Association of Twelve Immune-Related Genes with Performance of Three Broiler Lines in Two Different Hygiene Environments

Understanding G × E Interaction for Nutritional and Antinutritional Factors in a Diverse Panel of Vigna stipulacea (Lam.) Kuntz Germplasm Tested Over the Locations

Micronutrient malnutrition or hidden hunger is a serious challenge toward societal well-being. Vigna stipulacea (Lam.) Kuntz (known locally as Minni payaru), is an underutilized legume that has the potential to be a global food legume due to its rich nutrient profile. In the present study, 99 accessions of V. stipulacea were tested for iron (Fe), zinc (Zn), calcium (Ca), protein, and phytate concentrations over two locations for appraisal of stable nutrient-rich sources. Analysis of variance revealed significant effects of genotype for all the traits over both locations. Fe concentration ranged from 29.35-130.96 mg kg-1 whereas Zn concentration ranged from 19.44 to 74.20 mg kg-1 across both locations. The highest grain Ca concentration was 251.50 mg kg-1 whereas the highest grain protein concentration was recorded as 25.73%. In the case of grain phytate concentration, a genotype with the lowest value is desirable. IC622867 (G-99) was the lowest phytate containing accession at both locations. All the studied traits revealed highly significant genotypic variances and highly significant genotype × location interaction though less in magnitude than the genotypic variance. GGE Biplot analysis detected that, for grain Fe, Zn, and Ca concentration the 'ideal' genotypes were IC331457 (G-75), IC331610 (G-76), and IC553564 (G-60), respectively, whereas for grain protein concentration IC553521 (G-27) was the most "ideal type." For phytate concentration, IC351407 (G-95) and IC550523 (G-99) were considered as 'ideal' and 'desirable,' respectively. Based on the desirability index, Location 1 (Kanpur) was identified as ideal for Fe, Zn, Ca, and phytate, and for grain protein concentration, Location 2 (New Delhi) was the ideal type. A significant positive correlation was detected between grain Fe as well as grain Zn and protein concentration considering the pooled analysis over both the locations where as a significant negative association was observed between phytate and protein concentration over the locations. This study has identified useful donors and enhanced our knowledge toward the development of biofortified Vigna cultivars. Promoting domestication of this nutrient-rich semi-domesticated, underutilized species will boost sustainable agriculture and will contribute toward alleviating hidden hunger.

Associations between IGF1, IGFBP2 and TGFß3 Genes Polymorphisms and Growth Performance of Broiler Chicken Lines

Marker-assisted selection based on fast and accurate molecular analysis of individual genes is considered an acceptable tool in the speed-up of the genetic improvement of production performance in chickens. The objective of this study was to detect the single nucleotide polymorphisms (SNPs) in the IGF1, IGFBP2 and TGFß3 genes, and to investigate their associations with growth performance (body weight (BW) and average daily gain (ADG) at 14, 21, 28, 35 and 42 days of age) and carcass traits in broilers. Performance (carcass) data (weight before slaughter; weights of the trunk, giblets, abdominal fat, breast muscle and thigh muscle; slaughter value and slaughter percentage), as well as blood samples for DNA extraction and SNP analysis, were obtained from 97 chickens belonging to two different lines (Hubbard F15 and Cobb E) equally divided between the two sexes. The genotypes were detected using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) methods with specific primers and restrictase for each gene. The statistical analysis discovered significant associations (p < 0.05) between the TGFβ3 SNP and the following parameters: BW at 21, 28 and 35 days, trunk weight and slaughter value. Association analysis of BWs (at 21, 28 and 35 days) and SNPs was always significant for codominant, dominant and overdominant genetic models, showing a possible path for genomic selection in these chicken lines. Slaughter value was significant for codominant, recessive and overdominant patterns, whereas other carcass traits were not influenced by SNPs. Based on the results of this study, we suggested that the TGFβ3 gene could be used as a candidate gene marker for chicken growth traits in the Hubbard F15 and Cobb E population selection programs, whereas for carcass traits further investigation is needed.

Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken

Background

A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype.

Results

When genetic correlations (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{g}$$\end{document}rg) between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45% of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30%. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30% of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{g}$$\end{document}rg was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives.

Conclusions

If G × E interactions (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r_{g}$$\end{document}rg of 0.5 and 0.7) are strong, a genomic selection scheme in which 30% of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45%.

AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut

BACKGROUND

The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs affecting host peptides involved in the innate defences tend to be rare, but three non-synonymous SNPs in the avian β-defensin (AvBD1) gene encoding the variant peptides NYH, SSY and NYY were identified that segregated specifically to three lines of commercial broiler chickens Line X (LX), Line Y(LY) and Line Z. The impacts of such amino acid changes on peptide antimicrobial properties were analysed in vitro and described in relation to the caecal microbiota and gut health of LX and LY birds.

RESULTS

Time-kill and radial immune diffusion assays indicated all three peptides to have antimicrobial properties against gram negative and positive bacteria with a hierarchy of NYH > SSY > NYY. Calcein leakage assays supported AvBD1 NYH as the most potent membrane permeabilising agent although no significant differences in secondary structure were identified to explain this. However, distinct claw regions, identified by 3D modelling and proposed to play a key role in microbial membrane attachment, and permeation, were more distinct in the NYH model. In vivo AvBD1 synthesis was detected in the bird gut epithelia. Analyses of the caecal gut microbiota of young day 4 birds suggested trends in Lactobacilli sp. colonisation at days 4 (9% LX vs × 30% LY) and 28 (20% LX vs 12% LY) respectively, but these were not statistically significant (P > 0.05).

CONCLUSION

Amino acid changes altering the killing capacity of the AvBD1 peptide were associated with two different bird lines, but such changes did not impact significantly on caecal gut microbiota.

Extensive shared polymorphism at non-MHC immune genes in recently diverged North American prairie grouse

Gene polymorphisms shared between recently diverged species are thought to be widespread and most commonly reflect introgression from hybridization or retention of ancestral polymorphism through incomplete lineage sorting. Shared genetic diversity resulting from incomplete lineage sorting is usually maintained for a relatively short period of time, but under strong balancing selection it may persist for millions of years beyond species divergence (balanced trans-species polymorphism), as in the case of the major histocompatibility complex (MHC) genes. However, balancing selection is much less likely to act on non-MHC immune genes. The aim of this study was to investigate the patterns of shared polymorphism and selection at non-MHC immune genes in five grouse species from Centrocercus and Tympanuchus genera. For this purpose, we genotyped five non-MHC immune genes that do not interact directly with pathogens, but are involved in signaling and regulate immune cell growth. In contrast to previous studies with MHC, we found no evidence for balancing selection or balanced trans-species polymorphism among the non-MHC immune genes. No haplotypes were shared between genera and in most cases more similar allelic variants sorted by genus. Between species within genera, however, we found extensive shared polymorphism, which was most likely attributable to introgression or incomplete lineage sorting following recent divergence and large ancestral effective population size (i.e., weak genetic drift). Our study suggests that North American prairie grouse may have attained relatively low degree of reciprocal monophyly at nuclear loci and reinforces the rarity of balancing selection in non-MHC immune genes.

Genetic Variability, Genotype × Environment Interaction, Correlation, and GGE Biplot Analysis for Grain Iron and Zinc Concentration and Other Agronomic Traits in RIL Population of Sorghum (Sorghum bicolor L. Moench)

The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg^-1 and Zinc = 10.2 to 58.7 mg kg^-1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p < 0.01) indicating possibility of simultaneous effective selection for both the traits. The RIL population showed good variability and high heritabilities (>0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc.

Contrasting patterns of selection and drift between two categories of immune genes in prairie-chickens

Immune-receptor genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognizing specific pathogens and are known to have high rates of adaptive evolution, presumably as a consequence of rapid co-evolution between hosts and pathogens. In contrast, many 'mediating' genes of the immune system do not interact directly with specific pathogens and are involved in signalling (e.g. cytokines) or controlling immune cell growth. As a consequence, we might expect stronger selection at immune-receptor than mediating genes, but these two types of genes have not been compared directly in wild populations. Here, we tested the hypothesis that selection differs between MHC (class I and II) and mediating genes by comparing levels of population differentiation across the range of greater prairie-chickens (Tympanuchus cupido). As predicted, there was stronger population differentiation and isolation by distance at immune receptor (MHC) than at either mediating genes or neutral microsatellites, suggesting a stronger role of local adaptation at the MHC. In contrast, mediating genes displayed weaker differentiation between populations than neutral microsatellites, consistent with selection favouring similar alleles across populations for mediating genes. In addition to selection, drift also had a stronger effect on immune receptor (MHC) than mediating genes as indicated by the stronger decline of MHC variation in relation to population size. This is the first study in the wild to show that the effects of selection and drift on immune genes vary across populations depending on their functional role.

Possible Association of IFN-γ Gene -316A/G SNP with Humoral Immune Response to Killed H5N1 HPAI Vaccine in a Red Junglefowl Population

To understand the role of interferon (IFN)-γ gene (IFNG) single-nucleotide polymorphisms (SNPs) in the resistance to H5N1 highly pathogenic avian influenza (HPAI), we determined the SNPs, the log2-transformed specific antibody titers, and ex vivo recall antigen-specific IFN-γ production by peripheral blood mononuclear cells (PBMCs) in 62 red junglefowls (Gallus gallus) immunized twice with inactivated H5N1 HPAI vaccine. Consequently, 52 SNPs were detected in the amplified 1137-bp length covering the promoter region and all exons, with +2133A/T SNP in the coding DNA sequence that caused a missense mutation and was identified in G. gallus for the first time. For -316A/G SNP genotypes, the chi-squared test showed that the bird sample was in the Hardy-Weinberg equilibrium (P=0.369>0.05), and the least squares analysis revealed an increasing tendency in the antibody titers with G to A substitution so that a significant difference occurred between the AA genotype (8.031±0.247) and the GG genotype (6.571±0.528) (P=0.015<0.05, 95% confidence interval [CI]: 0.0004-0.0866), as basically consistent with the antigen-induced IFN-γ protein expression, which indicated possible association of the -316A/G SNP with a secondary humoral immune response to the HPAI vaccine in the bird population. These findings may help to improve genetic resistance using cross-breeding and enhance HPAI vaccine-induced immunity in chicken production.

The effects of polymorphisms in IL-2, IFN-γ, TGF-β2, IgL, TLR-4, MD-2, and iNOS genes on resistance to Salmonella enteritidis in indigenous chickens

Salmonella Enteritidis is a major cause of food poisoning worldwide, and poultry products are the main source of S. Enteritidis contamination for humans. Among the numerous strategies for disease control, improving genetic resistance to S. Enteritidis has been the most effective approach. We investigated the association between S. Enteritidis burden in the caecum, spleen, and liver of young indigenous chickens and seven candidate genes, selected on the basis of their critical roles in immunological functions. The genes included those encoding interleukin 2 (IL-2), interferon-γ (IFN-γ), transforming growth factor β2 (TGF-β2), immunoglobulin light chain (IgL), toll-like receptor 4 (TLR-4), myeloid differentiation protein 2 (MD-2), and inducible nitric oxide synthase (iNOS). Two Malaysian indigenous chicken breeds were used as sustainable genetic sources of alleles that are resistant to salmonellosis. The polymerase chain reaction restriction fragment-length polymorphism technique was used to genotype the candidate genes. Three different genotypes were observed in all of the candidate genes, except for MD-2. All of the candidate genes showed the Hardy-Weinberg equilibrium for the two populations. The IL-2-MnlI polymorphism was associated with S. Enteritidis burden in the caecum and spleen. The TGF-β2-RsaI, TLR-4-Sau 96I, and iNOS-AluI polymorphisms were associated with the caecum S. Enteritidis load. The other candidate genes were not associated with S. Enteritidis load in any organ. The results indicate that the IL-2, TGF-β2, TLR-4, and iNOS genes are potential candidates for use in selection programmes for increasing genetic resistance against S. Enteritidis in Malaysian indigenous chickens.

Genome-wide patterns of genetic variation in two domestic chickens

Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.

A novel SNP of the PNRC1 gene and its association with reproductive traits in Tsaiya ducks

Proline-rich nuclear receptor coactivator (PNRC)1 is a member of a new family of nuclear receptor coactivators capable of potentiating the transcriptional activity of nuclear receptors. The objective was to investigate the relationship between PNRC1 genotypes of single nucleotide polymorphism (SNP) and reproductive traits in ducks. Brown Tsaiya ducks (N = 305) from two lines, a control line with no selection and the selected line, were used. Polymerase chain reaction-single strand polymorphism and DNA sequencing were done to screen polymorphisms of the PNRC1 gene. A novel SNP (G98T) in 3'-untranslated region of the PNRC1 gene was identified and resulted in two genotypes, GG and GT. The frequencies of genotype GG and allele G were higher in both lines investigated. Regarding egg weight at first egg (EWFE), based on SNP trait association analysis, ducks with the GG genotype had a 4.48 g per egg greater egg weight at first egg when compared with ducks of the GT genotype in the control line (P < 0.05). In addition, this SNP was associated with the hatchability rate (HR) in the selected line; ducks with the GT genotype had a 6.70% higher hatchability rate than those with the GG genotype (P < 0.05). Therefore, we inferred that the PNRC1 gene could be a candidate locus or linked to a major gene that influenced egg weight-related and hatchability traits in Tsaiya ducks. Further investigations on additional duck populations with larger sample sizes are needed to confirm these results.

Genetic parameters of foot-pad dermatitis and body weight in purebred broiler lines in 2 contrasting environments

The aims of this study were to investigate the genetic background of foot-pad dermatitis (FPD) in 4 different broiler lines reared in 2 contrasting environments (pedigree or sib-test) and to evaluate the performance of simultaneous genetic selection for improved FPD and BW. Data were available for 4 generations from 4 broiler lines, bred with varying intensities of selection for growth. The average BW ranged from 1.7 to 2.4 kg at 5 wk of age. In the pedigree environment, the prevalence of FPD ranged from 14 to 37%, with 3 to 9% being severely affected; in the sib-test environment, these values were correspondingly 45 to 79% and 35 to 70%. Both traits showed re-ranking of the 4 lines in terms of phenotype across the 2 environments, indicating the existence of a genotype-by-environment interaction. In both environments, females showed higher prevalences of FPD than males. In line with their higher prevalence, heritabilities of FPD in the sib-test environment ranged from 0.22 to 0.32, compared with 0.18 to 0.24 for FPD in the pedigree environment (all SE ≤0.02). Estimates of the genetic correlation between FPD in the pedigree and in the sib-test environments were high (0.78-0.82), which suggests that selection against FPD in a highly biosecure environment can improve the genetic merit for birds reared under commercial conditions. Estimates of the genetic associations between FPD and BW were small and varied in sign. Predicted responses to selection showed a yearly reduction in average score of -3.4 to -7.5% for FPD in the pedigree environment and -0.5 to -6.6% for FPD in the sib-test environment, while maintaining improvement of BW of 2.6 to 3.2% and 2.6 to 3.8% of the average BW per year, respectively. This research indicates that balanced genetic selection for both BW and FPD in contrasting environments is an effective strategy to reduce the genetic disposition to develop FPD in broilers.

Association of TLR4 polymorphism with cytokine expression level and pulmonary lesion score in pigs

The toll-like receptor 4 (TLR4), recognizing lipopolysaccharide of gram-negative bacteria, plays an essential role in immune responses. Variation in TLR4 alters host immune responses to pathogen and is associated with resistance/susceptibility to infectious diseases, as suggested by studies in humans and agricultural species, including cattle and chicken. In this study, we analyzed association of single nucleotide polymorphisms (SNPs) of TLR4 with cytokine expression level and pulmonary lesion score in swine. The SNP c.611 T>A showed significant association with the transcription levels of IFNG, TNFA, and IL-6 (P < 0.05); the SNP c.962 G>A showed significant association with the transcription of IFNG, IL-2, and IL-4 (P < 0.05); the SNP c.1,027 C>A showed significant association with the transcription of IFNG and IL-6 (P < 0.05); the haplotypes showed significant association with the transcription of IFNG, IL-2, IL-4, IL-6, and TNFA (P < 0.05). Both SNPs c.611 T>A and c.962 G>A showed significant association with pulmonary lesion scores (P < 0.01); and the combination genotypes of 3 polymorphic sites were also significantly associated with pulmonary lesion scores (P < 0.01). The observed relationship between TLR4 polymorphism and the transcription levels of cytokines indicate that these SNPs are related to the modulation of the cytokine mediated immune response.

Drift and selection influence geographic variation at immune loci of prairie-chickens

Previous studies of immunity in wild populations have focused primarily on genes of the major histocompatibility complex (MHC); however, studies of model species have identified additional immune-related genes that also affect fitness. In this study, we sequenced five non-MHC immune genes in six greater prairie-chicken (Tympanuchus cupido) populations that have experienced varying degrees of genetic drift as a consequence of population bottlenecks and fragmentation. We compared patterns of geographic variation at the immune genes with six neutral microsatellite markers to investigate the relative effects of selection and genetic drift. Global F(ST) outlier tests identified positive selection on just one of five immune genes (IAP-1) in one population. In contrast, at other immune genes, standardized G'(ST) values were lower than those at microsatellites for a majority of pairwise population comparisons, consistent with balancing selection or with species-wide positive or purifying selection resulting in similar haplotype frequencies across populations. The effects of genetic drift were also evident as summary statistics (e.g., Tajima's D) did not differ from neutrality for the majority of cases, and immune gene diversity (number of haplotypes per gene) was correlated positively with population size. In summary, we found that both genetic drift and selection shaped variation at the five immune genes, and the strength and type of selection varied among genes. Our results caution that neutral forces, such as drift, can make it difficult to detect current selection on genes.

The differential evolutionary dynamics of avian cytokine and TLR gene classes

The potential for investigating immune gene diversity has been greatly enhanced by recent advances in sequencing power. In this study, variation at two categories of avian immune genes with differing functional roles, pathogen detection and mediation of immune mechanisms, was examined using high-throughput sequencing. TLRs identify and alert the immune system by detecting molecular motifs that are conserved among pathogenic microorganisms, whereas cytokines act as mediators of resulting inflammation and immunity. Nine genes from each class were resequenced in a panel of domestic chickens and wild jungle fowl (JF). Tests on population-wide genetic variation between the gene classes indicated that allele frequency spectra at each group were distinctive. TLRs showed evidence pointing toward directional selection, whereas cytokines had signals more suggestive of frequency-dependent selection. This difference persisted between the distributions considering only coding sites, suggesting functional relevance. The unique patterns of variation at each gene class may be constrained by their different functional roles in the immune response. TLRs identify a relatively limited number of exogeneous pathogenic-related patterns and would be required to adapt quickly in response to evolving novel microbes encountered in new environmental niches. In contrast, cytokines interact with many molecules in mediating the power of immune mechanisms, and accordingly respond to the selective stimuli of many infectious diseases. Analyses also indicated that a general pattern of high variability has been enhanced by widespread genetic exchange between chicken and red JF, and possibly between chicken and gray JF at TLR1LA and TLR2A.

Porcine Toll-like receptors: the front line of pathogen monitoring and possible implications for disease resistance

Toll-like receptors (TLRs) are the most famous pattern-recognition receptors (PRRs); they monitor pathogen-associated molecular patterns and play a critical role in activation of the immune system against infection. TLR gene mutations may affect the gene products in terms of their ligand-binding ability or their signal transduction ability after ligand binding; such changes have a great influence on pathogen monitoring and disease resistance. Thirteen mammalian TLRs have been identified, and genes corresponding to all 10 TLR genes identified in humans have been fully cloned in pigs. Porcine TLR gene coding sequences possess a large number of nonsynonymous single nucleotide polymorphisms (SNPs). They are concentrated in ectodomains, and may increase the variability of pathogen recognition in pig populations. We summarize the current knowledge of TLR molecules in mammals and livestock (particularly pigs) and speculate on the relationship between SNPs in porcine TLRs and their application to vaccine design and disease-resistance breeding.

Genome-assisted prediction of a quantitative trait measured in parents and progeny: application to food conversion rate in chickens

Accuracy of prediction of yet-to-be observed phenotypes for food conversion rate (FCR) in broilers was studied in a genome-assisted selection context. Data consisted of FCR measured on the progeny of 394 sires with SNP information. A Bayesian regression model (Bayes A) and a semi-parametric approach (Reproducing kernel Hilbert Spaces regression, RKHS) using all available SNPs (p = 3481) were compared with a standard linear model in which future performance was predicted using pedigree indexes in the absence of genomic data. The RKHS regression was also tested on several sets of pre-selected SNPs (p = 400) using alternative measures of the information gain provided by the SNPs. All analyses were performed using 333 genotyped sires as training set, and predictions were made on 61 birds as testing set, which were sons of sires in the training set. Accuracy of prediction was measured as the Spearman correlation (r¯S) between observed and predicted phenotype, with its confidence interval assessed through a bootstrap approach. A large improvement of genome-assisted prediction (up to an almost 4-fold increase in accuracy) was found relative to pedigree index. Bayes A and RKHS regression were equally accurate (r¯S = 0.27) when all 3481 SNPs were included in the model. However, RKHS with 400 pre-selected informative SNPs was more accurate than Bayes A with all SNPs.

Nonparametric methods for incorporating genomic information into genetic evaluations: an application to mortality in broilers

Four approaches using single-nucleotide polymorphism (SNP) information (F(infinity)-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14-42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods.

Machine learning classification procedure for selecting SNPs in genomic selection: application to early mortality in broilers

Genome-wide association studies using single nucleotide polymorphisms (SNPs) can identify genetic variants related to complex traits. Typically thousands of SNPs are genotyped, whereas the number of phenotypes for which there is genomic information may be smaller. When predicting phenotypes, options for statistical model building range from incorporating all possible markers into the specification to including only sets of relevant SNPs (features). In the latter case, an efficient method of selecting influential features is required. A two-step feature selection method for binary traits was developed, which consisted of filtering (using information gain), and wrapping (using naïve Bayesian classification). The filter reduces the large number of SNPs to a much smaller size, to facilitate the wrapper step. As the procedure is tailored for discrete outcomes, an approach based on discretization of phenotypic values was developed, to enable feature selection in a classification framework. The method was applied to chick mortality rates (0-14 days of age) on progeny from 201 sires in a commercial broiler line, with the goal of identifying SNPs (over 5000) related to progeny mortality. To mimic a case-control study, sires were clustered into two groups, low and high, according to two arbitrarily chosen mortality rate cut points. By varying these thresholds, 11 different 'case-control' samples were formed, and the SNP selection procedure was applied to each sample. To compare the 11 sets of chosen SNPs, predicted residual sum of squares (PRESS) from a linear model was used. The two-step method improved naïve Bayesian classification accuracy over the case without feature selection (from around 50 to above 90% without and with feature selection in each case-control sample). The best case-control group (63 sires above or below the thresholds) had the smallest PRESS statistic among groups with model p-values below 0.003. The 17 SNPs selected using this group accounted for 31% of the variation in raw mortality rates between sire families.

SHORT COMMUNICATION: Associations of BF2 alleles with antibody titres and production traits in commercial pure line broiler chickens

Three commercial broiler pure lines were evaluated for associations of sire BF2 (major histocompatibility complex class I) alleles with progeny phenotypic traits. Significant BF2 associations with a subset of traits were observed in two lines. The BF2*21 allele was positively associated with antibody titre to infectious bursal disease virus in both lines. Other associations were line-specific.

MX1 exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits

The Mx1 gene in mice is induced by type I interferons and is the major determinant of resistance to influenza virus and related orthomyxoviruses. It has been previously shown that a SNP in exon 13 of the chicken MX1 gene determines differential antiviral activity of the protein. We evaluated this SNP and two additional SNPs in elite broiler lines by PCR amplification and sequence analysis. Associations between MX1 exon 13 SNPs and several traits of economic interest were evaluated. Significant associations were found between the SNP determining antiviral activity and mortality in one line and leg defects in another line.