The Genetic Architecture of Early Body Temperature and Its Correlation With Salmonella Pullorum Resistance in Three Chicken Breeds

Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat

As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targeted sequencing (GBTS) technology. The source of SNPs in the panel were from the whole-genome resequencing of 110 dairy goats from three European and two Chinese indigenous dairy goat breeds. The performance of this liquid SNP chip panel was evaluated by genotyping 200 additional goats. Fifteen of them were randomly selected for whole-genome resequencing. The average capture ratio of the panel design loci was 98.41%, and the genotype concordance with resequencing reached 98.02%. We further used this chip panel to conduct genome-wide association studies (GWAS) to detect genetic loci that affect coat color in dairy goats. A single significant association signal for hair color was found on chromosome 8 at 31.52-35.02 Mb. The TYRP1 gene, which is associated with coat color in goats, was identified to be located at this genomic region (chromosome 8: 31,500,048-31,519,064). The emergence of high-precision and low-cost liquid microarrays will improve the analysis of genomics and breeding efficiency of dairy goats.

Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken

In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions.

Research Progress in the Early Warning of Chicken Diseases by Monitoring Clinical Symptoms

Global animal protein consumption has been steadily increasing as a result of population growth and the increasing demand for nutritious diets. The poultry industry provides a large portion of meat and eggs for human consumption. The early detection and warning of poultry infectious diseases play a critical role in the poultry breeding and production systems, improving animal welfare and reducing losses. However, inadequate methods for the early detection and prevention of infectious diseases in poultry farms sometimes fail to prevent decreased productivity and even widespread mortality. The health status of poultry is often reflected by its individual physiological, physical and behavioral clinical symptoms, such as higher body temperature resulting from fever, abnormal vocalization caused by respiratory disease and abnormal behaviors due to pathogenic infection. Therefore, the use of technologies for symptom detection can monitor the health status of broilers and laying hens in a continuous, noninvasive and automated way, and potentially assist in the early warning decision-making process. This review summarized recent literature on poultry disease detection and highlighted clinical symptom-monitoring technologies for sick poultry. The review concluded that current technologies are already showing their superiority to manual inspection, but the clinical symptom-based monitoring systems have not been fully utilized for on-farm early detection.

Body temperature is a repeatable trait in a free-ranging passerine bird

Body temperature (Tb) affects animal function through its influence on rates of biochemical and biophysical reactions, the molecular structures of proteins and tissues, and, ultimately, organismal performance. Despite its importance in driving physiological processes, there are few data on how much variation in Tb exists within populations of organisms, and whether this variation consistently differs among individuals over time (i.e. repeatability of a trait). Here, using thermal radio-frequency identification implants, we quantified the repeatability of Tb, both in the context of a fixed average environment (∼21°C) and across ambient temperatures (6-31°C), in a free-living population of tree swallows (Tachycineta bicolor, n=16). By experimentally trimming the ventral plumage of a subset of female swallows (n=8), we also asked whether the repeatability of Tb is influenced by the capacity to dissipate body heat. We found that both female and male tree swallow Tb was repeatable at 21°C (R=0.89-92), but female Tb was less repeatable than male Tb across ambient temperature (Rfemale=0.10, Rmale=0.58), which may be due to differences in parental investment. Trimmed birds had on average lower Tb than control birds (by ∼0.5°C), but the repeatability of female Tb did not differ as a function of heat dissipation capacity. This suggests that trimmed individuals adjusted their Tb to account for the effects of heat loss on Tb. Our study provides a first critical step toward understanding whether Tb is responsive to natural selection, and for predicting how animal populations will respond to climatic warming.

Identification of candidate genes associated with slaughter traits in F2 chicken population using genome-wide association study

Slaughter traits are crucial economic traits of chickens. We performed a GWAS to discover critical loci and candidate genes for 21 slaughter traits in an F2 chicken population resulting from crossing Luxi gamecocks and recessive white feather broilers. We found some SNPs and genes which were significantly associated with keel length, head length, body slope length, bilateral leg weight without shin, bilateral foot weight, subcutaneous fat thickness, heart weight, muscular stomach weight and glandular stomach weight. This study provides references for further investigation of slaughter traits and molecular breeding in chicken.