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

ABSTRACT: 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.

SUBMITTER: Shumaker S

PROVIDER: S-EPMC8000459 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background Understanding how Japanese quails respond to arginine intake has been an objective that previous studies have not fulfilled. The main responses to be quantified include the arginine requirement for maintenance (mg/kg0.67) and egg mass production (mg/g). Quantifying maintenance and production relationships are essential steps for predicting animal response. The current study aimed to describe how quails respond to arginine intake and determine arginine requirements for maintenance and egg production in Japanese quails. Methods The experiment was carried out in a completely randomized design, with seven treatments and seven replicates with individual birds as experimental units. The arginine levels were: 2.43, 3.64, 4.85, 6.07, 9.07, 12.13, and 14.56 g/kg. The experiment lasted for eight weeks. The variables analyzed were daily arginine intake, daily arginine deposition in eggs, and body weight. The data were analyzed using a mixed model, with the experimental unit being the random effect and the experimental levels of arginine as a fixed effect. When the effect of arginine levels was detected (P ≤ 0.05), saturation kinetics and an exponential model with four parameters (monomolecular) were adopted. ANOVA results indicated that dietary arginine levels significantly affected (P < 0.01) the analyzed variables. The formulation strategy of the experimental diets allowed amplitude in the dietary arginine levels, and according to bird responses, arginine was the limiting nutrient. Results The arginine requirement for body weight maintenance (BW0.67) was estimated to be 90 mg/kg BW0.67 by the monomolecular function. The requirement for egg mass (EM) production was estimated to be 25 mg/g per egg. A factorial model was parameterized as follows: daily arginine intake mg/bird = 90 × BW0.67 + 25 × EM ± 12 mg. The model was applied to data obtained from literature, and the resultant error was within the expected limit of 12 mg. The recommended daily arginine intake for the daily production of 11 g of egg and 180 g of BW was determined to be 304 mg/bird. The current study provides procedures that researchers can easily adopt.

Project description:BackgroundBehavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement, response to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production).ResultsWe report the results of the first genome-wide QTL detection based on a medium density SNP panel obtained from whole genome sequencing of a pool of individuals from each divergent line. A genetic map was constructed using 2145 markers among which 1479 could be positioned on 28 different linkage groups. The sex-averaged linkage map spanned a total of 3057 cM with an average marker spacing of 2.1 cM. With the exception of a few regions, the marker order was the same in Japanese Quail and the chicken, which confirmed a well conserved synteny between the two species. The linkage analyses performed using QTLMAP software revealed a total of 45 QTLs related either to behavioral (23) or production (22) traits. The most numerous QTLs (15) concerned social motivation traits. Interestingly, our results pinpointed putative pleiotropic regions which controlled emotional reactivity and body-weight of birds (on CJA5 and CJA8) or their social motivation and the onset of egg laying (on CJA19).ConclusionThis study identified several QTL regions for social and emotional behaviors in the Quail. Further research will be needed to refine the QTL and confirm or refute the role of candidate genes, which were suggested by bioinformatics analysis. It can be hoped that the identification of genes and polymorphisms related to behavioral traits in the quail will have further applications for other poultry species (especially the chicken) and will contribute to solving animal welfare issues in poultry production.

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

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