Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds

Epigenomic features associated with body temperature stabilize tissues during cold exposure in cold-resistant pigs

Cold stress in low-temperature environments can trigger changes in gene expression, but epigenomics regulation of temperature stability in vital tissues, including the fat and diencephalon, is still unclear. Here, we explore the cold-induced changes in epigenomic features in the diencephalon and fat tissues of two cold-resistant Chinese pig breeds, Min and Enshi black (ES) pigs, utilizing H3K27ac CUT&Tag, RNA-seq, and selective signature analysis. Our results show significant alterations in H3K27ac modifications in the diencephalon of Min pigs and the fat of ES pigs after cold exposure. Dramatic changes in H3K27ac modifications in Min pigs are primarily associated with genes involved in energy metabolism and hormone regulation, whereas those in ES pigs are primarily associated with immunity-related genes. Moreover, transcription factors PRDM1 and HSF1, which show evidence of selection, are enriched in genomic regions presenting cold-responsive alterations in H3K27ac modification in the Min pig diencephalon and ES pig fat, respectively. Our results indicate the diversity of epigenomic response mechanisms to cold exposure between Min and ES pigs, providing unique epigenetic resources for studies of low-temperature adaptation in large mammals.

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

BACKGROUND

Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures.

RESULTS

We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively.

CONCLUSIONS

In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

Transcriptome Analysis Revealed Potential Genes of Skeletal Muscle Thermogenesis in Mashen Pigs and Large White Pigs under Cold Stress

Pigs are susceptible to cold stress due to the absence of brown fat caused by the partial deletion of uncoupling protein 1 during their evolution. Some local pig breeds in China exhibit potential cold adaptability, but research has primarily focused on fat and intestinal tissues. Skeletal muscle plays a key role in adaptive thermogenesis in mammals, yet the molecular mechanism of cold adaptation in porcine skeletal muscle remains poorly understood. This study investigated the cold adaptability of two pig breeds, Mashen pigs (MS) and Large White pigs (LW), in a four-day cold (4 °C) or normal temperature (25 °C) environment. We recorded phenotypic changes and collected blood and longissimus dorsi muscle for transcriptome sequencing. Finally, the PRSS8 gene was randomly selected for functional exploration in porcine skeletal muscle satellite cells. A decrease in body temperature and body weight in both LW and MS pigs under cold stress, accompanied by increased shivering frequency and respiratory frequency, were observed. However, the MS pigs demonstrated stable physiological homeostasis, indicating a certain level of cold adaptability. The LW pigs primarily responded to cold stress by regulating their heat production and glycolipid energy metabolism. The MS pigs exhibited a distinct response to cold stress, involving the regulation of heat production, energy metabolism pathways, and robust mitochondrial activity, as well as a stronger immune response. Furthermore, the functional exploration of PRSS8 in porcine skeletal muscle satellite cells revealed that it affected cellular energy metabolism and thermogenesis by regulating ERK phosphorylation. These findings shed light on the diverse transcriptional responses of skeletal muscle in LW and MS pigs under cold stress, offering valuable insights into the molecular mechanisms underlying cold adaptation in pigs.

Distinct Transcriptional Responses of Skeletal Muscle to Short-Term Cold Exposure in Tibetan Pigs and Bama Pigs

Piglets are susceptible to cold, and piglet death caused by cold stress leads to economic losses in the pig industry in cold areas. Skeletal muscle plays a key role in adaptive thermogenesis in mammals, but the related mechanism in pigs is unclear. In this study, cold-tolerant Tibetan pigs and cold-sensitive Bama pigs were subjected to either a cold environment (4 °C) or a room temperature environment (25 °C) for 3 days. The biceps femoris (BF) and longissimus dorsi muscle (LDM) were collected for phenotypic analysis, and the BF was used for genome-wide transcriptional profiling. Our results showed that Tibetan pigs had a higher body temperature than Bama pigs upon cold stimulation. RNA-seq data indicated a stronger transcriptional response in the skeletal muscle of Tibetan pigs upon cold stimulation, as more differentially expressed genes (DEGs) were identified with the same criteria (p < 0.05 and fold change > 2). In addition, distinct pathway signaling patterns in skeletal muscle upon cold exposure were found between the breeds of pigs. Mitochondrial beta-oxidation-related genes and pathways were significantly upregulated in Tibetan pigs, indicating that Tibetan pigs may use fatty acids as the primary fuel source to protect against cold. However, the significant upregulation of inflammatory response- and glycolysis-related genes and pathways in the skeletal muscle of Bama pigs suggested that these pigs may use glucose as the primary fuel source in cold environments. Together, our study revealed the distinct transcriptional responses of skeletal muscle to cold stimulation in Tibetan pigs and Bama pigs and provided novel insights for future investigation of the cold adaptation mechanism in pigs.

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

BACKGROUND

The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes.

RESULTS

Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F_ST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF).

CONCLUSION

Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

Simple Summary

The search for genomic regions related to adaptive abilities preserved in the chicken gene pool of two breeds, which have not been under intensive selection pressure, is of great importance for breeding in the future. This study aimed to identify key candidate genes associated with the adaptation of chickens to cold environments (using the example of the Russian White breed) by using molecular genetic methods. A total of 12 key genes on breed-specific ROH (runs of homozygosity) islands were identified, which may be potential candidate genes associated with the high level of adaptability of chickens to cold environments in the early postnatal period. These genes were associated with lipid metabolism, maintaining body temperature in cold environments, non-shivering thermogenesis and muscle development and are perspectives for further research.

Abstract

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip^® chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.

Network Meta-Analysis of Chicken Microarray Data Following Avian Influenza Challenge—A Comparison of Highly and Lowly Pathogenic Strains

The current bioinformatics study was undertaken to analyze the transcriptome of chicken (Gallus gallus) after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually. Different undirected networks were constructed and their metrics determined e.g., degree centrality, closeness centrality, harmonic centrality, subgraph centrality and eigenvector centrality. The results showed that, based on criteria of centrality, the CMTR1, EPSTI1, RNF213, HERC4L, IFIT5 and LY96 genes were the most significant during HPAI challenge, with PARD6G, HMG20A, PEX14, RNF151 and TLK1L having the lowest values. However, for LPAI challenge, ZDHHC9, IMMP2L, COX7C, RBM18, DCTN3, and NDUFB1 genes had the largest values for aforementioned criteria, with GTF3C5, DROSHA, ATRX, RFWD2, MED23 and SEC23B genes having the lowest values. The results of this study can be used as a basis for future development of treatments/preventions of the effects of avian influenza in chicken.

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.

Endocrinology of thermoregulation in birds in a changing climate

The ability to maintain a (relatively) stable body temperature in a wide range of thermal environments by use of endogenous heat production is a unique feature of endotherms such as birds. Endothermy is acquired and regulated via various endocrine and molecular pathways, and ultimately allows wide aerial, aquatic, and terrestrial distribution in variable environments. However, due to our changing climate, birds are faced with potential new challenges for thermoregulation, such as more frequent extreme weather events, lower predictability of climate, and increasing mean temperature. We provide an overview on thermoregulation in birds and its endocrine and molecular mechanisms, pinpointing gaps in current knowledge and recent developments, focusing especially on non-model species to understand the generality of, and variation in, mechanisms. We highlight plasticity of thermoregulation and underlying endocrine regulation, because thorough understanding of plasticity is key to predicting responses to changing environmental conditions. To this end, we discuss how changing climate is likely to affect avian thermoregulation and associated endocrine traits, and how the interplay between these physiological processes may play a role in facilitating or constraining adaptation to a changing climate. We conclude that while the general patterns of endocrine regulation of thermogenesis are quite well understood, at least in poultry, the molecular and endocrine mechanisms that regulate, e.g. mitochondrial function and plasticity of thermoregulation over different time scales (from transgenerational to daily variation), need to be unveiled. Plasticity may ameliorate climate change effects on thermoregulation to some extent, but the increased frequency of extreme weather events, and associated changes in resource availability, may be beyond the scope and/or speed for plastic responses. This could lead to selection for more tolerant phenotypes, if the underlying physiological traits harbour genetic and individual variation for selection to act on - a key question for future research.

Are Dual-Purpose Chickens Twice as Good? Measuring Performance and Animal Welfare throughout the Fattening Period

Chickens are the world's most widely used farm animal and have a significant genetic diversity. In the current study, we investigated three strains for their suitability as dual-purpose chickens, with a focus on the fattening ability and welfare of the cockerels: 1. layer cockerels (Lohmann Brown, LB, n = 714); 2. cockerels of a dual-purpose hybrid (Lohmann Dual, LD, n = 844); and 3. cockerels of a native breed (Rhinelander, RL, n = 458). Chicks were raised under identical conditions and marked individually to compare focus and random sampling methods for weighing birds weekly. Because chicks of dual-purpose origins are usually raised mixed-sex, cockerels and pullets were weighed and observed together until sexes the were identifiable at week 10 of their life. During the 10th to 20th week of life, investigations were continued on 100 cockerels per genotype. Key figures for growth performance, such as feed conversion ratio (FCR) and European production efficiency factor (EPEF), were also calculated at weekly intervals. LD cockerels showed considerable growth performance (p < 0.001 compared to LB, RL, 2 kg at 9 weeks), whereas LB reached a live weight of 2 kg at 13 weeks and RL at 15 weeks of age. Genotype-dependent differences were also evident, with favorable FCR and EPEF for LD, intermediate for LB, and unfavorable for RL (all p < 0.001). The results of the FCR and EPEF suggest that cockerels should be slaughtered around week 8 of life, although only the carcass of the LD might be marketable. Thus, the optimal time of slaughter based on production parameters such as FCR and EPEF is different from the time when the animal reaches a marketable 2 kg live weight. Animal-based welfare indicators revealed that the RL are not adapted to production environments, including those that are extensive. Further research aimed at adapted feed management, including better FCR, and animals adapted to the respective production environments is necessary to improve alternative poultry production in the future.