The RXFP2 gene is a key regulator of horn morphology in sheep ( Ovis aries Linnaeus), with a 1.78-kb insertion in its 3′-untranslated region (UTR) previously linked to the polled phenotype. However, horned individuals homozygous for this insertion (1.78 kb +/ +) have been observed in typically polled breeds such as Hu sheep, suggesting additional regulatory mechanisms. In this study, a significant horn-associated quantitative trait locus (QTL) on chromosome 10 was identified through genome-wide association analysis which was consistent with previous study. We found that the 1.78-kb insertion in the 3′-UTR of RXFP2 is associated with horn status across sheep breeds, and that elevated RXFP2 expression correlates with horn development even in 1.78 kb +/ + individuals, as revealed by expression analyses in multiple breeds. RNA-seq and hormonal profiling further demonstrated that the INSL3/RXFP2 signaling axis, particularly its interactions with hormones such as testosterone, plays a central role in horn morphogenesis. These results indicate that horn development is modulated not only by structural variations in RXFP2, but also through its transcriptional and hormonal regulation, providing new insights into the polygenic basis of horn formation and informing breeding strategies for polled sheep.

The intramuscular fat (IMF) content is an important indicator of meat quality, affecting the sensory properties of meat. IMF is a complex trait with polygenic nature. This research aimed to identify differentially expressed (DE) genes and key transcription factors (TFs) associated with IMF deposition in the liver of two rabbit lines divergently selected for IMF (high-IMF: H and low-IMF: L). We used 48 rabbits (24 H and 24 L) belonging to the 9th generation of selection to determine their liver gene expression levels using 3′ RNA sequencing. We found 308 DE genes between H and L lines; 134 upregulated and 174 downregulated in the H line. Among them, ACBD4, ACOT1, ACOT4, AIFM2, CPT1A, CPT1B, CROT, CYP4B1, CYP4A6, HADHB, IGFBP1, IGFBP2, FABP4, GPAT3, MPZL2, MYLIP, MRPL15, NR4A2, PLIN2, PCTP, PRRG4, PAQR9, RAB34, SLC16A11, SLC18A1, SLC2A1, TPMT, and UBC, were related to lipid metabolism, energy metabolism, purine/thiopurine metabolism, and/or molecule transport that could influence the IMF deposition. Of the 308 DE genes, 210 target genes were predicted for 11 DE TFs through the gene regulatory networks. Notably, 3 TFs, namely ETV1, NR4A1, and IKZF3 appear to modulate gene expression of several putative targets (including common targets: CREM, NR4A2, and RRS1). Functional analysis of DE genes revealed an overrepresentation of 40 enriched terms, including the PPAR signalling pathway (associated genes: CPT1B, FABP4, and PLIN2) and other lipid metabolism bioprocesses. Collectively, our results enhance the understanding of the liver-muscle crosstalk that contributes to IMF deposition and improvement of rabbit meat quality.

Late-feathering phenotype can be divided into different subtypes based on the length difference between primary and primary-covert feathers of one-day old chicks. In this study, a chick with its primary feathers shorter than primary-covert feathers is identified as Subtype 1 (T1), a chick with its primary feathers as long as primary-covert feathers is Subtype 2 (T2). The objective of this study was to obtain candidate genes for late-feathering subtypes in Shouguang chickens. Fifty-three Shouguang chickens were genotyped with a 600 K SNP chip and two genomic regions in Chromosome 3 and 10 were identified to be associated with late-feathering subtypes by GWAS. Twelve hair follicle samples of flight feathers from 12 one-day old Shouguang chicks, including 6 of each subtype, were collected. RNA sequencing analysis was performed and no overlap genes were found between differentially expressed genes (DEGs) by differential expression analysis and candidate genes by GWAS. In order to find the relationship between the two set genes, a protein‐protein interaction (PPI) network was constructed using all protein-coding genes in the two sets and the result showed that four genes ( CDC40, EFL1, AK9, and ZBTB24 ) from GWAS and 28 DEGs were enriched in the top one cluster associated with muscle function. Considering the spatiotemporal characteristics of gene differential expression and the fact that two most significant SNP loci in GWAS were located on EFL1 and CDC40, we suggested that the two genes be more suitable as candidate genes for late-feathering subtypes.

This study evaluated the developmental competence of SCNT embryos produced from transfected cells and a transgenic cloned buffalo carrying the EGFP gene, as well as changes in transgene expression levels with aging. Cells collected from the transgenic buffalo at different ages were used for recloning, and the resulting SCNT embryos were assessed for developmental potential and expression patterns of key genes involved in development and telomere maintenance—including Oct-4, Sox2, Nanog, Cdx2, Gata3, E-cadherin, β-catenin, Tert, Terc, Terf1, and Terf2.The findings revealed that expression of the exogenous EGFP gene increased as the buffalo matured. Moreover, both SCNT and transfection procedures altered the expression of genes related to embryonic development and cell adhesion in blastocysts. These changes in gene expression may contribute to the reduced developmental competence typically observed in buffalo SCNT embryos compared to those produced by IVF.Keywords: Transgenic buffalo, re-cloning, EGFP, developmental competence, telomere

The combined use of in vitro fertilization and genomics contribute to increasing productive potential and genetic gain in dairy cattle. The aim of this study is to deepen the understanding of the genomic architecture of the dairy Gir breed by identifying variants associated with the number of oocytes and embryos. This study is a continuation of a previous family analysis study conducted in the dairy Gir, in which a region on chromosome 7 (BTA7) was associated with the number of oocytes and embryos. In the current study, a genomic variant call file (VCF) of 12 sires with positive Predicted Transmission Ability (PTA) for milk production was investigated. These bulls are widely used in dairy herds to produce Gir daughters, whose oocyte and embryo data were collected. This region on BTA 7 was analyzed using the online tool EnsemblVEP and four variants were classified as lead SNPs. Two lead SNPs were single-nucleotide substitutions and both caused the inclusion of a premature stop codon in XRCC4 and HAPLN1 genes. A third lead SNP regards the deletion of five sequential thymines in an intergenic region. The fourth lead SNP involves the deletion of one nucleotide in EDIL3 gene, causing frameshift. In conclusion, these lead SNPs may have a positive or negative impact on the production of oocytes and in vitro embryos in the dairy Gir, which can be verified through subsequent association studies. Therefore, it is extremely important to verify how genetic improvement and breeding programs can increase gains for the reproductive traits.

China is home to a vast array of local chicken breeds, including the LulingWu Chicken (LLW) from Hubei Province, which exhibits unique traits such as few or absent tail feathers, black bones, and black skin. Despite its long history of domestication, the genetic structure and diversity of the LLW remain largely unexplored. This study investigates the genetic variation and population structure of LLW chickens through genome-wide re-sequencing. A total of 20 blood samples from LLW chickens (10 yellow-feathered and 10 white-feathered) were analyzed alongside re-sequencing data from 111 individuals across 14 chicken breeds. Genetic diversity analysis revealed the highest inbreeding coefficients in white feather LLW and Red Jungle Fowl. Population structure analyses (neighbour-joining tree, PCA, and admixture) demonstrated that LLW forms a distinct monophyletic clade, separate from other Hubei and Chinese breeds, regardless of feather colour. Selective sweep analysis identified 10,578 candidate regions containing 297 genes, and among these genes, ARHGEF39, SMPD2, SV2C, THBS2, PTCH1, FBP1, FBP2, and GNAL were suspected in the regulation of tail feather development, pigmentation, and environmental adaptation. These findings provide new insights into the genetic uniqueness and adaptive traits of the LLW, supporting its conservation and potential use in future breeding programs. Further validation of identified genes and pathways will enhance our understanding of their role in chicken phenotypic adaptation.