Background: Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds. Results: Here, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip. Conclusions: The updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.

Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibetan Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. Of which, the haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with the haplotype A had an increased hemoglobin (Hb)–O₂ affinity compared to those carrying the haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed a varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

Background: Cultivated meat, an alternative to conventional meat, has substantial potential for alleviating environmental and ethical concerns. This method of manufacturing meat involves the isolation of skeletal muscle satellite cells (SMSCs) from donor animals, after which they proliferate in vitro and differentiate into primitive muscle fibers. The aim of this research was to evaluate how the insulin-like growth factor 1 (IGF1) gene regulates the myogenic differentiation of bovine skeletal muscle satellite cells (bSMSCs). Methods: bSMSCs isolated from newborn calves were cultured to the third generation in vitro and differentiated into myoblasts via the serum withdrawal method. An overexpression lentivirus and siRNA targeting the IGF1 gene were constructed and transduced into bSMSCs, which were subsequently analyzed via real-time fluorescence quantitative PCR(qRT–PCR) and Western blots. The mRNA and protein levels of the myogenic differentiation markers myosin heavy chain (MyHC) and myogenin (MyoG) were determined. Results: The results revealed that the lentivirus overexpressing the IGF1 gene significantly increased the expression of MyHC and MyoG, whereas the expression of both the MyHC and MyoG mRNAs and proteins was strongly reduced by si-IGF1. Conclusions: IGF1 positively regulates the myogenic differentiation of bSMSCs. This study provides a reference for further elucidating the molecular mechanism by which the IGF1 gene regulates the myogenic differentiation of bSMSCs via the PI3K/Akt signaling pathway and lays a foundation for establishing a regulatory network of bovine muscle growth and development.

Yanbian cattle are a native cattle breed originating from the Yanbian Korean Autonomous Prefecture in Jilin Province, northeastern China. Developed over centuries through natural and artificial selection under cold climatic conditions, this breed is highly adapted to harsh environments, including low temperatures, rugged terrain, and sparse forage. Here, we constructed a high-quality chromosome-level genome assembly for Yanbian cattle using HiFi, Hi-C and RNA-seq data. The genome sequence was anchored to 30 chromosomes, with a total genome length of 2.8 Gb, a contig N50 of 86.41 Mb and a scaffold N50 of 111.08 Mb. Short-read data showed the average 99.56% mapping ratio to the assembly, validating base-level accuracy. Also, 93% complete BUSCOs verified the integrity of the assembled genome. 51.94% repetitive elements of the genome and 20,421 protein-coding genes were annotated. This Yanbian cattle genome serves as an indispensable resource for bovine genomic studies and local breed conservation, enabling both evolutionary insights and genetic characteristic analyses.

Lamb meat has become very popular with consumers in recent years due to its nutritional benefits. As a lean red meat, lamb is an important natural source of polyunsaturated and saturated fatty acids, which can be modified by adjustments in livestock feed. This study used proteomic and metabolic analyses to compare a basal ration supplemented with either mulberry silage or corn silage. Supplementation with mulberry silage led to a reduction in subcutaneous carcass fatness compared with corn silage. Additionally, changes in the proteome associated with fatty acid metabolism and oxidation resulted in decreased levels of saturated and trans fatty acids, while significantly increasing the levels of α-linolenic acid (ALA) and oleic acid and reducing linoleic acid content.