Chicken Genome Study Pinpoints Variants Shaping Antibody Responses to Two Major Poultry Viruses

A genome-wide association study of 572 chickens from an advanced intercross line has identified specific genetic variants linked to the strength and persistence of antibody responses against avian influenza virus and Newcastle disease virus, two of the most economically damaging pathogens in global poultry production. The study, published in Genetics Selection Evolution, measured antibody titers at four time points around vaccination and mapped them against more than 1.3 million SNP markers across the chicken genome, revealing loci on several chromosomes that appear to influence how long and how strongly vaccinated birds mount humoral immunity.

The research team, led by Haile Berihulay and Wei Luo, worked with the F19 advanced intercross line, a population created by crossing the slow-growing Chinese indigenous Huiyang Bearded chicken with a fast-growing commercial broiler line and then intercrossing the offspring randomly for 19 generations. This design matters for genetic mapping because the many generations of recombination break down long stretches of inherited DNA, which sharpens the resolution with which associated variants can be located. Although the line was originally developed to study growth traits, its high genetic diversity and substantial phenotypic variation also make it well suited for dissecting complex immune phenotypes.

The experimental setup was unusual in several respects. The birds received a commercial live Newcastle disease vaccine of the LaSota strain together with inactivated vaccines covering avian influenza subtypes H5, H7, and H9, applied as separate formulations rather than a combined vector vaccine. Blood samples were collected one day before immunization and then at 20, 40, and 60 days afterward, allowing the researchers to track baseline levels, the peak response, and the decay of antibody over two months.

Antibody titers were quantified with the hemagglutination inhibition assay following World Organization for Animal Health guidelines. The phenotypic data showed a consistent pattern across all four antigens: titers rose sharply from baseline to the first post-vaccination measurement at 20 days and then remained relatively stable or declined only slightly through day 60. For the H5 subtype, mean titers increased from 2.62 at baseline to 3.21 at day 20 and held near 3.13 thereafter. Newcastle disease titers peaked later, at day 40, reaching 3.40 before easing to 3.21 at day 60, with notably low coefficients of variation indicating a fairly uniform response across individuals. Genome-wide association testing at the pre-immunization baseline detected no significant associations, which the authors interpreted as expected given the absence of a vaccination stimulus at that point.

Heritability estimates, calculated by partitioning phenotypic variance into genetic and residual components using restricted maximum likelihood, ranged from 0.15 to 0.35 for avian influenza antibody responses and from 0.23 to 0.35 for Newcastle disease responses. The highest estimate, 0.35 with a standard error of 0.05, was observed for the H5 subtype at the day-40 time point. Across the board, environmental variance exceeded genetic variance, meaning that non-genetic factors contributed substantially to the variation in antibody titers even in this controlled population. Newcastle disease responses showed a somewhat higher average heritability, 0.28 versus 0.23 for avian influenza, and the mid and late post-vaccination periods emerged as the stages where genetic predictability was greatest.

The association analysis itself relied on a mixed linear model that included sex, immunization stage, and the top three principal components as fixed effects, with a genomic relationship matrix capturing additive polygenic background and controlling for population structure. After quality control filtering removed individuals with high genetic relatedness or incomplete records and pruned SNPs for linkage disequilibrium, 1,359,927 independent markers remained for testing in 572 birds. Significance thresholds were set by Bonferroni correction at a genome-wide level of P less than 3.7 times ten to the minus eight, with a suggestive threshold an order of magnitude looser. Quantile-quantile plots closely followed the expected diagonal, suggesting minimal inflation from stratification.

In total, 22 significant SNPs were identified, 14 for avian influenza responses distributed across ten chromosomes and 8 for Newcastle disease responses on six chromosomes. Three variants exceeded the strict genome-wide threshold: rs312870707 on chromosome 3, associated with H5 titers; rs316474025, also on chromosome 3, associated with H7; and rs737164663 on chromosome 10, associated with H9. A fourth variant, rs318005864 on chromosome 27, reached genome-wide significance for Newcastle disease antibody titers at the day-40 midpoint and explained 17 percent of the phenotypic variance, the largest single effect reported in the study. Estimated additive effects of the significant SNPs accounted for 13 to 28 percent of variance in avian influenza responses and 6 to 17 percent in Newcastle disease responses, figures considerably higher than the roughly 5 percent effects reported in earlier chicken immune-response GWAS.

Several of the flagged loci sit near genes with plausible immunological roles. The chromosome 3 signal near rs316474025 lies close to NFKBIE, which encodes an inhibitor of the NF-kappaB transcription pathway critical to immune regulation and B-cell development, and near SLC35B2, a transporter required for sulfation reactions involved in STING-mediated antiviral signaling. The rs312870707 region contains ATG5, essential for autophagosome formation and MHC class II antigen presentation. On chromosome 10, rs737164663 lies near FRMD5 and GLCE, and on chromosome 27, rs318005864 is close to CDK12 and RPL19, genes implicated in cell cycle regulation and innate immune responses during viral infection. Notably, rs737164663 and rs318005864 were associated with both avian influenza and Newcastle disease titers at different time points, hinting at pleiotropic regulation that spans antigens.

Functional enrichment analysis of 130 candidate genes within 50-kilobase windows flanking the significant SNPs painted a picture of broad regulatory involvement rather than direct antibody machinery. The most significant Gene Ontology term was positive regulation of the MAPK cascade, and enriched KEGG pathways included metabolic pathways, adherens junctions, calcium signaling, tight junctions, and cell adhesion molecules. The absence of enrichment for immunoglobulin synthesis or B-cell receptor signaling led the authors to characterize vaccine-induced antibody titers as polygenic traits shaped primarily by upstream signaling, cellular coordination, and immune kinetics. They also noted that no strong signals emerged on chromosome 16, where the chicken major histocompatibility complex resides, possibly because the high polymorphism of that region is not fully captured by SNP-based GWAS under stringent multiple-testing correction.

The authors are careful to frame the findings as putative rather than proven determinants. They acknowledge that some significant SNPs appeared as isolated signals with minor allele frequencies near the filtering threshold of 0.05, a situation that can generate spurious associations when few allele carriers dominate phenotypic extremes, although they argue that the recombination-rich advanced intercross design and the mixed model framework reduce this risk. More consequentially, the abstract states explicitly that before any implementation in breeding programs, the efficacy and long-term persistence of selecting these antibody response traits should be validated in larger independent cohorts. Within that caveat, the study supplies a genetic framework for a possible route to more resilient flocks: because antibody titers are measurable, moderately heritable, and interpretable quantitative traits, the loci identified here, particularly the prioritized variants rs316474025 and rs318005864, represent candidate targets for genomic selection aimed at improving the magnitude and durability of vaccine-induced immunity in chickens, pending confirmation of their effects across other populations and production environments.

Subject of Research: Genetic variants associated with longitudinal antibody responses to avian influenza and Newcastle disease vaccination in chickens

Article Title: Genome-wide association study reveals putative genetic determinants of longitudinal immune responses to avian influenza and Newcastle disease in chickens

Article References: Berihulay, H., Luo, W., Lao, A., Chuxiao, L., Jebessa, E., Zou, X., Ji, J., Qu, H., Chen, P., Cai, M., Shu, D., & Luo, C. (2026). Genome-wide association study reveals putative genetic determinants of longitudinal immune responses to avian influenza and Newcastle disease in chickens. Genetics Selection Evolution, 58(1), Article 56. https://doi.org/10.1186/s12711-026-01077-2

Image Credits: AI Generated

DOI: 10.1186/s12711-026-01077-2

Keywords: GWAS, chickens, avian influenza, Newcastle disease, antibody response, heritability, genomic selection, advanced intercross line, SNPs, poultry immunogenetics, vaccination, candidate genes