Copy number variation study in Japanese quail associated with stress related traits using whole genome re-sequencing data

Copy number variation (CNV) is a major driving factor for genetic variation and phenotypic diversity in animals. To detect CNVs and understand genetic components underlying stress related traits, we performed whole genome re-sequencing of pooled DNA samples of 20 birds each from High Stress (HS) and Low Stress (LS) Japanese quail lines using Illumina HiSeq 2×150 bp paired end method. Sequencing data were aligned to the quail genome and CNVnator was used to detect CNVs in the aligned data sets. The depth of coverage for the data reached to 41.4x and 42.6x for HS and LS birds, respectively. We identified 262 and 168 CNV regions affecting 1.6 and 1.9% of the reference genome that completely overlapped 454 and 493 unique genes in HS and LS birds, respectively. Ingenuity pathway analysis showed that the CNV genes were significantly enriched to phospholipase C signaling, neuregulin signaling, reelin signaling in neurons, endocrine and nervous development, humoral immune response, and carbohydrate and amino acid metabolisms in HS birds, whereas CNV genes in LS birds were enriched in cell-mediated immune response, and protein and lipid metabolisms. These findings suggest CNV genes identified in HS and LS birds could be candidate markers responsible for stress responses in birds.

拷贝数变异（Copy number variation, CNV）是动物遗传变异与表型多样性的主要驱动因素之一。为检测CNV并解析应激相关性状的潜在遗传机制，本研究针对高应激（High Stress, HS）与低应激（Low Stress, LS）两个日本鹌鹑品系，各选取20只个体的混合DNA样本，采用Illumina HiSeq 2×150 bp双端测序策略开展全基因组重测序。将测序数据比对至鹌鹑参考基因组后，借助CNVnator工具对比对数据集进行CNV检测。HS与LS组的测序覆盖度分别达到41.4倍与42.6倍。本研究分别在HS与LS组中鉴定出262个和168个CNV区域，这些区域分别覆盖参考基因组的1.6%与1.9%，且完全覆盖454个和493个独有的功能基因。Ingenuity通路分析（Ingenuity Pathway Analysis）结果显示，HS组的CNV相关基因显著富集于磷脂酶C信号通路、神经调节蛋白信号通路、神经元Reelin信号通路、内分泌与神经发育、体液免疫应答以及碳水化合物与氨基酸代谢过程；而LS组的CNV相关基因则富集于细胞介导免疫应答、蛋白质与脂质代谢过程。上述研究结果表明，本研究在HS与LS组鹌鹑中鉴定得到的CNV相关基因，可作为鸟类应激响应的候选分子标记。