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

Abstract

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.

Identification of SNPs Associated with Stress Response Traits within High Stress and Low Stress Lines of Japanese Quail

“…For the purposes of this study, two different lines of Japanese quail—a high stress (HS) line and a low stress (LS) line—have been utilized. These two lines have been selected since the 1980s for divergent blood corticosterone response to restraint-induced stress in order to serve as models for stress responses in poultry [ 6 ]. The differences between the two lines include higher sociability, lower fear, higher body weight, increased egg production, and a reduced heterophil/lymphocyte ratio in the LS line compared to the HS line.…”

“…The differences between the two lines include higher sociability, lower fear, higher body weight, increased egg production, and a reduced heterophil/lymphocyte ratio in the LS line compared to the HS line. Additionally, the LS line had decreased stress-induced osteoporosis, accelerated onset of puberty, heightened male sexual activity and efficiency, and a decrease in corticosterone levels of approximately one-third when compared to the HS line [ 6 ].…”

“…The development of HS and LS lines of Japanese quail up to the 12th generation is documented by Satterlee and Johnson (1988) [ 7 ]. Each line was selected for its plasma corticosterone response to immobilization [ 6 , 7 ]. An independent random mating condition has since been used for their maintenance [ 8 , 9 , 10 ].…”

“…Bird selection and DNA sequencing was performed in direct accordance with Khatri et al (2019) [ 6 ]. Male HS and LS birds were chosen for this study as they have a more stable physiology as a result of having fewer hormonal changes when compared to females.…”

“…Twelve samples showing highest quality per line were pooled to represent each line. Library preparation and Illumina sequencing for the pooled DNA samples were performed by the Research Technology Support Facility at Michigan State University (East Lansing, MI, USA) using Illumina HiSeq 2 × 150 bp paired end read technology [ 6 ].…”