷酸距离之间的反比关系不再显着时，两个集群的Adh内含子位点被排除在分析之外。最有可能的解释是两个集群的连锁不平衡的上位性选择之间的网站在集群中，以保持前mRNA的二级结构。
The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D(ij), D2, r(ij), r2 and D(ij) were compared to theoretical distributions. The observed distributions of D(ij), D2, r(ij) and r2 were consistent with the theoretical distribution given an infinite sites model. The observed distribution of D(ij) differed from the theoretical distribution because of an excess of values at -1 and 1. No spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure.