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The economic significance of ruminants in agriculture underscores the need for advanced research methodologies to enhance their traits. This review aims to elucidate the transformative role of pan-omics technologies in ruminant research, focusing on their application in uncovering the genetic mechanisms underlying complex traits such as growth, reproduction, production performance, and rumen function. Pan-omics analysis not only helps in identifying key genes and their regulatory networks associated with important economic traits but also reveals the impact of environmental factors on trait expression. By integrating genomics, epigenomics, transcriptomics, metabolomics, and microbiomics, pan-omics enables a comprehensive analysis of the interplay between genetics and environmental factors, offering a holistic understanding of trait expression. We explore specific examples of economic traits where these technologies have been pivotal, highlighting key genes and regulatory networks identified through pan-omics approaches. Additionally, we trace the historical evolution of each omics field, detailing their progression from foundational discoveries to high-throughput platforms. This review provides a critical synthesis of recent advancements, offering new insights and practical recommendations for the application of pan-omics in the ruminant industry. The broader implications for modern animal husbandry are discussed, emphasizing the potential for these technologies to drive sustainable improvements in ruminant production systems. [ABSTRACT FROM AUTHOR]

Simple Summary: This article first introduces the basic principles and analysis process of genome-wide association studies and metabolome genome-wide association studies, then summarizes the latest research progress regarding their applications in animal genetic breeding, and finally briefly compares and elaborates on the advantages and disadvantages of genome-wide association studies and metabolome genome-wide association studies. Given the current emphasis on the analysis of genome-wide association studies and metabolome genome-wide association studies as a focal point of scientific research, our aim in publishing this review is to provide a resource for fellow scientists to efficiently grasp the advancements within our domain. In recent years, genome-wide association studies (GWAS) and metabolome genome-wide association studies (mGWAS) have emerged as crucial methods for investigating complex traits in animals and plants. These have played pivotal roles in research on livestock and poultry breeding, facilitating a deeper understanding of genetic diversity, the relationship between genes, and genetic bases in livestock and poultry. This article provides a review of the applications of GWAS and mGWAS in animal genetic breeding, aiming to offer reference and inspiration for relevant researchers, promote innovation in animal genetic improvement and breeding methods, and contribute to the sustainable development of animal husbandry. [ABSTRACT FROM AUTHOR]

At present, there are few reports about the proteomics changes provoked by butylated hydroxytoluene (BHT) supplementation on cryopreserved semen in mammals. Thus, we aimed to evaluate the effects of different concentrations of BHT on goat sperm and to investigate the proteomics changes of adding BHT to cryopreserved goat (Capra hircus) sperm. Firstly, semen samples were collected from four goats, and frozen in the basic extenders containing different concentrations of BHT (0.5 mM, 1.0 mM, 2.0 mM) and a control without BHT, respectively. After thawing, the protective effects of dose-dependent replenished BHT to the freezing medium on post-thaw sperm motility, integrities of plasma membrane and acrosome, reactive oxygen species levels were confirmed, with 0.5 mM BHT being the best (B group) as compared to the control (without BHT, C group). Afterwards, TMT-based quantitative proteomic technique was performed to profile proteome of the goat sperm between C group and B group. Parallel reaction monitoring was used to confirm reliability of the data. Overall, 2,476 proteins were identified and quantified via this approach. Comparing the C and B groups directly (C vs. B), there were 17 differentially abundant proteins (DAPs) po-tentially associated with sperm characteristics and functions were identified, wherein three were upregulated and 14 were downregulated, respectively. GO annotation analysis demonstrated the potential involvement of the identified DAPs in metabolic process, multi-organism process, reproduction, reproductive process, and cellular process. KEGG enrichment analysis further indicated their potential roles in renin-angiotensin system and glutathione metabolism pathways. Together, this novel study clearly shows that BHT can effectively improve quality parameters and fertility potential of post-thawed goat sperm at the optimal concentration, and its cryoprotection may be realized through regulation of sperm metabolism and antioxidative capability from the perspective of sperm proteomic modification. [ABSTRACT FROM AUTHOR]

In the intricate tapestry of Yunnan Province's biodiversity, the Lanping black-boned sheep (LPBB) emerges as a captivating enigma, distinguished by its profound melanin pigmentation adorning both its skin and its internal organs. Initially cataloged in the 1950s within the confines of Lanping County, this exceptional mammalian species presents a scarcity and uniqueness that extends beyond its geographic origins. Here, we collected 100 blood samples from Lanping black-boned sheep along with 50 samples each from Lanping normal sheep (LPN) and Huize normal sheep (HZN), all sourced from Yunnan Province. Our investigation focused on the association between the platelet-derived growth factor receptor-like gene (PDGFRL) polymorphism and the distinctive melanin characteristics observed in Lanping black-boned sheep. Utilizing UV–visible spectrophotometry, we assessed the melanin indexes present, such as tyrosinase activity and true melanin in the sheep blood, and the results demonstrated a significant elevation in melanin indexes for Lanping black-boned sheep compared to the control group (P<0.05). We also identified three synonymous mutation sites within a partial 1128 bp exon fragment of the gene-encoding PDGFRL (EX2-G408A, EX5-T184C, and EX5-G222T). Notably, Lanping black-boned sheep, harboring genotypes GG, TT, and GG at these specific sites, showcased a pronounced surge in tyrosinase activity, eumelanin / total melanin ratios, and plasma colorimetric values when contrasted with the control group (P<0.05). The discernment of GG, TT, and GG as the prevailing genotypes at their respective genetic loci in Lanping black-boned sheep heralds a breakthrough in our understanding of the genetic markers associated with black pigmentation. However, all three loci are silent mutations and do not alter the phenotypic changes. Whether they affect changes in melanin content through other metabolic pathways requires further study. In conclusion, the PDGFRL gene was silenced by mutations in our study and affected blood melanin levels. However, the gene did not undergo a missense mutation that altered the phenotypic changes, and the exact channel through which the changes in melanin content were affected needs to be further verified. [ABSTRACT FROM AUTHOR]

Among the numerous transmissible spongiform encephalopathies (TSEs), bovine spongiform encephalopathy (BSE) is the most well-known TSEs. It is a potential Creutzfeldt–Jakob (CJD) disease mutation that can be transferred through cattle to humans. In several animals, the prion protein gene (PRNP) is recognized to take active part in TSE vulnerability or tolerance. Previous studies have found indels polymorphism in PRNP gene promoter and intron1 region linked to BSE vulnerability. It's linked with 23 bp indels polymorphism in putative promoter and 12 bp indel in intron 1 of the PRNP gene. The aim of this study was to compare the allele, genotype and haplotype frequencies of PRNP indel polymorphisms in Zhongdian Yak (Bos grunniens) (YK), Zhongdian Yellow cattle (Bos taurus) (YC) and Zhongdian Yakow (Bos primigenius taurus × Bos grunniens) (PK) with worldwide reported healthy or affected BSE cattle, in order to assess their potential resistance to BSE. A comparison of Chinese bovine populations with healthy and BSE-affected German and Swiss cattle from globally was conducted, and result indicating significant difference (p <.001) between healthy and affected cattle. Additionally, as compared to prior studies with Chinese bovine population, the significant results were found. In this study, the allelic frequency D23 finding high deletion in all analyzed Chinese bovine species, and haplotype D12–D23 exhibited a less significant inclination toward susceptibility to BSE. [ABSTRACT FROM AUTHOR]

Tyrosinase-related protein 2 (TYRP2) plays a pivotal role in the biosynthesis of eumelanin. Black-boned sheep have excessive melanin and eumelanin, resulting in dark (black) muscles and organs. This study was designed to investigate the effects of variants of the TYRP2 gene on black traits and coat colour of black-boned sheep. Melanin traits were measured in three populations of sheep (Nanping black-boned, Nanping normal, and Romney Marsh) and compared in this study. From the TYRP2 cDNA, all 8 exons and their flanking regions were amplified and characterized. Fifteen single nucleotide polymorphisms (SNPs) were identified in the exons and their flanking regions. Five exonic polymorphic sites, including two synonymous (c.93T>G and c.1140C>T) and three non-synonymous mutations (c.163C>T (p.R55W), c.605G>A (p.R202H), and c.1141A>G (p.T381A)), were retrieved. PCR-RFLP analysis of c.605G>A showed that the frequencies of allele G in the Nanping black-boned, Nanping normal, and Romney Marsh sheep were 0.632, 0.603, and 0.886, respectively. Sheep with the GG genotype had significantly (P < 0.05) lower tyrosinase activity, alkali-soluble melanin content, and ratio of eumelanin : total melanin than sheep with GA and AA genotypes when measured across all investigated samples but not when samples within each population of sheep were compared. However, there was no association of TYRP2 genotype at a single SNP position with coat colour across populations. Nonetheless, the two breeds with higher overall tyrosinase activity did produce darker and more varied coat colours than the breed with lower tyrosinase activity. Key words: black-boned sheep, TYRP2 gene, black traits, association analyses. La proteine 2 apparentee a la tyrosinase (TYRP2) joue un role important dans la biosynthese de l'eumelanine. Les moutons a chair noire ont des quantites excessives de melanine et d'eumelanine ce qui leur confere des muscles et des organes fonces (noirs). Cette etude a ete concue pour investiguer les effets de differents variants du gene TYRP2 sur les caracteres noirs et la couleur du pelage chez les moutons a chair noire. Dans ce travail, les caracteres affectes par la melanine ont ete mesures et compares chez trats populations du mouton (Nanping black-boned, Nanping normal et Romney Marsh). L'ADNc, les huit exons et les regions bordantes du gene TYRP2 ont ete amplifies et caracterises. Quinze SNP ont ete identifies au sein des exons et des regions bordantes. Cinq sites polymorphes dans les exons, deux mutations synonymes (c.93T>G et c.1140C>T) et trais non-synonymes (c.163C>T (p.R55W), c.605G>A (p.R202H) et c.1141A>G (p.T381A)), ont ete releves. Par analyse PCR-RFLP du polymorphisme c.605G>A, il a ete montre que les frequences de l'allele G au sein des populations Nanping black-boned, Nanping normal et Romney Marsh etaient respectivement 0,632, 0,603 et 0,886. Les moutons de genotype GG affichaient une activite tyrosinase, une teneur en melanine soluble en conditions alcalines et un ratio eumelanine : melanine totale significativement (P < 0,05) plus faibles que chez les moutons de genotype GA ou AA lorsque les mesures compaees etaient prises sur l'ensemble des animaux mais pas au sein de chaque population. Cependant, aucune association n'a ete observee entre le genotype de TYRP2 a une seine position SNP et la couleur du pelage chez ces populations. Neanmoins, les deux races avec une activite tyrosinase globalement plus elevee presentaient des pelages plus fonces et plus varies que la race a faible activite tyrosinase. Mots-cles : moutons a chair noire, gene TYRP2, caracteres fonces, analyses d'association. [Traduit par la Redaction], Introduction Melanin is found naturally in a wide range of species from microbes to humans and is present as a mixture of the black-brown pigment eumelanin and the yellow-red pigment [...]

Dogs represent such a rich potential resource to further understand diseases and genetic traits. Comparing the genomes of three species of canine, human, and rat in terms of genome analysis, it is found that dogs are highly conservative with humans and rats. The special population structure of dogs makes it a good model for studying the diversity of morphology and behavior, the genetic basis of mammalian evolution, and diseases. This article gives a brief review of recent advances in domestic dog origin and evolution, genomic structure, genetic variation in dog phenotypic characteristics, and gene mapping. These research results are expected to provide a better theoretical basis for canine genetic breeding research and provide new ideas and methods for the prevention, diagnosis and treatment of human diseases. [ABSTRACT FROM AUTHOR]