Genomewide association study of immune traits in chicken F2 resource population

Abstract

Immune traits play pivotal roles in animal immune capacity development and disease resistance. Single nucleotide polymorphisms (SNPs) are common forms of genetic variations among individuals, which are thought to account for the majority of inherited phenotypic variations. In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10(-6) ) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10(-5) ) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10(-5) ) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven suggestive SNPs). Three significant SNPs (GGaluGA151406, Gga_rs14554319 and Gga_rs13593979) and candidate genes (LYRM4 and KTN1) were found to be associated with avian influenza antibody titres, and the first two SNPs are from the results of two-model analysis. For the immune organs, through the analysis of GLM, 19 SNPs were found to be significantly associated with the thymus weight, 61 SNPs were significantly associated with the bursa of Fabricius weight, six of which were located within a 34-Mb region (125 846 474-159 649 698 bp) on chicken chromosome 1 (GGA1). A candidate region relevant to haematological traits from GLM was found in GGA4 and 9 loci were located on it. Three loci (GGaluGA348521, Gga_rs16098446 and GGaluGA348518) within 179 kb (16 286 868-16 466 134 bp) on GGAZ from GLM provided evidence that this genomic segment may be relevant to red blood cell volume distribution width (RDW). Our study provides a list of significant SNPs and candidate genes that will be valuable information for unveiling the underlying molecular mechanism of immune regulation.

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

“…Thus, we also compared our gene lists (Tables 1, 2 and 3) with gene entries in the ChickenQTLdb (https://www.animalgenome.org/cgi-bin/QTLdb/GG/ index) related to QTL for production traits and only identified a single gene. LPP, noteworthy one of the genes found in common between FPD and pEFP (Table 3), has been reported to be linked to shank length and diameter [21] as well as Bursa of Fabricius weight [22]. The latter finding might correspond the observation of feather pecking being related to the immune system, but this is speculative and needs to be further investigated.…”

In-depth 15 H7N9 Human Serum Proteomics Profiling Study

“…The remaining 7 singleton 163 proteins were TNFSF12-TNFSF13, AC073610.3 (Novel Protein), C1RL, FBLN2, OLFML3, SBSN 164 and C4orf54. They may play an important role in avian influenza infection, for instance, protein 165 AC073610.3 acts as GTP binding and obsolete signal transducer activity, the most related GGA2 166 protein associated with avian influenza antibody titers [18]. There were still 51 proteins that were not 167 annotated by the String system.…”

Genome-Wide Association Studies Provide Insight Into the Genetic Determination for Hyperpigmentation of the Visceral Peritoneum in Broilers

“…Currently, a large amount of candidate genes were identified as causal markers associated with growth performance, meat quality, carcass traits, feather colors, and disease resistance ability in the Chinese indigenous chicken population ( Luo et al, 2014 ; Zhang et al, 2015 ; Mao et al, 2019 ; Guo et al, 2020 ; Zhang et al, 2020 ). For example, GWAS in an F 2 resource population was conducted to identify two novel candidate genes related to three single-nucleotide polymorphisms (SNPs) associated with avian influenza antibody titers ( Sun et al, 2016 ). Another study reported that 21 candidate genes were proved to be associated with chicken bone growth based on GWAS in an F 2 crossbred experimental population ( Li et al, 2021 ).…”