Genetic effects analysis of myeloid leukemia factor 2 and T cell receptor-β on resistance to coccidiosis in chickens

Genomic heterozygosity is associated with parasite abundance, but the effects are not mediated by host condition

Whether, when, and how genetic diversity buffers individuals and populations against infectious disease risk is a critical and open question for understanding wildlife disease and zoonotic disease risk. Several, but not all, studies have found negative relationships between infection and heterozygosity in wildlife. Since they can host multiple zoonotic infections, we sampled a population of wild deer mice (Peromyscus maniculatus), sequenced their genomes, and examined their fecal samples for coccidia and nematode eggs. We analyzed coccidia infection status, abundance, and coinfection status in relation to per-locus and per-individual measures of heterozygosity, as well as identified SNPs associated with infection status. Since heterozygosity might affect host condition, and condition is known to affect immunity, it was included as a co-variate in the per-individual analyses and as response variable in relation to heterozygosity. Not only did coccidia-infected individuals have lower levels of genome-wide per-locus diversity across all metrics, but we found an inverse relationship between genomic diversity and severity of coccidia infection. We also found weaker evidence that coinfected individuals had lower levels of private allelic variation than all other groups. In the per-individual analyses, relationships between heterozygosity and infection were marginal but followed the same negative trends. Condition was negatively correlated with infection, but was not associated with heterozygosity, suggesting that effects of heterozygosity on infection were not mediated by host condition in this system. Association tests identified multiple loci involved in the inflammatory response, with a particular role for NF-κB signaling, supporting previous work on the genetic basis of coccidia resistance. Taken together, we find that increased genome-wide neutral diversity, the presence of specific genetic variants, and improved condition positively impact infection status. Our results underscore the importance of considering host genomic variation as a buffer against infection, especially in systems that can harbor zoonotic diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10682-022-10175-8.

Genetic resilience in chickens against bacterial, viral and protozoal pathogens

The genome contributes to the uniqueness of an individual breed, and enables distinctive characteristics to be passed from one generation to the next. The allelic heterogeneity of a certain breed results in a different response to a pathogen with different genomic expression. Disease resistance in chicken is a polygenic trait that involves different genes that confer resistance against pathogens. Such resistance also involves major histocompatibility (MHC) molecules, immunoglobulins, cytokines, interleukins, T and B cells, and CD4+ and CD8+ T lymphocytes, which are involved in host protection. The MHC is associated with antigen presentation, antibody production, and cytokine stimulation, which highlight its role in disease resistance. The natural resistance-associated macrophage protein 1 (Nramp-1), interferon (IFN), myxovirus-resistance gene, myeloid differentiation primary response 88 (MyD88), receptor-interacting serine/threonine kinase 2 (RIP2), and heterophile cells are involved in disease resistance and susceptibility of chicken. Studies related to disease resistance genetics, epigenetics, and quantitative trait loci would enable the identification of resistance markers and the development of disease resistance breeds. Microbial infections are responsible for significant outbreaks and have blighted the poultry industry. Breeding disease-resistant chicken strains may be helpful in tackling pathogens and increasing the current understanding on host genetics in the fight against communicable diseases. Advanced technologies, such as the CRISPR/Cas9 system, whole genome sequencing, RNA sequencing, and high-density single nucleotide polymorphism (SNP) genotyping, aid the development of resistant breeds, which would significantly decrease the use of antibiotics and vaccination in poultry. In this review, we aimed to reveal the recent genetic basis of infection and genomic modification that increase resistance against different pathogens in chickens.

Establishing a Model for Evaluating Chicken Coccidiosis Resistance Based on Principal Component Analysis

Simple Summary

Avian coccidiosis, an infectious disease caused by seven species of Eimeria that can infect a bird’s digestive tract and significantly retard its growth, is a serious economic disease for chickens. Many studies have demonstrated that host resistance to coccidiosis related to genetic variations can be improved by selective breeding. The parameters for evaluation of resistance to coccidiosis could be objective indicators, such as body weight gain and cecal lesion score, or biochemical indices, such as immune factors or cytokines in the plasma or serum. The aim of the study is to establish an optimal comprehensive evaluation model including a resistance index that can be detected in live chickens (slaughter traits cannot be selected in breeding) based on principal component analysis. The value of individual chickens calculated with the optimal evaluation model is associated with the cecum lesion score; the larger the value, the stronger the resistance to coccidiosis. This illustrated that the optimal model is effective in coccidiosis resistance selection.

Abstract

To establish a coccidiosis resistance evaluation model for chicken selection, the different parameters were compared between infected and control Jinghai yellow chickens. Validation parameters were selected for principal component analysis (PCA), and an optimal comprehensive evaluation model was selected based on the significance of a correlation coefficient between coccidiosis resistance parameters and principal component functions. The following six different parameters were identified: body weight gain 3–5 days post infection and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), malondialdehyde (MDA) and γ-interferon (IFN-γ) concentrations on the eight day post inoculation. Six principal components and one accumulated contribution of up to 80% of the evaluation models were established by PCA. The results showed that the first model was significantly or highly significantly related to nine resistance parameters (p < 0.01 or p < 0.05), especially to cecal lesions (p < 0.01). The remaining models were related to only 2–3 parameters (p < 0.01 or p < 0.05) and not to cecal lesions (p > 0.05). The values calculated by the optimal model (first model) were significantly negatively correlated with cecal lesion performance; the larger the value, the more resistant to coccidiosis. The model fi1 = −0.636 zxi1 + 0.311 zxi2 + 0.801 zxi3 − 0.046 zxi4 − 0.076 zxi5 + 0.588 zxi6 might be the best comprehensive selection index model for chicken coccidiosis resistance selection.

Genetic analysis of SNPs in the MLF2 and TCR-β genes for growth traits in Korean native chickens

The myeloid leukemia factor 2 (MLF2) and T-cell receptor β (TCR-β) genes are associated the development of resistance towards coccidiosis infection. Five single-nucleotide polymorphisms (SNPs) located on these genes (SNP_892 and intron 7 (10) of MLF2 and SNP_88, 434, and 561 of TCR-β) were identified and considered to be the genetic markers for resistance to coccidiosis. In this study, we investigated the association between these SNPs and the body weight of Korean native chicken (KNC) and the possibility of using these SNPs as genetic markers for improving growth in KNCs. KNC specimens (798) were genotyped using high-resolution melting analysis, and single-marker association tests were performed; body weights of KNC were also measured every 2 weeks. Three SNPs [892 and intron 7 (10) of MLF2 and 88 of TCR-β] had significant associations with body weight in some period of growth of KNC. Further, 2 SNPs (434 and 561) of TCR-β were linked and significantly associated with the overall growth of KNCs. Conclusively, the findings of the present study suggested that SNPs in the MLF2 and TCR-β genes could be used as combinations of genetic markers for selecting high growth performance specimens of KNCs.

Co-evolution with chicken class I genes

The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC.

The long view: a selective review of 40 years of coccidiosis research

This selective review of 40 years of coccidiosis research is one of a number on important diseases of poultry to celebrate the 40th anniversary of the birth of Avian Pathology, the journal of the World Veterinary Poultry Association, and is written for the non-specialist. The intention is to provide a flavour of the field problems and intellectual challenges, with emphasis in the areas of immunology and vaccinology that drove research in the 1970s, and to reflect on research progress since.

Identification of parental line specific effects of MLF2 on resistance to coccidiosis in chickens

BACKGROUND

MLF2 was the candidate gene associated with coccidiosis resistance in chickens. Although single marker analysis supported the association between MLF2 and coccidiosis resistance, causative mutation relevant to coccidiosis was not identified yet. Thus, this study suggested segregation analysis of MLF2 haplotype and the association test of the other candidate genes using improved data transformation.

RESULTS

A haplotype probably originated from one parental line was found out of 4 major haplotypes of MLF2. Frequency of this haplotype was 0.2 in parental chickens and its offspring in 12 families. Allele substitution effect of the MLF2 haplotype originated from a specific line was associated with increased body weight and fecal egg count explaining coccidiosis resistance. Nevertheless Box-Cox transformation was able to improve normality; association test did not produce obvious different results compared with analysis with log transformed phenotype.

CONCLUSION

Allele substitution effect analysis and classification of MLF2 haplotype identified the segregation of haplotype associated with coccidiosis resistance. The haplotype originated from a specific parental line was associated with improving disease resistance. Estimating effect of MLF2 haplotype on coccidiosis resistance will provide useful information for selecting animals or lines for future study.