Enhancing host immunity is an effective way to reduce morbidity in chickens.  Heterophil to lymphocyte ratio (H/L) is associated with host disease resistance in birds.  Chickens with different H/L levels show different disease resistances.  However, the utility of the H/L as an indicator of immune function needs to be further analyzed.  In this study, a H/L directional breeding chicken line (Jingxing yellow chicken) was constructed, which has been bred for 12 generations.  We compared the function of heterophils, and combined statistical analysis to explore the candidate genes and pathways related to H/L.  The oxidative burst function of the heterophils isolated from the H/L selection line (G12) was increased (P=0.044) compared to the non-selection line (NS).  The 22.44 Mb genomic regions which annotated 300 protein-coding genes were selected in the genome of G9 (n=92) compared to NS (n=92) based on a genome-wide selective sweep.  Several selective regions were identified containing genes like interferon induced with helicase C domain 1 (IFIH1) and moesin (MSN) associated with the intracellular receptor signaling pathway, C–C motif chemokine receptor 6 (CCR6), dipeptidyl peptidase 4 (DPP4) and hemolytic complement (HC) associated with the negative regulation of leukocyte chemotaxis and tight junction protein 1 (TJP1) associated with actin cytoskeleton organization.  In addition, 45 genome-wide significant indels containing 29 protein-coding genes were also identified as associated with the H/L based on genome-wide association study (GWAS).  The expression of protein tyrosine phosphatase non-receptor type 5 (PTPN5) (r=0.75, P=0.033) and oxysterol binding protein like 5 (OSBPL5) (r=0.89, P=0.0027) were positively correlated with H/L.  Compared to the high H/L group, the expressions of PTPN5 and OSBPL5 were decreased (P<0.05) in the low H/L group of Beijing you chicken.  The A/A allelic frequency of indel 5_13108985 (P=3.85E–06) within OSBPL5 gradually increased from the NS to G5 and G9, and the individuals with A/A exhibited lower H/L than individuals with heterozygote A/ATCT (P=4.28E–04) and homozygous ATCT/ATCT (P=3.40E–05).  Above results indicated oxidative burst function of heterophils were enhanced, and 22.44 Mb genomic regions were selected with the directional selection of H/L.  In addition, PTPN5 and OSBPL5 genes were identified as H/L-related candidate genes.  These findings revealed the complex genetic mechanism of H/L related to immunity and will allow selection for improving chicken immunity based on the H/L

The interaction between myocytes and intramuscular adipocytes is a hot scientific topic.  Using a co-culture system, this study aims to investigate the regulation of intramuscular fat deposition in chicken muscle tissue through the interaction between myocyte and adipocyte and identify important intermediary regulatory factors.  Our proteomics data showed that the protein expression of tissue inhibitor of metalloproteinases 2 (TIMP2) increased significantly in the culture medium of the co-culture system, and the content of lipid droplets was more in the co-culture intramuscular adipocytes.  In addition, TIMP2 was significantly upregulated (P<0.01) in muscle tissue of individuals with high intramuscular fat content.  Weighted gene co-expression network analysis revealed that TIMP2 was mainly involved in the extracellular matrix receptor interaction signaling pathway and its expression was significantly correlated with triglyceride, intramuscular fat, C14:0, C14:1, C16:0, C16:1, and C18:1n9C levels.  Additionally, TIMP2 was co-expressed with various representative genes related to lipid metabolism (such as ADIPOQ, SCD, ELOVL5, ELOVL7, and LPL), as well as certain genes involved in extracellular matrix receptor interaction (such as COL1A2, COL4A2, COL5A1, COL6A1, and COL6A3), which are also significantly upregulated (P<0.05 or P<0.01) in muscle tissue of individuals with high intramuscular fat content.  Our findings reveal that TIMP2 promotes intramuscular fat deposition in muscle tissue through the extracellular matrix receptor interaction signaling pathway.

Linoleic acid is an essential polyunsaturated fatty acid that cannot be synthesized by humans or animals themselves and can only be obtained externally.  The amount of linoleic acid present has an impact on the quality and flavour of meat and indirectly affects consumer preference.  However, the molecular mechanisms influencing the deposition of linoleic acid in organisms are not clear.  As the molecular mechanisms of linoleic acid deposition are not well understood, to investigate the main effector genes affecting the linoleic acid content, this study aimed to screen for hub genes in slow-type yellow-feathered chickens by transcriptome sequencing (RNA-Seq) and weighted gene coexpression network analysis (WGCNA).  We screened for candidate genes associated with the linoleic acid content in slow-type yellow-feathered broilers.  A total of 399 Tiannong partridge chickens were slaughtered at 126 days of age, fatty acid levels were measured in pectoral muscle, and pectoral muscle tissue was collected for transcriptome sequencing.  Transcriptome sequencing results were combined with phenotypes for WGCNA to screen for candidate genes.  KEGG enrichment analysis was also performed on the genes that were significantly enriched in the modules with the highest correlation.  A total of 13 310 genes were identified after quality control of transcriptomic data from 399 pectoral muscle tissues.  WGCNA was performed, and a total of 26 modules were obtained, eight of which were highly correlated with the linoleic acid content.  Four key genes, namely, MDH2, ATP5B, RPL7A and PDGFRA, were screened according to the criteria |GS|>0.2 and |MM|>0.8.  The functional enrichment results showed that the genes within the target modules were mainly enriched in metabolic pathways.  In this study, a large-sample-size transcriptome analysis revealed that metabolic pathways play an important role in the regulation of the linoleic acid content in Tiannong partridge chickens, and MDH2, ATP5B, RPL7A and PDGFRA were screened as important candidate genes affecting the linoleic acid content.  The results of this study provide a theoretical basis for selecting molecular markers and comprehensively understanding the molecular mechanism affecting the linoleic acid content in muscle, providing an important reference for the breeding of slow-type yellow-feathered broiler chickens.

Omega-3 (linolenic acid (ALA), docosapentaenoic acid, eicosapentaenoic acid) and omega-6 (linoleic acid (LA), arachidonic acid) polyunsaturated fatty acids are essential for health and normal physiological functioning in humans.  Here we report a genome-wide association study (GWAS) on LA content in chicken meat.  The 19 significant single nucleotide polymorphisms (SNPs) identified by the GWAS approach were annotated in VILL, PLCD1 and OXSR1 genes with highly polymorphic linkage blocks, and explained 4.5% of the phenotypic variation in the LA content.  Specifically, the PLCD1 mRNA expression level was negatively correlated with the LA content, and significantly higher in chickens with low LA content than in those with high LA content.  In addition, PLCD1 was found to be involved in metabolic pathways, etc.  Furthermore, the LA content was correlated with volatile organic compounds (e.g., octanal, etc.), but no relationship was found with intramuscular fat and triglycerides in chicken meat.  The results indicated that there are key SNPs in PLCD1 that regulate the content of LA, and it has no significant effect on fat deposition, but may affect the content of volatile organic compounds (VOCs).

Salmonella is one of the most common food-borne pathogens and its resistance in chicken can be improved through genetic selection.  The heterophils/lymphocytes (H/L) ratio in the blood reflects the immune system status of chicken.  We compared the genome data and spleen transcriptomes between the H/L ratio-selected and non-selected chickens, after Salmonella infection, aiming to identify the key genes participating in the antibacterial activity in the spleen.  The results revealed that, the selected population had stronger (P<0.05) liver resistance to Salmonella typhimurium (ST) than the non-selected population.  In the selected and non-selected lines, the identified differentiation genes encode proteins involved in biological processes or metabolic pathways that included the TGF-beta signaling pathway, FoxO signaling pathway, and Salmonella infection pathway.  The results of the analysis of all identified differentially expressed genes (DEGs) of spleen revealed that the G protein-coupled receptor (GPCR) and insulin-like growth factor (IGF-I) signaling pathways were involved in the Salmonella infection pathway.  Integrated analysis of DEGs and F_ST (fixation index), identified candidate genes involved in Salmonella infection pathway, such as GPR39, NTRK2, and ANXA1.  The extensive genomic changes highlight the polygenic genetic of the immune response in these chicken populations.  Numerous genes related to the immune performance are differentially expressed in the selected and non-selected lines and the selected lines has a higher resistance to Salmonella. 

  The safety of feeding transgenic cry1Ab/cry1Ac rice (a genetically modified (GM) rice variety) to broilers was examined from an immunological perspective. Hatchling Arbor Acres chickens (240) were assigned to two dietary treatments (diets containing GM or non-GM rice) with 12 replicates per group and 10 birds per replicate. Traits were measured on one randomly selected bird from each replicate at d 21 and 42. The 42-d feeding trial revealed that cry1Ab/cry1Ac rice had no significant effect relative to non-GM rice on body weight and the immune organ indices. No significant pathological lesion in the spleen and bursa of Fabricius was found in the GM rice group. There were no significant differences in serum concentrations of immunoglobulin Y (IgY), IgM, interleukin 4 (IL-4) and IL-6 between the two groups at d 21 or 42, except for IL-6 being higher (P<0.05) in the GM-fed chickens at d 42. There were no differences in the T and B lymphocyte transformation rate and CD4+/CD8+ ratio between the two groups at d 42. Additionally, there was no significant difference between the two diets in expression of relevant genes viz. the major histocompatibility complex class II beta chain (BLB2), interferon beta 1 (IFNβ), tumour necrosis factor alpha-like (TNFα) and toll-like receptor 4 (TLR4) in the spleen and bursa of Fabricius. All the data demonstrated that transgenic cry1Ab/cry1Ac rice had no adverse effect on these aspects of immune function of broilers during 42-d feeding trial. Transgenic rice was therefore indistinguishable from non-GM rice in terms of short-term feeding in chickens.