Data from: Deep sequencing of a candidate region harboring the SOX9 gene for the canine XX disorder of sex development

A disorder of sex development (DSD) in dogs with female sex chromosomes (78, XX), a lack of the SRY gene and the presence of testes or ovotestes is commonly diagnosed in numerous breeds. The molecular background of DSD is not fully recognized but has been linked to the copy number variation in the region harboring the SOX9 gene. We applied a genome-wide association study and targeted next-generation sequencing techniques to compare DSD and normal female dogs. The genome-wide association study did not indicate a significant chromosome region. Targeted next-generation sequencing of a 1.5-Mb region on canine chromosome 9 harboring the SOX9 gene revealed two putatively DSD-associated copy number variations 355 kb upstream and 691 kb downstream of SOX9, four blocks of low polymorphism and two blocks of an elevated heterozygosity. An initial next-generation sequencing analysis showed an association with two SNPs, but validation in larger cohorts did not confirm this result. We identified a large homologous fragment (over 243.8 kb), named hfMAGI2, located upstream of SOX9, that overlaps a known copy number variation region. It shows a high sequence similarity with the 5′ flanking region of the MAGI2 gene located on canine chromosome 18 that encodes a protein involved in ovary formation during early embryonic development. Our study showed that the identified copy number variation region located upstream of the SOX9 gene contains potential regulatory sequences (long non-coding RNA and hfMAGI2) and led to the assumption that a multiplication of this element may alter expression of the SOX9 gene, triggering the DSD phenotype.携带雌性染色体核型（78, XX）、缺失SRY基因（sex-determining region Y gene）且存在睾丸或卵睾体的犬类性别发育异常（disorder of sex development, DSD），在众多犬品种中均有高发诊断报道。目前该类DSD的分子机制尚未完全阐明，但已被证实与SOX9基因所在区域的拷贝数变异（copy number variation, CNV）相关。本研究采用全基因组关联分析（genome-wide association study, GWAS）与靶向下一代测序（next-generation sequencing, NGS）技术，对比了DSD患犬与正常雌性犬的基因组特征。全基因组关联分析未筛选到显著关联的染色体区域。针对犬9号染色体上包含SOX9基因的1.5 Mb区域开展靶向下一代测序，结果发现SOX9基因上下游分别355 kb和691 kb处存在2个疑似与DSD相关的拷贝数变异，同时检测到4个低多态性区域与2个杂合性升高区域。初步下一代测序分析显示存在2个单核苷酸多态性（single nucleotide polymorphism, SNP）位点与DSD相关，但扩大队列验证实验未证实该关联结果。本研究在SOX9基因上游区域鉴定出一段长243.8 kb以上的同源片段，命名为hfMAGI2，该片段与已知拷贝数变异区域存在重叠。该片段与犬18号染色体上MAGI2基因的5'侧翼区域序列相似度极高；MAGI2基因编码的蛋白参与早期胚胎发育过程中的卵巢形成。本研究证实，SOX9基因上游的拷贝数变异区域包含潜在调控序列（长链非编码RNA（long non-coding RNA, lncRNA）与hfMAGI2），据此推测该区域的拷贝数扩增可能会改变SOX9基因的表达水平，进而诱发DSD表型。