Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens

Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.

Meta-analysis identifying gut microbial biomarkers of Qinghai-Tibet Plateau populations and the functionality of microbiota-derived butyrate in high-altitude adaptation

The extreme environmental conditions of a plateau seriously threaten human health. The relationship between gut microbiota and human health at high altitudes has been extensively investigated. However, no universal gut microbiota biomarkers have been identified in the plateau population, limiting research into gut microbiota and high-altitude adaptation. 668 16s rRNA samples were analyzed using meta-analysis to reduce batch effects and uncover microbiota biomarkers in the plateau population. Furthermore, the robustness of these biomarkers was validated. Mendelian randomization (MR) results indicated that Tibetan gut microbiota may mediate a reduced erythropoietic response. Functional analysis and qPCR revealed that butyrate may be a functional metabolite in high-altitude adaptation. A high-altitude rat model showed that butyrate reduced intestinal damage caused by high altitudes. According to cell experiments, butyrate may downregulate hypoxia-inducible factor-1α (HIF-1α) expression and blunt cellular responses to hypoxic stress. Our research found universally applicable biomarkers and investigated their potential roles in promoting human health at high altitudes.

Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation

Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation.

Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments.

Probiotic fermented feed improved the production, health and nutrient utilisation of yellow-feathered broilers reared in high altitude in Tibet

1. Probiotic fermented feed (PFF) has been widely used in poultry production. The current study was designed to investigate whether PPF could alleviate the negative effects of hypoxia on yellow-feathered broilers reared at high altitude on the Tibet Plateau. 2. A total of 480, one-day-old male Lingnan yellow-feathered broilers were divided into four treatment groups with six replicates, each containing 20 broiler chickens. Broilers in the four groups were offered either a basal diet (without antibiotics) or test diets containing 5, 10 and 15% of PFF respectively. The experiment lasted for eight weeks. 3. Birds fed the 10% PFF diet exhibited increased (P < 0.05) average daily gain (ADG) on d 28 and 56, body weight (BW) on d 56, total tract apparent digestibility (TTAD) of dry matter (DM), crude protein (CP) and gross energy (GE). Feeding diets supplemented with 10% PFF increased (P < 0.05) digestive activity and gut development in duodenum and jejunum. Supplementation with 10% or 15% PFF significantly increased (P < 0.05) the caecal populations of Lactobacilli and Bifidobacteria spp. and decreased (P < 0.05) caecal E. coli and Salmonella spp. on d 28 and 56. 4. The ADG and BW on d 56, protease activity in duodenum on d 56 and jejunum on d 28 and 56, villus height and villi absorptive area in duodenum and jejunum and caecal Bifidobacteria spp. showed a quadratic (P < 0.05) dose response as supplemental PFF level increased. The TTAD of DM and CP and caecal Lactobacilli spp. increased linearly with PFF level. The caecal populations of E. coli and Salmonella spp. decreased linearly with PFF level. 5. In conclusion, addition of PFF in broiler diets had the potential to improve production performance, nutrient utilisation, intestinal digestive function and caecal microflora in yellow broiler chickens raised at high altitude.

Proteome-based identification of chicken egg yolk proteins associated with antioxidant activity on the Qinghai-Tibetan Plateau

In this study, a proteome analysis of Tibetan chicken egg yolk as well as the comparison to that of lowland chicken were performed by label-free quantitative proteomics. A total of 135 proteins were identified and abundances of 19 of these proteins were significantly different between these two groups. These differential proteins were mainly associated with oxidative stress, defense, energy metabolism and tissue development through bioinformatics analysis. To further verify the species-specific diversity of the antioxidant capacity, the antioxidative activities of egg yolk proteins were further invested in vitro and in Caco-2 cells. It was observed that both Tibetan and lowland chicken egg yolk proteins showed antioxidant activities, but the former exerted a much stronger effect. PIT54 and glutathione peroxidase 3 were considered to be antioxidant-related candidate proteins. These results provide substantial evidence for the molecular mechanisms of enhancing physical activity levels of egg yolk proteins, especially with regard to the cross-species protective mechanisms against oxidative stress.

Optimization of Antioxidant Hydrolysate Produced from Tibetan Egg White with Papain and Its Application in Yak Milk Yogurt

The objective of the present study was to produce antioxidant hydrolysate from Tibetan egg white protein hydrolyzed with papain, and to investigate the effect of added papain egg white hydrolysate (PEWH) on the quality characteristics and amino acid profiles of yak milk yogurt. A response surface methodology (RSM) was utilized to analyze the effects of hydrolysis time (X₁), the ratio of enzymes to substrates, and enzyme dosage (X₃) on the superoxide anion radical (O₂⁻) scavenging activity of hydrolysates. The predicted maximum value of O₂⁻ scavenging activity (89.06%) was obtained an X₁ of 2.51 h, X₂ of 4.13%, and X₃ of 4500 U/g of substrate, almost approaching the experimental value (88.05 ± 1.2%). Furthermore, it was found that the addition of PEWH to yak milk can enhance acidification, sensory score, the number of lactic acid bacteria (LAB), and the amino acid content in yak milk yogurt. The results suggested that PEWH displayed an exceptional potential to be developed as a functional food ingredient that could be applied during the manufacturing process of yak milk yogurt.

Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos

Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31.2 gigabases of sequence data were generated from six MeDIP-seq libraries. We identified 1,049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs are involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia-related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB2, BMPR1B, BMPRII, and ITGA2) might play key regulatory roles in the adaptation to hypoxia in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.

High altitude hypoxia as a factor that promotes tibial growth plate development in broiler chickens

Tibial dyschondroplasia (TD) is one of the most common problems in the poultry industry and leads to lameness by affecting the proximal growth plate of the tibia. However, due to the unique environmental and geographical conditions of Tibet, no case of TD has been reported in Tibetan chickens (TBCs). The present study was designed to investigate the effect of high altitude hypoxia on blood parameters and tibial growth plate development in chickens using the complete blood count, morphology, and histological examination. The results of this study showed an undesirable impact on the overall performance, body weight, and mortality of Arbor Acres chickens (AACs) exposed to a high altitude hypoxic environment. However, AACs raised under hypoxic conditions showed an elevated number of red blood cells (RBCs) and an increase in hemoglobin and hematocrit values on day 14 compared to the hypobaric normoxia group. Notably, the morphology and histology analyses showed that the size of tibial growth plates in AACs was enlarged and that the blood vessel density was also higher after exposure to the hypoxic environment for 14 days, while no such change was observed in TBCs. Altogether, our results revealed that the hypoxic environment has a potentially new role in increasing the blood vessel density of proximal tibial growth plates to strengthen and enhance the size of the growth plates, which may provide new insights for the therapeutic manipulation of hypoxia in poultry TD.