Whole-Genome Resequencing-Based Selection-Signal and Association Analyses Prioritize Candidate Genes and Haplotypes for PRRS Resistance-Related Traits in Pigs
Simple Summary Porcine reproductive and respiratory syndrome is a serious infectious disease that causes reproductive problems, breathing illness, and major economic losses in pig production. Vaccines and farm management help control the disease, but they do not always provide enough protection because the virus changes easily. This study aimed to find inherited genetic features that may help identify pigs with better natural resistance to this disease. Pigs were first screened after vaccination and then after exposure to the virus, and animals with clearly different disease-response patterns were selected for detailed genetic analysis. By comparing genetic differences between resistant and susceptible pigs and combining these results with public data showing how genes behave during infection, this study identified several candidate genes and genetic regions related to disease response. A region on chromosome 8, especially around genes named NFXL1 and NIPAL1, was highlighted, and a specific genetic pattern in this region was more common in resistant pigs. These findings provide useful clues for future testing and may support breeding programs aimed at improving disease resistance in pigs.
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.
The findings should be considered exploratory and require validation in larger, independent, genetically comparable populations, because the observed differences between survivor and non-survivor groups cannot be unambiguously separated from underlying population structure.
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Cross-beaks are deemed a threat to poultry health, productivity, and animal welfare. Nevertheless, due to sporadic cases, heterogeneity of gene loci and incomplete dominance, the molecular mechanism of cross-beak formation, especially the degree of cross, is not yet clear. Thus, we screen key genes and reveal the possible phenotypic formation mechanism of cross-beak by comparison with different degrees of deformity in Huiyang Bearded chickens by compare whole-genome resequencing-based variant analysis. Comparative analysis between cross-beak and normal-beaked chickens identified differential variants in several candidate genes, including CDH11, CTNNAL1, NRXN3, NRXN1, CDH5, SDC3, and DHFR. Genes harboring these variants were enriched in pathways related to cell adhesion molecules and metabolic processes, with functional annotations involving cell–cell adhesion and neural crest cell migration. Comparative analysis between chickens with severe and slight cross-beak deformities identified additional candidate genes, including MRPL21, NSUN2, DDX55, GNB3, and NFKB2. These genes were associated with enriched terms and pathways related to focal adhesion, amyotrophic lateral sclerosis, steroid 7 α-hydroxylase activity, and skin-barrier establishment. These findings provide a preliminary catalogue of genetic variants and candidate genes for future functional studies of cross-beak development and severity in chickens.
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