LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

文献类型： 外文期刊

第一作者： Comai, Luca

作者： Comai, Luca;Amundson, Kirk R.;Ordonez, Benny;Zhao, Xin;Henry, Isabelle M.;Comai, Luca;Amundson, Kirk R.;Ordonez, Benny;Zhao, Xin;Henry, Isabelle M.;Braz, Guilherme Tomaz;Jiang, Jiming;Jiang, Jiming;Zhao, Xin

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关键词： structural variation; chromosome; translocation; DNA sequence; copy number variation; linkage disequilibrium

期刊名称：GENETICS （ 影响因子：4.402； 五年影响因子：4.795 ）

ISSN： 0016-6731

年卷期： 2021 年 219 卷 3 期

页码：

收录情况： SCI

摘要： Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between chromosomes (chr.) 7 and 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. "Alca Tarma," the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.

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