Jul 2026· Veterinary Parasitology: Regional Studies and Reports· Vol 73, pp.
101538
· 0 citations
Medicine
TL;DR
Two genome-wide strongly associated SNPs were detected on chromosomes 2 and 3, located near FEC associated QTLs and immune-related genes, supporting their relevance as candidate genes for GIN-resistance selection in Pelibuey hair-sheep.
Abstract
The aim of this study was to detect genomic regions and genes associated with gastrointestinal nematodes (GIN) resistance in Pelibuey sheep, based in deworming necessity (NOD) estimated by fecal egg count (FEC). During a ten-months period, deworming criterion was based on GIN eggs per gram (EPG), then animals exceeding 1000 EPG were dewormed, and individuals were classified as cases (dewormed at least once) or controls (non-deworming at all). Animals were genotyped with the GGP Ovine50k genome profiler microarray. Quality control of dataset and case-control GWAS were carried to identify associated candidate genes and quantitative trait loci (QTL). Two genome-wide strongly associated SNPs were detected on chromosomes 2 and 3, located near FEC associated QTLs and immune-related genes: GALNT6, KLRK1, KLRD1, CLEC1B, FGF13, TMEM52B, OLR1, and CLEC7A. The identified genes are involved in key defense mechanisms such as mucus synthesis, immune signaling, and natural-killer cell activation, supporting their relevance as candidate genes for GIN-resistance selection in Pelibuey hair-sheep.
Background: This study aimed to identify genomic regions under selection in Kangayam cattle of Tamil Nadu using a de-correlated composite of multiple signals (DCMS) framework. Methods: BovineHD SNP array data were retrieved from the WIDDE repository and the ICAR Krishi-Kosh portal. After quality control, autosomal SNPs were used for subsequent analyses. Fixation index, integrated haplotype score, modified haplotype homozygosity, Tajima’s D and nucleotide diversity, were calculated and integrated using the DCMS approach. Genomic windows with false discovery rate (FDR) adjusted q less than 0.001 scores were considered for subsequent analysis. Functional annotation, QTL enrichment, protein–protein interaction (PPI) network analysis and hub gene identification were performed to interpret biological relevance. Result: Genomic regions identified after DCMS analysis, harbored genes related to muscle development, metabolism, immunity, thermotolerance, reproduction and milk composition, including MSTN, BMP7, PRKAG3, BoLA-DRB3, IL8R, ABCA1 and members of the SLCO gene family. PPI and hub gene analyses highlighted transport and metabolic pathways, with SLC22A7 and ABCC9 emerging as key nodes. This study presents the first DCMS-based selection signature map for Kangayam cattle, uncovering coordinated selection across interconnected biological pathways.
Asad Khan, Ishmeet Kumar, J. Vyas et al.· Indian Journal of Animal Res...· 0 citations
Background: The major histocompatibility complex (MHC) is a well-known gene complex that plays a fundamental role in immune recognition; however, its influence on reproductive processes in cattle is not yet fully established, particularly regarding how it modulates the female response to the embryo. Therefore, this study aimed to investigate the relationship between MHC genes and reproductive processes in cattle and to identify potential molecular targets involved in these mechanisms. Methods: Data from four studies identified through a systematic review were integrated. MHC genes associated with reproduction were identified, neighboring genomic regions were explored to detect candidate genes and transcription factors, and biological process networks were constructed using differentially expressed genes associated with cattle. Results: The integrated analysis led to the identification of six MHC genes associated with reproduction, along with 54 candidate genes from genome-wide association studies and 46 from transcriptomic studies located in neighboring regions. Among these, BoLA-DQB and BoLA-DQA5 stood out in all analyses, while the transcription factors FOXA1, FOXO3, ELF5, and STAT3 appeared across the different datasets. These genes and factors may represent potential targets for future functional validations and could be explored using genome editing technologies to better understand their roles in reproductive processes. The identified biological pathways were related to embryonic development and reproductive organ formation, providing a preliminary foundation for future investigations. Conclusions: This work integrates currently available evidence and highlights potential molecular targets that can be explored in cattle breeding and reproductive biology, associating MHC genes with these roles and advancing innovative perspectives in the field of molecular genetics.
Louíse B. Faverzani, Andreia K. Zwirtes, D. Rodrigues et al.· Genes· 0 citations
Early postnatal growth is a critical determinant of meat production efficiency and long-term genetic improvement in goats; however, the molecular mechanisms underlying individual variation in growth performance remain poorly understood. In this study, a total of 123 Hechuan white goats were included. First, a genome-wide association study (GWAS) for average daily gain (ADG) was performed using all 123 individuals. Subsequently, based on the coefficient of variation of ADG (CV = 65.6%), an extreme phenotype sampling (EPS) strategy was applied to select 39 individuals with extreme growth phenotypes for subsequent metabolomic, microbiome, and integrated mGWAS analyses.The results showed that ADG approximately followed a normal distribution across the 123 goats. GWAS identified 22 loci significantly associated with ADG, mapping to genes including DLK1, NCAPG2, LCORL, CNTNAP2, and SLC8A1, which are involved in pathways related to skeletal muscle development, cell cycle regulation, ion transport, and immune function. Metabolomic profiling detected 1,589 putative metabolites, revealing differential enrichment of lipid, amino acid, and bile acid metabolic pathways between fast- and slow-growing goats. Gut microbiome analysis demonstrated that Christensenellaceae_R-7_group and Monoglobus were significantly enriched in fast-growing individuals, whereas Desulfovibrio was more abundant in slow-growing goats.Integrated mGWAS analysis further revealed extensive effects of host genetic variation on gut microbiota and fecal metabolites. Specifically, 11 bacterial genera were significantly associated with host genomic variants, among which Desulfovibrio exhibited the highest number of associated loci. Integration of multiple variant types consistently linked Desulfovibrio, Eubacterium_hallii_group, and Candidatus_Saccharimonas with genes such as ARHGAP24 and IGF2BP2. In addition, 14 metabolites were significantly associated with host genetic variants, with Lysopc(14:1(9Z)/0:0) and glycocholic acid showing the strongest associations. Notably, the peak signal for Lysopc was located within HMGA2.Collectively, these findings define a coordinated host genome–gut microbiota–metabolite network underlying early growth variation in goats and provide a mechanistic foundation for precision breeding and targeted nutritional strategies in goat production systems.
This narrative review synthesizes major advances in sheep genetic mapping, functional genomics, and GS relevant to economically important traits to provide researchers, breeders, and students with a balanced, evidence-based resource to guide future genomic improvements in sustainable sheep production.
Mostafa Ghaderi-Zefrehei, Effat Nasre Esfahani, Hassan Amini Pozveh et al.· Frontiers in Genetics· 0 citations
Avian Influenza virus (AIV) and Newcastle disease virus (NDV) are highly contagious immunosuppressive pathogens that cause high mortality rates and economic losses in the global poultry industry. Although vaccination to enhance the host antibody response remains the main control strategy, the genetic basis of this variation is poorly understood. In this study, we used a genome-wide association study (GWAS) to investigate the genetic architecture of the longitudinal antibody responses to AIV (subtypes H5, H7, and H9) and NDV in chickens. To identify the genomic regions and candidate genes associated with the longitudinal antibody response to AIV and NDV after immunization, we conducted a GWAS using 1,359,927 SNP markers in an advanced intercross line (AIL) of the F19 resource population. We found moderate heritability for both the traits. Based on these associations, we identified the genomic regions and candidate genes for both traits. Association analysis revealed two significant SNPs located on chromosome 3, rs316474025 near NFKBIE and SLC35B2 [rs316474025], and rs312870707 near ATG5 gene, that are associated with viral antibody titers against AIV subtypes H5 and H7, respectively. Additionally, one variant on chromosome 27, rs318005864 near DDK12 and RPL19 genes, was strongly linked to the antibody response associated with NDV at mid-phase (40 days post-immunization). Furthermore, another variant, rs737164663, near FRMD5 and GLCE genes, was strongly linked to the antibody titer associated with both AIV subtype H9 and NDV in the late phase (60 days post-immunization). Genes located in these regions may be responsible for the immune response in chickens. Before implementation in breeding programs, the efficacy and long-term persistence of selecting these antibody response traits should be validated in larger independent cohorts. We confirmed the presence of genetic variability and identified SNPs significantly associated with antibody titer traits in F19 chickens. These findings highlight genomic regions contributing to variation in antibody responses and provide valuable information for improving antibody-related traits through selective breeding programs.
Objective
Litter size is a key trait for evaluating reproductive performance of goats, which can directly influence the breeding efficiency and profitability of production cycles. However, a comprehensive understanding of its genetic architecture, including the causative mutations and their functional impacts, remains scarce, thus hindering its application in precision breed-ing.
Methods
A total of 92 female Leizhou goats were genotyped through whole-genome se-quencing (WGS), and their litter size were measured for three consecutive births. Subsequently, based on the genotype and phenotype data, population genetic structure analysis, selection signature analysis, and genome-wide association study (GWAS) were performed.
Results
We identified a total of 20,802,514 SNPs in the 92 Leizhou goats. Analysis of genetic structure revealed that the high-litter-size group exhibited greater genetic diversity than the low-litter-size group, although no significant genetic differentiation was detected between them. We identified 340 putative selective regions and 346 candidate genes across the genome. A total of 37 candidate genes were identified as being closely associated with reproductive traits, including BMP6, MAPK8, RPTOR, etc. In GWAS results, we identified 63 quantitative trait loci (QTLs) for litter size at suggestive significance (P＜1×10-5). After, 207 candidate genes were annotated, and 4 of them were highlighted that have been previously reported to be associated with reproductive processes (e.g., TMEM100, PDGFD, NLRP9, and ARHGAP22). By integrating the results from both approaches, we identified MAPK8 as a potential candidate gene associated with litter size. Furthermore, our findings from motif recognition, transcrip-tion factor prediction, and previous studies lead us to propose that the BMP6-GATA4-MAPK8 signaling pathway may play a key role in regulating litter size in goats.
Conclusion
Our findings identify several candidate genes and putative associated variants for litter size, providing valuable insights into the genetic basis of reproductive traits in goats.
Da Feng, Siyi Hu, Jian Ma et al.· Animal bioscience· 0 citations