EXPERIMENTAL-DESIGN AND ERROR-DETECTION FOR POLYPLOID RADIATION HYBRID MAPPING
EXPERIMENTAL-DESIGN AND ERROR-DETECTION FOR POLYPLOID RADIATION HYBRID MAPPING
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DOI：
10.1101/gr.5.2.151
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发表时间：
1995-09-01
期刊：
影响因子：
7
通讯作者：
COX, DR
中科院分区：
文献类型：
--
作者：
LUNETTA, KL;BOEHNKE, M;COX, DR
在本文中，我们考虑的问题，实验设计和错误检测和校正多倍体辐射杂种作图。使用分析方法和计算机模拟，我们首先考虑片段留存率、倍性和标记间距的组合，这些组合提供了对标记进行排序的最佳机会。我们发现，在一般情况下，倍性和染色体特异性保留率的组合，导致每个杂交留存率的类似50%的结果在最大的权力，以秩序标记。我们还发现，分析多倍体辐射杂种，如果他们是单倍体不妥协的能力，以标记，但不太准确的标记间距离估计结果。其次，我们研究了两个位点的信息，排序多个位点的能力，和估计的标记间距离和总的地图长度的打字错误的影响。即使是低水平的错误导致大量的信息损失的破损概率，显着降低的能力，顺序位点，和膨胀的估计标记间的距离和总的地图长度。我们比较了排序的准确性，结果从重复类型的混合动力车，以单一类型的两倍多的混合动力车，并发现重复类型的结果在一个更高的概率确定的真实顺序作为一个最好的订单，但单一类型的两倍多的混合动力车的结果在更强的支持真实的顺序。对于低错误率，从较大的单类型面板构建的框架图仅稍微不太可能是正确的，并且包括比较小的双类型面板多得多的标记。第三，我们开发了一种方法来计算一个多倍体辐射杂种在给定的基因座顺序的专性染色体断裂的数量的分布，并讨论如何使用这种方法可以用来确定杂交与可疑大量的染色体断裂。
In this paper we consider issues of experimental design and error detection and correction for polyploid radiation hybrid mapping. Using analytic methods and computer simulation, we first consider the combinations of fragment retention rate, ploidy, and marker spacing that provide the best chance to order markers. We find that in general, combinations of ploidy and chromosome-specific retention rates that lead to a per-hybrid retention rate of similar to 50% result in the greatest power to order markers. We also find that analyzing polyploid radiation hybrids as if they were haploid does not compromise the ability to order markers but does result in less accurate intermarker distance estimates. Second, we examine the effect of typing errors on two-locus information, ability to order multiple loci, and estimation of intermarker distances and total map length. Even low levels of error result in large losses of information about breakage probabilities, markedly reduce ability to order loci, and inflate estimates of intermarker distances and total map length. We compare the ordering accuracy that results from duplicate typing of hybrids to that of single typing twice as many hybrids and find that duplicate typing resuts in a higher probability of identifying the true order as one of the best orders, but that single typing of twice as many hybrids results in stronger support for the true order. For low error rates, framework maps constructed from the larger single-typed panels are only slightly less likely to be correct and include substantially more markers than the smaller double-typed panels. Third, we develop a method to calculate the distribution of the number of obligate chromosome breaks for a polyploid radiation hybrid under a given locus order and discuss how this method may be used to identify hybrids with suspiciously large numbers of chromosome breaks.