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Background: Olfactory receptor (OR) genes are highly polymorphic and form extensive families that recognize a wide range of vertebrate odorants. To explore the genetic diversity of MHC-linked OR genes and their connection to MHC genes, we conducted a combined haplotype analysis of MHC-linked OR and MHC class I genes to determine the influence of MHC on OR diversity, which could be associated with MHC-based mate selection. Results: We selected nine MHC-linked OR genes based on their expression levels in pig testes and developed a sequence-based typing method for these genes. We then performed high-resolution typing of these OR genes, along with three major classical MHC class I genes (SLA-1, -2, and − 3), in 48 pigs across six breeds. We observed significantly higher allelic diversity (P < 0.01) in ORs with strong linkage disequilibrium (LD) to SLA compared to those with weak or no LD, and we identified 48 SLA class I-OR haplotypes using the expectation-maximization algorithm. The genetic diversity of SLA-linked ORs was positively correlated with their expression levels in the testis. Specifically, SLA-linked ORs with higher testicular expression (FPKM ≥ 0.1) exhibited an increase in the number of codons under mutually diversifying selection with SLA compared to those with lower expression (FPKM < 0.1). Conclusions: The presence of evolutionary interactions between MHC and linked OR genes supports the potential involvement of MHC-linked ORs in MHC-based mate selection. The use of combined haplotype information for MHC and linked ORs could provide new insights into the reproductive biology of animals. [ABSTRACT FROM AUTHOR]

Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species. [ABSTRACT FROM AUTHOR]

Bovine prolactin (PRL) gene is essential for the initiation and maintenance of lactation and exerts multiple effects on mammary alveoli to promote the synthesis and secretion of major components of milk. The objectives of this study were to identify mutations in PRL gene and to evaluate the mutations as potential markers of milk performance traits in cattle populations of Ethiopia. For this purpose, genomic DNA from whole blood was extracted through salting out procedure from 87 animals of five cattle populations of Ethiopia. Accordingly, three single nucleotide polymorphisms (SNPs) were identified of which one SNP g.8323T > A showed missense mutation while the other two SNPs revealed silent mutations. FST values showed statistically significant genetic differentiation among the studied populations. Intermediate polymorphic information content was noted for most SNPs, which indicates the presence of sufficient genetic variation at this locus. Two SNPs showed heterozygote deficiency as a result of positive FIS values. Only g.8398A > G SNP have statistically significant (p < 0.05) effect on average daily milk yield, fat and solid not fat percentage in all studied cattle populations. Therefore, g.8398A > G SNP identified in this study influences cattle milk production and may be used as possible candidate SNP for marker-assisted selection programs in cattle populations of Ethiopia. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMP) are innate immune molecules with antimicrobial activity that are important to defend against pathogenic infection. We performed genome‐level analyses of the AMP family gene repertories for six terrestrial (Homo sapiens, Bos taurus, Sus scrofa, Capra hircus, Canis lupus, and Loxodonta africana) and five aquatic (Balaenoptera acutorostrata, Tursiops truncatus, Lipotes vexillifer, Odobenus rosmarus, and Trichechus manatus) mammals and identified 59 (30 partial or pseudogenes) previously unannotated β‐defensin (BD) sequences from those aquatic species. Extreme reduction in BD genes was evident in Odontoceti. NK‐lysin and granulysin among AMP family genes were absent from aquatic mammals, except O. rosmarus. A phylogenetic tree constructed with 296 amino acid sequences of BD from 11 species suggested a broad expansion of this gene family with extensive genetic diversity in mammals. We determined a pair of evolutionarily conserved flanking genes for each of four BD containing intervals and defined them as PGK2‐TFAP2D, BCL2L1‐ZCCHC3, AGPAT5‐GPM6A, and ADAM29‐CTSB intervals. The characterization of BD syntenic regions revealed conservation of homologous synteny blocks and reuse of evolutionary breakpoint regions. Phylogenetic reconstruction of BD gene evolution showed that the major expansion events of BD genes occurred four times in the mammalian lineage. Taken together, the findings of this study show the occurrence of significant differences in the number of AMP family genes in diverse mammalian species, including aquatic species, likely due to their environmental adaptation. [ABSTRACT FROM AUTHOR]