Genotyping of major histocompatibility complex Class II DRB gene in Rohilkhandi goats by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing

The goat PRLR gene: mRNA expression, association analysis of InDel variants with body weight and growth traits

Prolactin is a single-chain peptide hormone produced by the anterior pituitary gland and plays an important role in the reproductive development of mammals. Therefore, we investigated the expression of the PRLR gene in various goat tissues during distinct developmental stages, as well as the correlation between the 16 bp InDel and growth traits in goats. The study findings demonstrated a consistent expression and distribution of PRLR in both yearling and adult goat tissues, with the highest levels observed in the testis. Association analysis showed that in the yearling IMWC goat population (n = 463), this 16 bp InDel variation was associated with body weight (P = 0.026), body height (P = 0.005), body length (P = 0.008), heart girth (P = 0.001), chest depth (P = 0.000075), and chest width (P = 0.005); In the adult IMWC goat population (n = 211), the 16 bp InDel variation was associated with body height (P = 0.011), height across the hip (P = 0.0003), chest depth (P = 0.001), and cashmere fineness (P = 0.022); In all IMWC goat populations (n = 674), this 16 bp InDel was related to body weight (P = 0.042), body height (P = 0.001), body length (P = 0.013), heart girth (P = 0.012), height across the hip (P = 0.038), chest depth (P = 0.001), and chest width (P = 0.006). The bioinformatics analysis has revealed that the significant impact of a 16 bp InDel on growth traits in goats may be attributed to its specific binding to the transcription factors AP-2α and Sp1. These findings suggest that this genetic variant plays a crucial role in the growth and development of goats, making it a valuable DNA marker for selecting goats with superior growth traits.

The Goat Cytotoxic T Lymphocyte-Associated Antigen-4 Gene: mRNA Expression and Association Analysis of Insertion/Deletion Variants with the Risk of Brucellosis

The cytotoxic T lymphocyte-associated antigen-4 (CTLA4) gene, a member of the immunoglobulin superfamily, is crucial for maintaining immune homeostasis and preventing autoimmune diseases. Studies have shown that polymorphisms in the CTLA4 gene are linked to an increased risk of brucellosis in humans, but its association with brucellosis in goats remains unexplored. In this study, the tissue expression profile of CTLA4 in goats was investigated, and the correlation between InDel polymorphisms in the CTLA4 gene and susceptibility to brucellosis in goats was examined. The findings reveal the widespread expression of CTLA4 in goat tissues, particularly in the spleen and testes. The tested goat populations presented genotypes insertion/insertion (II), insertion/deletion (ID), and deletion/deletion (DD) at both the P1 and P2 loci, and an association analysis revealed significant differences in the distribution of genotypes and allele frequencies at the P1 and P2 loci of the CTLA4 gene between the Brucella goat case and the control groups (p < 0.05). Specifically, compared with the II genotype, the P1 and P2 loci were significantly associated with an elevated risk of brucellosis development in goats under both the codominant (ID/II) and dominant (ID + DD/II) models (P1, p = 0.042, p = 0.016; P2, p = 0.011, p = 0.014). Additionally, haplotype analysis indicated that haplotypes IP1DP2, DP1IP2, and DP1DP2 were significantly associated with an increased risk of brucellosis in goats compared to the reference haplotype IP1IP2 (p = 0.029, p = 0.012, p = 0.034). Importantly, the Lipopolysaccharide (LPS) stimulation of peripheral blood monocytes and/or macrophages from goats with the II, ID, and DD genotypes resulted in increased CTLA4 expression levels in the II genotype, leading to a robust LPS-induced inflammatory response. Through bioinformatic analysis, the observed effect of the InDel locus on Brucella pathogenesis risk in goats could be attributed to the differential binding of the transcription factors nuclear factor kappaB (NF-κB) and CCAAT/enhancer-binding protein α (C/EBPα). These findings offer potential insights for breeding strategies against brucellosis.

Documentation of extensive genetic diversity in the Ovar-DRB1 gene in native Turkish sheep

Indigenous breeds have a high level of genetic diversity that might contribute to develop animal breeds with desired traits such as disease resistance and high productivity. Major histocompatibility complex (MHC) is a key component of adaptive immune system and consists of highly polymorphic genes that take part in adaptive immune response and disease resistance. Exploring and understanding the effect of polymorphisms in MHC could be beneficial to future animal breeding strategies. In this study, we sequenced the highly polymorphic Exon2 of the ovine DRB1 gene using Sanger sequencing to explore the diversity of this gene in six indigenous Turkish sheep breeds and two crossbreeds. In total, 894 haplotypes from 447 sheep were investigated, and 69 different haplotypes including 27 novel ones were identified. Among the identified haplotypes there were common and breed specific haplotypes. There was a relatively high diversity of the alleles within indigenous breeds. Allelic diversity patterns were mostly associated with geographical differences. The results of this study highlight the genetic variation within indigenous breeds which has important implications for biodiversity and the adaptability of breeds to specific environments. There is value to further studies which include other genomic regions and traits, and these could guide breeding strategies.

A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma

Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We demonstrate that cell-free genomic DNA (cfDNA) may be extracted and amplified from archived plasma samples, allowing retrospective analysis of host genetic diversity. This technique was also applicable to archived serum samples up to 35 years old and to different ruminant species. As proof of concept, we used this cfDNA approach to genotype the major histocompatibility complex (MHC) class II DRB1 locus of 224 Merino sheep which had participated in field trials of a commercial Haemonchus contortus vaccine, Barbervax^®, in Australia. This identified a total of 51 different DRB1 alleles and their relative frequencies. This is the first study to examine host MHC diversity using DNA extracted from archived plasma samples, an approach that may be applied to retrospective analyses of genetic diversity and responses to vaccination or infection across different species and populations.