Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
Plant J. 2012 Aug;71(3):517-26. doi: 10.1111/j.1365-313X.2012.04993.x. Epub 2012 May 14.
Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.
基于测序的作图（SHOREmap，SHORE 映射）大大加快了因果突变的鉴定速度。最初基于混池分离群体重测序的 SHOREmap 方法需要高度准确和完整的参考序列。然而，当前非模式生物的下一代测序数据的全基因组或转录组组装并不能产生染色体长度的支架。因此，我们开发了一种利用与相关基因组的同线性进行遗传作图的方法。我们首先展示了如何使用较少的标记进行基于测序的作图，以及如何通过富集标记序列来补偿标记数量的减少。作为概念验证，我们将这种方法应用于拟南芥基因模型，这些基因模型按照与远亲芸薹属基因组序列的同线性进行排序，而芸薹属基因组相对于拟南芥有几个大规模的重排。我们的方法为缺乏完成的基因组参考序列的物种或只有 RNA-seq 组装的物种提供了一种高分辨率遗传作图的替代方法。最后，为了通过精细作图提高因果突变的鉴定能力，我们引入了一种新的似然比检验统计量，将局部等位基因频率估计值转换为置信区间，类似于传统的作图区间。
