Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA.
Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
Genes (Basel). 2021 Mar 12;12(3):405. doi: 10.3390/genes12030405.
Mitigation of stress is of great importance in poultry production, as chronic stress can affect the efficiency of production traits. Selective breeding with a focus on stress responses can be used to combat the effects of stress. To better understand the genetic mechanisms driving differences in stress responses of a selectively bred population of Japanese quail, we performed genomic resequencing on 24 birds from High Stress (HS) and Low Stress (LS) lines of Japanese quail using Illumina HiSeq 2 × 150 bp paired end read technology in order to analyze Single Nucleotide Polymorphisms (SNPs) within the genome of each line. SNPs are common mutations that can lead to genotypic and phenotypic variations in animals. Following alignment of the sequencing data to the quail genome, 6,364,907 SNPs were found across both lines of quail. 10,364 of these SNPs occurred in coding regions, from which 2886 unique, non-synonymous SNPs with a SNP% ≥ 0.90 and a read depth ≥ 10 were identified. Using Ingenuity Pathway Analysis, we identified genes affected by SNPs in pathways tied to immune responses, DNA repair, and neurological signaling. Our findings support the idea that the SNPs found within HS and LS lines of quail could direct the observed changes in phenotype.
减轻应激在禽类生产中非常重要，因为慢性应激会影响生产性状的效率。通过专注于应激反应的选择性育种，可以用来对抗应激的影响。为了更好地了解遗传机制在选择育种的日本鹌鹑群体中的应激反应差异，我们使用 Illumina HiSeq 2 × 150 bp 配对末端读取技术对来自日本鹌鹑高应激（HS）和低应激（LS）品系的 24 只鸟进行了基因组重测序，以便分析每个品系基因组内的单核苷酸多态性（SNP）。SNP 是常见的突变，可导致动物的基因型和表型变异。对测序数据与鹌鹑基因组进行比对后，在两条鹌鹑品系中共发现了 6364907 个 SNP。其中 10364 个 SNP 发生在编码区，从中鉴定出了 2886 个独特的、非同义的 SNP，SNP%≥0.90，读深度≥10。使用 Ingenuity Pathway Analysis，我们确定了受 SNP 影响的基因，这些 SNP 与免疫反应、DNA 修复和神经信号转导相关的途径有关。我们的研究结果支持了这样一种观点，即鹌鹑 HS 和 LS 品系中发现的 SNP 可能导致表型观察到的变化。
