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Novel Y Chromosome Retrocopies in Canids Revealed through a Genome-Wide Association Study for Sex

机译:通过性别全基因组关联研究揭示犬科动物中的新型Y染色体逆转录

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摘要

The lack of an annotated reference sequence for the canine Y chromosome has limited evolutionary studies, as well as our understanding of the role of Y-linked sequences in phenotypes with a sex bias. In genome-wide association studies (GWASs), we observed spurious associations with autosomal SNPs when sex was unbalanced in case-control cohorts and hypothesized that a subset of SNPs mapped to autosomes are in fact sex-linked. Using the Illumina 230K CanineHD array in a GWAS for sex, we identified SNPs that amplify in both sexes but possess significant allele frequency differences between males and females. We found 48 SNPs mapping to 14 regions of eight autosomes and the X chromosome that are Y-linked, appearing heterozygous in males and monomorphic in females. Within these 14 regions are eight genes: three autosomal and five X-linked. We investigated the autosomal genes (MITF, PPP2CB, and WNK1) and determined that the SNPs are diverged nucleotides in retrocopies that have transposed to the Y chromosome. MITFY and WNK1Y are expressed and appeared recently in the Canidae lineage, whereas PPP2CBY represents a much older insertion with no evidence of expression in the dog. This work reveals novel canid Y chromosome sequences and provides evidence for gene transposition to the Y from autosomes and the X.
机译:犬Y染色体缺少带注释的参考序列已限制了进化研究,以及我们对Y连锁序列在具有性别偏见的表型中的作用的了解。在全基因组关联研究(GWAS)中,我们观察到病例对照队列中性别不平衡时与常染色体SNP的虚假关联,并假设映射到常染色体的SNP的一部分实际上与性别相关。在用于性别的GWAS中使用Illumina 230K CanineHD阵列,我们鉴定了在两个性别中均可扩增但在雄性和雌性之间具有明显等位基因频率差异的SNP。我们发现48个SNP映射到8个常染色体和X染色体的14个区域,这些区域是Y连锁的,在雄性中表现为杂合而在雌性中表现为单态。在这14个区域中,有八个基因:三个常染色体基因和五个X连锁基因。我们研究了常染色体基因(MITF,PPP2CB和WNK1),并确定SNPs是转位到Y染色体的复本中的分歧核苷酸。 MITFY和WNK1Y最近在Canidae谱系中表达并出现,而PPP2CBY代表了一个更老的插入物,没有在狗中表达的证据。这项工作揭示了新的犬科动物Y染色体序列,并提供了将基因从常染色体和X转移到Y的证据。

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