Genetic and phenotypic parameter estimates for body weights and egg production in Horro chicken of Ethiopia

Comparative population genomics analysis uncovers genomic footprints and genes influencing body weight trait in Chinese indigenous chicken

Body weight of chicken is a typical quantitative trait, which shows phenotypic variations due to selective breeding. Despite some QTL loci have been obtained, the body weight of native chicken breeds in different geographic regions varies greatly, its genetic basis remains unresolved questions. To address this issue, we analyzed 117 Chinese indigenous chickens from 10 breeds (Huiyang Bearded, Xinhua, Hotan Black, Baicheng You, Liyang, Yunyang Da, Jining Bairi, Lindian, Beijing You, Tibetan). We applied fixation index (FST) analysis to find selected genomic regions and genes associated with body weight traits. Our study suggests that NELL1, XYLT1, and NCAPG/LCORL genes are strongly selected in the body weight trait of Chinese indigenous chicken breeds. In addition, the IL1RAPL1 gene was strongly selected in large body weight chickens, while the PCDH17 and CADM2 genes were strongly selected in small body weight chickens. This result suggests that the patterns of genetic variation of native chicken and commercial chicken, and/or distinct local chicken breeds may follow different evolutionary mechanisms.

Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits

Monitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-term data from small experimental populations selected for a handful of traits. Here, we used a large dataset from a commercial breeding line spread over a period of twenty-three years. A total of 2,059,869 records and 2,062,112 animals in the pedigree were used for the estimations of variance components for the traits: body weight (BWT; 2,059,869 records) and hen-housed egg production (HHP; 45,939 records). Data were analysed with three estimation approaches: sliding overlapping windows, under frequentist (restricted maximum likelihood (REML)) and Bayesian (Gibbs sampling) methods; expected variances using coefficients of the full relationship matrix; and a "double trait covariances" analysis by computing correlations and covariances between the same trait in two distinct consecutive windows. The genetic variance showed marginal fluctuations in its estimation over time. Whereas genetic, maternal permanent environmental, and residual variances were similar for BWT in both the REML and Gibbs methods, variance components when using the Gibbs method for HHP were smaller than the variances estimated when using REML. Large data amounts were needed to estimate variance components and detect their changes. For Gibbs (REML), the changes in genetic variance from 1999-2001 to 2020-2022 were 82.29 to 93.75 (82.84 to 93.68) for BWT and 76.68 to 95.67 (98.42 to 109.04) for HHP. Heritability presented a similar pattern as the genetic variance estimation, changing from 0.32 to 0.36 (0.32 to 0.36) for BWT and 0.16 to 0.15 (0.21 to 0.18) for HHP. On the whole, genetic parameters tended slightly to increase over time. The expected variance estimates were lower than the estimates when using overlapping windows. That indicates the low effect of the drift-selection process on the genetic variance, or likely, the presence of genetic variation sources compensating for the loss. Double trait covariance analysis confirmed the maintenance of variances over time, presenting genetic correlations >0.86 for BWT and >0.82 for HHP. Monitoring genetic variance in broiler breeding programmes is important to sustain genetic progress. Although the genetic variances of both traits fluctuated over time, in some windows, particularly between 2003 and 2020, increasing trends were observed, which warrants further research on the impact of other factors, such as novel mutations, operating on the dynamics of genetic variance.

Genotype by Environment Interactions (G*E) of Chickens Tested in Ethiopia Using Body Weight as a Performance Trait

Ethiopia is a developing nation that could highly benefit from securing food via improved smallholder poultry farming. To support farmer and breeding decisions regarding which chicken strain to use in which Ethiopian environment, G*E analyses for body weight (BW) of growing male and female chickens were conducted. Research questions were (1) if a G*E is present for BW and (2) which strain performs best in which environment in terms of predicted BW. Analyses were performed using predicted BW at four different ages (90, 120, 150, and 180 days) of five strains (Horro, Koekoek, Kuroiler, Sasso-Rhode Island Red (S-RIR), and Sasso) tested in five Ethiopian regions (Addis Ababa, Amhara, Oromia, South Region, and Tigray) that are part of three Agro-Ecological Zones (AEZ) (cool humid, cool sub-humid, and warm semi-arid). The indigenous Horro strain was used as a control group to compare four other introduced tropically adapted strains. The dataset consisted of 999 female and 989 male farm-average BW measurements. G*E was strongly present (p < 0.001) for all combinations of strain and region analyzed. In line with previous research, Sasso was shown to have the highest predicted BW, especially at an early age, followed by Kuroiler. Horro had the lowest predicted BW at most ages and in most regions, potentially due to its young breeding program. The highest predicted BW were observed in Tigray, Oromia, and Amhara regions, which are in the main part of the cool sub-humid AEZ.

Genetic and phenotypic parameter estimates for selection within Ugandan indigenous chickens

The high genetic variation within indigenous chickens (IC) which provides an opportunity to select superior stock for sustainable production and conservation is under-exploited. This study is aimed at estimating heritability and genetic and phenotypic correlation coefficients of productive and reproductive traits of Ugandan IC as a basis for selection. Data on traits were collected across two consecutive generations, weight (W) and shank length (SL) of chicks at hatching (HW) as well as at 2 (W2; SL2), 4 (W4; SL4), 6 (W6; SL6), 8 (W8; SL8), and 12 (W12; SL12) weeks of growth. Body weights at onset of lay (WFE) were also measured. In addition, egg number (EN-60), egg weight (EW), clutch number (CLN-60), and clutch size (CLS-60) over a period of 60 days were recorded. Genetic parameters were estimated using the univariate animal model analysis with restricted maximum likelihood procedure using the variability package of R, version 4.1.1. Heritability of traits ranged from 0.30 and 0.72 except SL4 (0.02), SL12 (0.14), and EN-60 (0.17). The traits EN-60 and W4 were negatively phenotypically correlated (- 0.49). Body weight at first egg was highly genetically correlated (0.99) with SL8. Egg number was significantly, negatively, and genetically correlated (- 0.96) with SL12. In conclusion, shank length is a potential phenotypic marker when selecting for live weight at onset of lay and egg yield. The shank length could, therefore, permit selection of superior chickens at an early age.

The genetic impact of heat stress on the egg production of Thai native chickens (Pradu Hang dum)

Sustainable poultry production in adverse weather conditions is a widely debated issue, which has led to research into the development of breeds of poultry that are genetically resistant to heat. This study aimed to investigate the effects of heat stress on the genetics of monthly egg production and examine the threshold point of heat stress for preventing thermal stress and its effects on chicken productivity. The data of 5,965 monthly egg production records of 629 Thai native Pradu Hang dum chickens were used for analysis in combination with the temperature-humidity index (THI) calculated by meteorological data near the testing station. The average THI throughout the year was 76.6, and the highest was 82. The THI data were subsequently used to find the threshold point of heat stress. The THI equation used in this study was chosen by its highest correlation (-0.306) between THI values and monthly egg production. At a THI of 74, the lowest -2 logL was found and was considered the threshold point of heat stress. This means that monthly egg production would start decreasing when the THI was 74. Heritability was 0.15±0.03, and genetic and permanent environmental correlations were -0.29 and -0.48, respectively. The threshold point was used to estimate the estimated breeding values (EBVs) of the monthly egg production and heat stress individually, and EBVs were calculated into the selection index. The selection index values when the animal was selected for the replacement herd for all chickens (top 50%, 30%, 20%, and 10%) were 0.14, 0.90, 1.27, 1.53, and 1.91, respectively, and the genetic progress was 0.55, 0.60, 0.68, 0.75, and 0.77, respectively. This shows that the selection index values are lower if there are many selected animals. The recommendation for animal genetic selection is that the top 10% is appropriately because it seems to be most preferred. Therefore, using a selection index for high egg production and heat tolerance in Thai native chickens is possible to achieve genetic assessment in a large population.

Role of SNPs located in the exon 9 of ATAPA1 gene on goose egg production

The meat and egg of goose is one of the main components of human food supply. The improvement of goose egg production is particularly important for the increasing human population. However, limited information is available about the effective molecular markers and mechanisms of egg production in goose. In this study, we jointly utilized the data of genome resequencing in different egg production Sichuan white goose and transcriptome at different follicle development stages to identified the molecular markers and mechanisms of egg production. The coefficient of variation of individual egg production in Sichuan white goose population is 0.42 to 0.49. Fifty individuals with the highest (laying 365 days egg number, LEN365 = 79-145) and 50 individuals with the lowest (LEN365 = 8-48) egg production were divided into high and low egg production groups. Based on whole-genome sequencing data of the selected samples, 36 SNPs (annotation novel.12.470, CELF2, ATP1A1, KCNJ6, RAB4A, UST, REV3L, DHX15, CAVN2, SLC5A9, Cldn5, MRPS23, and Tspan2) associated with the LEN365 were identified, involving multiple pathways such as metabolism and endocrinology. Notably, 5 SNPs located in the exon9 of ATP1A1 were identified by GWAS analysis. The association analysis with LEN365 showed the phenotypic variance explained of this haplotype consisting of 5 SNPs is 20.51%. Through transcriptome data analysis, we found the expression of ATP1A1 in the granular layers was increased in the stage of small yellow follicle to large yellow follicle (LYF) and LYF to F5, while decreased in F2 to F1. For the first time, we report the haplotype region formed by 5 SNPS on exon9 of ATP1A1 is associated with egg production in goose and involved in follicle selection and maturation processes.

Genetic and phenotypic correlations among feed efficiency, immune and production traits in indigenous chicken of Kenya

This study aimed at estimating genetic and phenotypic relationships among feed efficiency, immune and production traits measured pre- (9-20 weeks of age) and post- (12 weeks from on-set of lay) maturity. Production traits were average daily gain (ADG) and average daily feed-intake (ADFI₁) in the pre-maturity period and age at first egg (AFE), average daily feed-intake (ADFI₂) and average daily egg mass (EM) in the post-maturity period. Feed efficiency comprised of residual feed intake (RFI) estimated in both periods. Natural antibodies binding to keyhole limpet hemocyanin (KLH-IgM) and specific antibodies binding to Newcastle disease virus (NDV-IgG) measured at 16 and 28 weeks of age represented immune traits pre- and post-maturity, respectively. In the growing period, 1,820 records on ADG, KLH-IgM and NDV-IgG, and 1,559 records on ADFI₁ and RFI were available for analyses. In the laying period, 1,340 records on AFE, EM, KLH-IgM and NDV-IgG, and 1,288 records on ADFI₂ and RFI were used in the analyses. Bi-variate animal mixed model was fitted to estimate (co)variance components, heritability and correlations among the traits. The model constituted sex, population, generation, line and genotype as fixed effects, and animal and residual effects as random variables. During the growing period, moderate to high heritability (0.36-0.68) was estimated for the production traits and RFI while the antibody traits had low (0.10-0.22) heritability estimates. Post-maturity, the production traits and RFI were moderately (0.30-0.37) heritable while moderate to high (0.25-0.41) heritability was estimated for the antibody traits. Genetic correlations between feed efficiency and production traits in both periods showed that RFI had negative genetic correlations with ADG (-0.47) and EM (-0.56) but was positively correlated with ADFI₁ (0.60), ADFI₂ (0.74) and AFE (0.35). Among immune and production traits, KLH-IgM and NDV-IgG had negative genetic correlations with ADG (-0.22; -0.56), AFE (-0.39; -0.42) and EM (-0.35; -0.16) but were positively correlated with ADFI₁ (0.41; 0.34) and ADFI₂ (0.47; 0.52). Genetic correlations between RFI with KLH-IgM (0.62; 0.33) and NDV-IgG (0.58; 0.50) were positive in both production periods. Feed intake, RFI and antibody traits measured in both production periods were positively correlated with estimates ranging from 0.48 to 0.82. Results from this study indicate selection possibilities to improve production, feed efficiency and immune-competence in indigenous chicken. The genetic correlations suggest that improved feed efficiency would be associated with high growth rates, early maturing chicken, high egg mass and reduced feed intake. In contrast, improved general (KLH-IgM) and specific (NDV-IgG) immunity would result in lower growth rates and egg mass but associated with early sexual maturation and high feed intake. Unfavorable genetic correlations between feed efficiency and immune traits imply that chicken of higher productivity and antibody levels will consume more feed to support both functions. These associations indicate that selective breeding for feed efficiency and immune-competence may have genetic consequences on production traits and should therefore be accounted for in indigenous chicken improvement programs.

Estimation of genetic parameters for production, reproduction, and growth curve of Fars indigenous chicken

Iranian native chicken, including Fars indigenous chicken, is an important genetic resource due to its adaptation to stressful environmental conditions, good endurance and resistance to disease. The aim of this research was to determine the genetic infrastructure of Fars indigenous chicken using several nonlinear functions. The dataset included body weight at hatch (BW1), body weight at the 8th week (BW8), body weight at the 12th week (BW12), weight at sexual maturity (WSM), age at sexual maturity (ASM), number of eggs in the first 12 weeks of laying period (EN), egg weight at the first day of laying (EW1), average egg weight at the 28thday of laying (EW28), and average egg weight at weeks 28, 30, and 32 of the laying period (AEW). Growth models were fitted using the NLIN procedure and WOMBAT software was used to predict variance components for the best fit model parameters. Results suggested three-parameter models, for example, Gompertz, fitted better to the data than others. The maturity weight (A), initial weight (B), and maturity rate (K) parameters in the Gompertz model were 1996.8 ± 6.63, 4.11 ± 0.03, and 0.021 ± 0.0001, respectively. The heritability of A, B, and K parameters were 0.03, 0.05, and 0.12, respectively.

Genetic Comparisons of Body Weight, Average Daily Gain, and Breast Circumference between Slow-Growing Thai Native Chickens (Pradu Hang dum) Raised On-Site Farm and On-Station

To ensure that any new technology developed within an experimental station is appropriate to the community’s needs and compatible with the existing systems, on-site farm research is an important component in examining the effectiveness of agricultural research. The present study examined the growth performance and genetics of Thai native chickens under conditions typically experienced by farmers on smallholder farms (on-site farms) compared with at an experimental unit (on-station). There were 1694 Thai native chickens (Pradu Hang dum) used in this experiment, and they were divided into 613 chickens for the on-station and 1081 chickens for the on-site farm experiments. The individual chicken data included the birth weight (BW0) and body weight at 4, 8, 12, and 16 weeks of age (BW4, BW8, BW12, and BW16, respectively), ADG from 0−4, 4−8, 8−12, 12−16 weeks of age (ADG0−4, ADG4−8, ADG8−12, ADG12−16, respectively), and breast circumference at 8, 12, and 16 weeks of age (BrC8, BrC12, BrC16, respectively). A multiple traits animal model and a selection index were used to estimate the variance components, genetic parameters, and breeding values of growth traits. The results showed that the body weight, average daily gain, and breast circumference at 8, 12, and 16 weeks of age of Thai native chickens raised on-station were higher than those raised on-site at the farm among mixed-sex and sex-segregated chickens, while the birth weight and body weight at four weeks of age (BW0 and BW4) and ADG from 0−4 weeks of age (ADG0−4) were not significantly different (p > 0.05). The heritability estimates of body weight, average daily gain, and breast circumference in the chickens raised at the on-site farm and on-station were moderate to high, with on-station values slightly higher than on-site farm values. The heritability estimates of body weight were 0.236 to 0.499 for the on-site farm, and 0.291 to 0.499 for on-station. For average daily gain, the heritability estimates were 0.274 to 0.283 for the on-site farm and 0.298 to 0.313 for on-station; meanwhile, and for breast circumference, the heritability estimates were 0.204 to 0.268 for the on-site farm and 0.278 to 0.296 for on-station. Both phenotypic and genetic correlations among and between growth traits were positive and ranged from low to high values. The top 20% of the estimated breeding values and selection indices in the on-site farm and on-station experiments showed that the body weight at eight weeks of age (BW8), ADG from 4−8 weeks of age (ADG4−8), and breast circumference at eight weeks of age (BrC8) should be used as selection criteria for Thai native chicken breeding programs. In conclusion, the genetic parameters and breeding values in on-station experiments showed that the breeding program by selection index for improving growth performance is valid. Therefore, to implement such a breeding program in an on-site farm, an intensive or semi-intensive farm system should be considered to minimize the effect of genotype-environment interaction.

Feed and nutrient utilization efficiency and juvenile traits of Vezaguda chicken of Odisha in floor rearing system

A study was conducted to evaluate the performance of Vezaguda, an indigenous chicken population of Odisha, up to 8 weeks of age in floor rearing system. Unsexed day-old chicks (100) were selected for this study. Mortality and feed intake were recorded daily while body weight was recorded weekly. Body conformation traits such as shank length, shank circumference, shank width, thigh length, chest girth, keel length, body length, height, back length, wing length, folded wing length, wing span, neck length, head length, skull length, head width, beak length and breast angle were measured at 6th and 8th weeks of age. The 8th week body weight of male and female chicks were 501.58±21.64 g and 423.35±13.44 g, respectively. The cumulative feed conversion ratio (FCR), energy efficiency ratio (EER), and protein efficiency ratio (PER) at 8th week were 4.00±0.06, 8.73±0.12, and 1.25±0.02, respectively. An index of productivity, production efficiency factor (PEF) was calculated taking into account final weight, liveability %, age of the bird and FCR. The PEF at 8th week was 16.38±0.46. At 6th week of age, all recorded conformation traits were higher in male chicks than that of female chicks. At 8th week of age, chest girth, skull length and beak length were significantly higher in male chicks than that of female chicks.

Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia)

The Tigray region is an ancient entry route for the domestic chickens into Africa. The oldest African chicken bones were found in this region at Mezber, a pre-Aksumite rural farming settlement. They were dated to around 800–400 BCE. Since then, the farming communities of the region have integrated chicken into their livelihoods. The region is also recognised for its high chicken-to-human population ratio and diverse and complex geography, ranging from 500 to 4,000 m above sea level (m.a.s.l.). More than 15 agro-ecological zones have been described. Following exotic chicken introductions, the proportion of indigenous chicken is now 70% only in the region. It calls for the characterisation of indigenous Tigrayan chicken ecotypes and their habitats. This study reports an Ecological Niche Modelling using MaxEnt to characterise the habitats of 16 indigenous village chicken populations of Tigray. A total of 34 ecological and landscape variables: climatic (22), soil (eight), vegetation, and land cover (four), were included. We applied Principal Component Analysis correlation, and MaxentVariableSelection procedures to select the most contributing and uncorrelated variables. The selected variables were three climatic (bio5 = maximum temperature of the warmest month, bio8 = mean temperature of the wettest quarter, bio13 = precipitation of the wettest month), three vegetation and land cover (grassland, forest land, and cultivated land proportional areas), and one soil (clay content). Following our analysis, we identified four main chicken agro-ecologies defining four candidates indigenous Tigrayan chicken ecotypes. The study provides baseline information for phenotypic and genetic characterisation as well as conservation interventions of indigenous Tigrayan chickens.

Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions

Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.

Comparative Study of Phenotypes and Genetics Related to the Growth Performance of Crossbred Thai Indigenous (KKU1 vs. KKU2) Chickens under Hot and Humid Conditions

To improve the body weight and growth performance traits of crossbred Thai indigenous chickens, phenotypic performance and genetic values were estimated. Crossbred Thai indigenous chickens, designated KKU1 and KKU2, were compared. The data included 1375 records of body weight (BW0, BW2, BW4, and BW16), breast circumference at 6 weeks of age (BrC6), and average daily gain (ADG0−2, ADG0−4, and ADG0−6). A multi-trait animal model with the average information-restricted maximum likelihood (AI-REML) was used to estimate the genetic parameters and breeding values. The results showed that the body weight and breast circumference traits (BW2, BW4, BW6, and BrC6) for the mixed sex KKU1 chickens were higher than for the KKU2 chickens (p < 0.05). For the growth performance traits, the KKU1 chickens had higher average daily gain and feed intake and a lower feed conversion ratio than the KKU2 chickens (p < 0.05). The survival rates were not different except at up to 6 weeks of age, when that of the KKU1 chickens was slightly lower. The specific combining ability, heritability, genetic and phenotypic correlations, and estimated breeding values showed that the KKU1 chickens had better genetics than the KKU2 chickens. In conclusion, KKU1 chickens are suitable for development as crossbred Thai indigenous chickens for enhanced growth performance and for commercial use.

Genetic parameters of growth traits, trend of production and reproduction traits, and meat quality status of Ghagus, an indigenous chicken of India

Indigenous chickens play a vital role in providing nutritional security and economic support for the rural and tribal people in tropical countries like India. Ghagus, an indigenous chicken breed of India, was characterized for growth, production, and reproduction (fertility and hatchability) traits over different generations and for carcass and meat quality traits. Heritability, and genetic and phenotypic correlations among growth traits were estimated using mixed model least squares and maximum likelihood methods. Estimates of heritability of growth traits such as bodyweights at different age and 8-week shank length were high (0.32 to 0.39) in initial generation and moderate to high during latest generation (0.20 to 0.42). The correlations of growth traits with 40-week egg production were positive and significant (P < 0.001). There was improvement in 8-week bodyweight (559.3 ± 4.40 g) by 177 g over the generations. The average egg production up to 40 weeks over the generations was 35.66 eggs. There was also a significant (P < 0.001) increase in egg weights over the generations. The fertility (mean 89.3%) ranged from 85.2 to 92.3%. The hatchability on fertile egg set (mean 90.8%) ranged from 86.5 to 94.1% and it was improved by 3.9% over the generations. The carcass and meat quality study revealed that this breed has the lean meat, high protein, and attractive meat color with desirable meat quality characteristics. The study concluded that the Ghagus breed with self-propagation capacity has the potential to be improved as an indigenous meat-type breed to meet the ever-increasing demand for indigenous chickens' meat in the country.

Genetic Evaluation of Body Weights and Egg Production Traits Using a Multi-Trait Animal Model and Selection Index in Thai Native Synthetic Chickens (Kaimook e-san2)

To improve the genetics of both growth and egg production, which are limitations in purebred native chickens, new genetic lines can be developed using an appropriate genetic approach. The data used in this study included 2713 body weight (BW0, BW4, BW6, BW8, and BW10), breast circumference (BrC6), chicken age at first egg (AFE), and egg production (240EP, 270EP, 300EP, and 365EP) records covering the period 2015 to 2020. A multi-trait animal model with the average information-restricted maximum likelihood (AI-REML) and a selection index was used to estimate the variance components, genetic parameters, and breeding values. The results showed that males had significantly higher weights than females (p < 0.05) from 4 to 10 weeks of age and that this difference increased over the generations. The differences between BW0 and BrC6 by sex and generation were not significant (p > 0.05). The estimated heritability of body weight ranged from 0.642 (BW0) to 0.280 (BW10); meanwhile, the estimated heritability of BrC6 was moderate (0.284). For egg production traits, the estimated heritability of 240EP, 270EP, 300EP, and 365EP was 0.427, 0.403, 0.404, and 0.426, respectively, while the estimated heritability of AFE was 0.269. The genetic and phenotypic correlations among the growth traits (BW0 to BW10) were low to highly positive. The genetic and phenotypic correlations between growth (BW0 to BW10) and BrC6 traits were positive, and the genetic correlations between BW6 (0.80), BW8 (0.84), BW10 (0.93), and BrC6 were strongly positive. Genetic correlations among the egg production traits (240EP, 270EP, 300EP, and 365EP) were low to highly positive and ranged from 0.04 to 0.86. The genetic correlations between AFE and all egg production traits were low to moderately negative and ranged from −0.14 to −0.29. The positive genetic correlations between body weight (BW6, BW8, and BW10) and egg production traits were found only in 240EP. The average genetic progress of body weight traits ranged from −0.38 to 30.12 g per generation for BW0 to BW10 (p < 0.05); the genetic progress was 0.28 cm per generation for BrC6 (p > 0.05). The average genetic progress of cumulative egg production traits ranged from 4.25 to 12.42 eggs per generation for 240EP to 365EP (p < 0.05), while the average genetic progress of AFE was −7.12 days per generation (p < 0.05). In conclusion, our study suggests that the body weight at six weeks of age (BW6), breast circumference at six weeks of age (BrC6), cumulative egg production at 240 days of age (240EP), and age at first egg (AFE) are the traits that should be used as selection criteria, as they have a positive effect on the development of growth and egg production.

Genetic parameters for production traits in F1 reciprocal crossbred Chee Fah and Fah Luang chickens

ContextRecently, Chee Fah and Fah Luang chickens have been registered as a black-bone native chicken in Thailand. Only a few studies revealed genetic information about them. No publication has reported any data related to their cross-mating, particularly, genetic parameters.AimsThis study aimed to estimate genetic parameters for production traits of F1 generation of reciprocal crossbred Chee Fah and Fah Luang chickens.MethodsA dataset of production traits of two crossbred groups was used in the present study. Effects of breed, month-day of incubation and sex were tested at P&lt;0.05. Genetic parameters were estimated using the restricted maximum likelihood method with multi-trait animal model.Key resultsThe crossbred Chee Fah×Fah Luang was significantly heavier and consumed more feed than Fah Luang×Chee Fah (P&lt;0.05). Male chickens had significantly better 20-week-old bodyweight, feed conversion ratio and average daily gain compared with females for both crossbred groups (P&lt;0.05). The effect of month-day of incubation had a significant influence on production traits (P&lt;0.05), except for day-old bodyweight. Heritabilities for production traits of crossbred chickens were low to high. The highest estimate was observed for day-old bodyweight (0.97), followed by feed intake (0.40), 20-week-old bodyweight (0.06), average daily gain (0.05) and feed conversion ratio (0.03), respectively. Both positive and negative genetic correlations were found among their production traits. Favourable relationships were found between average daily gain versus bodyweight and versus feed conversion ratio (rgg=0.99 and −0.90, respectively). Similarly, production traits showed phenotypic correlations in both directions, which ranged from −0.95 to 0.99.ConclusionsHeritability estimations for production traits were found in low to high magnitude. The desirable genetic relationships were found between feed conversion ratio and day-old bodyweight, 20-week-old bodyweight and average daily gain, and between 20-week-old bodyweight and average daily gain.ImplicationsThese findings could be considered as a source of genetic data for enhancing production traits of crossbred black-bone native chickens.

Analysis of (co) variance components and estimation of breeding value of growth and production traits in Dahlem Red chicken using pedigree relationship in an animal model

Variance and covariance components of growth and production traits were analyzed employing REML animal model to assess the Dahlem Red (PD-3) chicken population for direct additive genetic, maternal effects and to estimate the estimated breeding value (EBV), genetic parameters, genetic trends and rate of inbreeding (ΔF) utilizing seven generation’s data. The generation and hatch had significant (P≤0.01) effect on the body weight at 0 day (BW0), 2 (BW2), 4 (BW4) and 6 weeks (BW6) and shank length at six weeks of age (SL6). The average least squares means (LSM) for BW6 and SL6 were 273.93±0.62 g and 53.97±0.05 mm, respectively. All the production traits were significantly (P≤0.01) influenced by generation and hatch. The average LSM for age at sexual maturity (ASM), egg production up to 40 weeks (EP40) and egg mass up to 40 weeks (EM40) were 168.82±0.25 d, 72.60±0.41 eggs and 4.21±0.07 kg, respectively. Model 5 with additive direct, maternal genetic, maternal permanent environmental and residual variance components was the best for BW0, BW2 and BW4 based on the AIC values obtained in WOMBAT. Model 4 was the best model for BW6, SL6, ASM, EP40 and EM40 with additive direct, maternal permanent environmental and residual variance components. Maternal effects were higher during early age, decreased with age, and remained present until 20 weeks of age. The heritability (h²) estimates were low to moderate in magnitude for all the growth traits and ranged from 0.02±0.03 to 0.19±0.03. The maternal heritability was high at hatch (0.35±0.06), decreased gradually until 4^th week (0.02±0.01) and ceased afterwards. The heritabilities of EP40 (0.11±0.03) and EM40 (0.12±0.04) were low. The direct additive genetic correlations (r_a) between BW2, BW4, BW6 and SL6 were high and positive (P≤ 0.05). The additive genetic and maternal permanent environmental correlation between EP40 and EM40 were high and positive (P≤ 0.05). The EBV of EM40 was significant (P≤ 0.05) with 0.48 kg/generation in PD-3 chicken at the end of the seventh generation. The EBV of EP40 showed an increasing trend with a genetic gain of 1.87 eggs per generation. The average inbreeding coefficient of the population was 0.019 and average ΔF was 0.007 over the last seven generations of selection. The EBV trends for primary and associated traits showed linear trends in the desired direction and negligible inbreeding.

The Effects of Weather on Avian Growth and Implications for Adaptation to Climate Change

Climate change is forecasted to generate a range of evolutionary changes and plastic responses. One important aspect of avian responses to climate change is how weather conditions may change nestling growth and development. Early life growth is sensitive to environmental effects and can potentially have long-lasting effects on adult phenotypes and fitness. A detailed understanding of both how and when weather conditions affect the entire growth trajectory of a nestling may help predict population changes in phenotypes and demography under climate change. This review covers three main topics on the impacts of weather variation (air temperature, rainfall, wind speed, solar radiation) on nestling growth. Firstly, we highlight why understanding the effects of weather on nestling growth might be important in understanding adaptation to, and population persistence in, environments altered by climate change. Secondly, we review the documented effects of weather variation on nestling growth curves. We investigate both altricial and precocial species, but we find a limited number of studies on precocial species in the wild. Increasing temperatures and rainfall have mixed effects on nestling growth, while increasing windspeeds tend to have negative impacts on the growth rate of open cup nesting species. Thirdly, we discuss how weather variation might affect the evolution of nestling growth traits and suggest that more estimates of the inheritance of and selection acting on growth traits in natural settings are needed to make evolutionary predictions. We suggest that predictions will be improved by considering concurrently changing selection pressures like urbanization. The importance of adaptive plastic or evolutionary changes in growth may depend on where a species or population is located geographically and the species’ life-history. Detailed characterization of the effects of weather on growth patterns will help answer whether variation in avian growth frequently plays a role in adaption to climate change.

Inheritance of growth traits and impact of selection on carcass and egg quality traits in Vanashree, an improved indigenous chicken

The present study was carried out to assess the inheritance of growth traits and to study the effect of selection on carcass characteristics and egg quality traits in Vanashree, an improved indigenous chicken. Estimates of heritability were high for body weights recorded at 4, 5 and 6 weeks of age and 8th week shank length, while it was moderate for 8th week body weight. Estimates of heritability on sire component of variance declined as age increased from 4 to 8 weeks of age. The genetic and phenotypic correlations among various growth traits were positive and high in magnitude. The body weight continued to increase up to 40 weeks of age particularly in male birds, while there was little increase in shank length from 20 to 40 weeks of age particularly in hens. There was no significant change in carcass characteristics and egg quality traits except that there was some improvement in dressing percentage over the generations. Sex effect was significant on relative weights of the breast, legs, gizzard, liver and heart and abdominal fat percentage. There was increase in Haugh unit and albumen index, yolk percentage, yolk to albumen ratio and yolk colour in the present generation. The results suggest that there is adequate additive genetic variation for growth traits in the population and that Vanashree chicken could continue to be improved so as to make it a promising dual purpose purebred indigenous chicken for increasing the productivity of free range or semi-intensive systems of production.

Estimation of additive genetic, dominance, and mate sire variances for fertility traits in Thai native (Pradu Hang Dam) chickens

The objective of this study was to compare the appropriate models used to estimate the value of genetic parameters in fertility traits: fertility (FER), hatchability of fertile eggs (HOF), and hatchability of eggs set (HOS) in Thai native (Pradu Hang Dam) chickens. Data were collected for each fertility trait from 3435 test-week records from 715 hens, 158 mate sires, and 972 pedigree animals. Three random regression models were analyzed: model 1 (M1: A + PE) was adjusted by using additive genetic and permanent environmental effects. Model 2 (M2: A + PE + D) was adjusted by using the dominance effect. Finally, model 3 (M3: A + MS + PE + D) was adjusted by using the mate sire effect. The results found the low heritability of FER (M1 to M3), HOF (M1 to M3), and HOS (M1 to M3) ranged from 0.031-0.040, 0.037-0.066, and 0.040-0.059, respectively. Adjustment for the dominance and mate sire effects in M3 reduced the upward bias in heritability and improved the accuracy of variance component estimates compared to M1 and M2. In conclusion, the genetic evaluation for FER, HOF, and HOS can include the dominance and MS effects to increase the accuracy of evaluation of breeding values and plan for mate selection in breeding programs.

Estimation of breeding value, genetic parameters and maternal effects of economic traits in rural male parent line chicken using pedigree relationships in an animal model

Breeding value (BV), genetic parameters and additive genetic, and maternal effects were evaluated on growth and production traits utilizing data from eight generations employing animal model in a rural male parent line (PD-6) chicken at ICAR-Directorate of Poultry Research, Hyderabad, India. The least squares means (LSM) for body weight (BW) and shank length (SL) up to 6 weeks of age varied significantly (p ≤ .01) among the generations and hatches. BW increased significantly (p ≤ .01) over the generations and decreased with the hatches. Sex also had a significant effect on BW and shank length except for BW at 0 day (BW0). LSM for BW (BW6) and Shank length (SL6) at 6 weeks of age were 598.84 ± 0.79 g and 74.57 ± 0.04 mm, respectively. Males recorded significantly (p ≤ .01) higher BWs and shank length. All the production traits were significantly (p ≤ .01) influenced by the generation effect. The overall LSM for age at sexual maturity (ASM), egg production at 40 weeks (EP40) and egg weight at 40 weeks (EW40) were 164.93 ± 0.23 days, 74.66 ± 0.40 eggs and 54.79 ± 0.08 g, respectively. Model 3 with additive, maternal permanent environmental and residual effects was the appropriate model for BW2, BW4, BW6, SL4 and SL6, whereas Model 4 with maternal effects was the best for BW0. The heritability estimates for BW6 and SL6 were 0.22 ± 0.02 and 0.18 ± 0.02, respectively. Model 1 with additive direct and residual effects was the best appropriate model for all the production traits. The heritability estimates of EP40 and EW40 were 0.16 ± 0.04 and 0.34 ± 0.05, respectively. BW and shank length were highly correlated with significant (p ≤ .05) positive association from different components. The correlation coefficient from direct additive component between egg production and BW40 was negative, while it was positive with less magnitude between egg production and BW20. The egg production and egg weights had a negative association at different ages. BV of SL6, the primary trait of selection, was significant (p ≤ .05) across the generations and increased linearly with an average genetic gain of 1.05 mm per generation. BV of BW6 was also significant (p ≤ .05) and increased linearly as correlated response with an average genetic response of 22.34 g per generation. BV of EP40 showed an increasing trend with a genetic gain of 0.02 eggs per generation. The EW 40 also increased linearly with an average genetic gain of 0.06 g. The average inbreeding coefficient of the population was 0.015. The study concluded that the population was in ideal status with a linearly increasing trend of average BV with negligible inbreeding over the eight generations of selection.

Local Chicken Breeds of Africa: Their Description, Uses and Conservation Methods

There has been a research gap in the genetic, physiological, and nutritional aspects of indigenous chickens of Africa over the past decade. These chickens are known to be economically, socially, and culturally important to the people of Africa, especially those from marginalised communities. Although they are associated with poor productivity in terms of the number of eggs laid, most consumers prefer their flavoursome meat. Several local chickens have been classified into breeds or ecotypes, but many remain unidentified and are facing extinction. To prevent this, the Food and Agriculture Organization has launched an indigenous poultry conservation programme. In addition, the Agricultural Research Council in South Africa has established a programme to protect four local chicken breeds. The purpose of this review is to provide a detailed understanding of the description, uses and conservation methods of local chicken breeds of Africa. Several studies have been conducted on the nutritional requirements of local chickens, but the results were inconclusive and contradictory. This review concludes that local chickens play a significant role in improving livelihoods, and strategies to preserve and sustain them must be intensified.

Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens

Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek's Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity [body weight and body condition score (BCS)]. Combined data from the two chicken ecotypes, Horro (n = 384) and Jarso (n = 376), were jointly analyzed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22-0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection.

Multiphasic nonlinear mixed growth models for laying hens

Appropriate evaluation of BW and gain during rearing is required for optimal extended laying performance in laying hens. The objective of this study was to compare monophasic, diphasic, and triphasic Gompertz and logistic models describing BW and gain in individually fed free-run laying hens and to study the variation between individuals in shape parameters. Fifteen Lohmann Brown Lite hens were fed ad libitum from week 0 to 43 with a precision feeding system, measuring feed intake and BW individually in a group housed setting. Random variables related to mature weight and timing of maximum gain during the pubertal growth phase were introduced into the multiphasic model for BW with the best fit. For both the weight-age and gain-age functions, the diphasic and triphasic Gompertz and logistic model models fitted the data better than the monophasic models. The Gompertz model was able to identify the ages at the highest gain at similar time points for both BW and gain, whereas the logistic models failed to do so. The derivative of the multiphasic Gompertz models for the gain-age relationship identified age at the highest gain at similar ages as compared with the logistic models for gain. The mixed models predicted that the individual mature BW ranged from 1.83 kg to 2.10 kg and the variability in the timing of the highest rate of gain during the pubertal growth spurt ranged from 15.26 wk to 19.79 wk. Including random terms associated with the mature BW and the second inflection point of the diphasic Gompertz growth model allowed for identification of variability in the growth curve shape between individuals, which can be a tool to study the relationship between the individual growth curve shape and performance parameters.

Evaluation of growth performance of Sasso and Kuroiler chickens fed three diets at varying levels of supplementation under semi-intensive system of production in Tanzania

The experiment was conducted to evaluate the effect of breed, diet, and level of feed supplementation on growth performance, feed conversion ratio, and survivability of Sasso and Kuroiler chicken. The study was conducted in two separate phases, i.e., the starter phase (0-6 weeks of age) and grower phase (6-20 weeks of age). One thousand sixty-day-old Sasso and Kuroiler chicks were raised until 6 weeks under intensive management system with three dietary treatments. At the age of 6 weeks, a total of 960 birds (480 Sasso and 480 Kuroiler) were randomly selected from each treatment diet and assigned to four feed supplementation levels, i.e., 25%, 50%, 75%, and 100% with two replicates each having 20 birds. Beginning week 7, birds were allowed to semi-scavenge from 6:00 am in the morning to 6:00 pm in the evening with free access to open grass area of 1 bird/4 m². Grower rations based on the three categories, i.e., commercial, medium-cost, and low-cost formulation, were fed from 7th to the 20th week of age. During 0 to 6 weeks of the growing phase, the breed and diet significantly (p < 0.05) influenced 6-week live weight, live weight gain, and feed conversion ratio. Birds given commercial diet (D1) excelled in live weight, total live weight gains, and feed conversion ratio followed by medium-cost (D2) and low-cost (D3) diet respectively. During the 7th to 20th weeks of the growing phase, the breed, diet, and supplementation levels had a significant influence (p < 0.05) on the live weight and weight gain at 20 weeks of age. Feed cost per kilogram gain increased with an increase in the level of supplementation. Days taken by birds to reach market weight (2 kg) with 100%, 75%, 50%, and 25% level of dietary supplementation were 16, 18, 20, and more than 20 weeks respectively. The survival rate for Sasso and Kuroiler was 99.80% and 97.13% respectively. It is concluded that appreciable growth performance can be attained for semi-scavenging Sasso and Kuroiler chickens when supplemented with medium- or low-cost diets at the level of 50 to 75% of their daily feed requirements.

Using random regression models to estimate genetic variation in growth pattern and its association with sexual maturity of Thai native chickens

1. Genetic (co)variances and parameters between body weights (BW) across the growth trajectory were estimated using a univariate random regression (RR) animal model. The effect of growth rates (GH) on age at first egg (AFE) and egg weight at first egg (EWFE) were explored using a series of univariate and bivariate analyses. 2. Body weights were taken from Thai native chickens at hatch day to 168 days of age. The model included interactions between age with hatch nested within year and sex as fixed effects, and random effects of direct additive genetic, direct permanent environmental, maternal genetic and maternal permanent environmental effects. All random effects were fitted as regressions to animals' age via quadratic Legendre polynomials and fitting six classes of residual variances was identified as an optimal variance structure to estimate parameters. 3. Genetic and phenotypic variances for BW increased with increasing age. Estimated heritabilities for direct additive (h² _a) and maternal genetic (h² _m) effects on BW traits ranged from 0.34 to 0.54, and 0.04 to 0.06, respectively. Estimated variance ratios for direct (c² _ape) and maternal permanent environmental (c² _mpe) effects ranged from 0.19 to 0.48 and 0.10 to 0.12, respectively. Estimated correlations between weights at different ages were high for all random effects. 4. Estimated h² _a for six GH traits ranged from 0.06 to 0.28, while for AFE and EWFE these were 0.24 and 0.16, respectively. Estimated h² _m and c² _mpe were low for GH. Estimated genetic correlations between GH and AFE ranged from -0.22 to 0.02 and, between GH and EWFE, ranged from -0.05 to 0.40. These estimates suggested that selecting high GH chickens at 28 days of age can be expected to reduce AFE and to increase EWFE.

Quantifying the effect of inbreeding on average daily gain and Kleiber ratio in Mazandaran native chickens

The aims of this study was to evaluate inbreeding effects for growth rate (average daily gain from hatch to 8 weeks of age (ADG1-8), average daily gain from hatch to 12 weeks of age (ADG1-12), average daily gain from 8 weeks of age to 12 weeks (ADG8-12), average daily gain from hatch to sex maturity (ADG1-SM), average daily gain from 8 weeks of age to sex maturity (ADG8-SM), average daily gain from 12 weeks to sex maturity (ADG12-SM), and Kleiber ratios (KR1-8, KR1-12, KR8-12) in Mazandaran native chickens. The data set of 82,446 pedigreed individuals over 21 generations was analyzed. All individuals were grouped into three classes based on the inbreeding coefficient: First class contained non-inbred birds (F = 0) and second and third classes contained inbred individuals (0 < F ≤ 5% and F > 5%, respectively). The effects of inbreeding coefficient on the studied traits were estimated by the restricted maximum likelihood method (REML) applying the WOMBAT software and fitting individual increase in inbreeding coefficient (ΔFi) of birds as linear covariates under 6 different animal models. ADG8-SM and ADG12-SM increased non-significantly by 0.003 and 0.005 g, respectively, due to 1% increase in ΔFi, while ADG1-8, ADG1-12, ADG8-12, ADG1-SM, KR1-8, and KR1-12 decreased (P < 0.001), respectively, by 0.012 g, 0.011 g, 0.010 g, 0.014 g, 0.003 g, and 0.002 g. Also, KR8-12 non-significantly decreased by 0.001 g. Estimates of direct heritability of traits based on the most appropriate models ranged from 0.05 (KR8-12) to 0.26 (ADG12-SM). Results showed that it is important to regularly analyze inbreeding level in the herd in an attempt to prevent the reduction of performance.

Estimation of heritability and genetic correlation of egg production traits using animal model in commercial layer

Traditionally, heritability has been estimated by correlations of close kin. It is likely to be biased by determinants such as non genetic factors, inbreeding, selection and shared environment. Whereas, an animal model takes into account all relationships in a pedigree and is therefore expected to provide estimates of quantitative genetic parameters with higher precision. Therefore, the egg production data in the current study was analyzed using animal model to have more precise and accurate estimates of genetic parameters. The heritability of growth and egg weight traits was moderate to high. Whereas the heritability was lower for egg number and ASM traits. The body weights were positively correlated with egg weights and negatively correlated with egg numbers traits. The egg number produced at different age intervals was positively correlated. The genetic correlation of EP40 and EP52 with EP64 were 0.83 and 0.92, respectively. Therefore, the part period egg production of EP52 would give better selection response for egg production at 64 than EP40. Therefore, the selection of higher egg numbers can be done earlier at 52 weeks rather than waiting for EP64.

Genetic analysis on body weight at different ages in broiler chicken raised in commercial environment

A multivariate model was developed and used to estimate genetic parameters of body weight (BW) at 1-6 weeks of age of broilers raised in a commercial environment. The development of model was based on the predictive ability of breeding values evaluated from a cross-validation procedure that relied on half-sib correlation. The multivariate model accounted for heterogeneous variances between sexes through standardization applied to male and female BWs differently. It was found that the direct additive genetic, permanent environmental maternal and residual variances for BW increased drastically as broilers aged. The drastic increase in variances over weeks of age was mainly due to scaling effects. The ratio of the permanent environmental maternal variance to phenotypic variance decreased gradually with increasing age. Heritability of BW traits ranged from 0.28 to 0.33 at different weeks of age. The direct genetic effects on consecutive weekly BWs had high genetic correlations (0.85-0.99), but the genetic correlations between early and late BWs were low (0.32-0.57). The difference in variance components between sexes increased with increasing age. In conclusion, the permanent environmental maternal effect on broiler chicken BW decreased with increasing age from weeks 1 to 6. Potential bias of the model that considered identical variances for sexes could be reduced when heterogeneous variances between sexes are accounted for in the model.

Use of genomic information to exploit genotype-by-environment interactions for body weight of broiler chicken in bio-secure and production environments

BACKGROUND

The increase in accuracy of prediction by using genomic information has been well-documented. However, benefits of the use of genomic information and methodology for genetic evaluations are missing when genotype-by-environment interactions (G × E) exist between bio-secure breeding (B) environments and commercial production (C) environments. In this study, we explored (1) G × E interactions for broiler body weight (BW) at weeks 5 and 6, and (2) the benefits of using genomic information for prediction of BW traits when selection candidates were raised and tested in a B environment and close relatives were tested in a C environment.

METHODS

A pedigree-based best linear unbiased prediction (BLUP) multivariate model was used to estimate variance components and predict breeding values (EBV) of BW traits at weeks 5 and 6 measured in B and C environments. A single-step genomic BLUP (ssGBLUP) model that combined pedigree and genomic information was used to predict EBV. Cross-validations were based on correlation, mean difference and regression slope statistics for EBV that were estimated from full and reduced datasets. These statistics are indicators of population accuracy, bias and dispersion of prediction for EBV of traits measured in B and C environments. Validation animals were genotyped and non-genotyped birds in the B environment only.

RESULTS

Several indications of G × E interactions due to environmental differences were found for BW traits including significant re-ranking, heterogeneous variances and different heritabilities for BW measured in environments B and C. The genetic correlations between BW traits measured in environments B and C ranged from 0.48 to 0.54. The use of combined pedigree and genomic information increased population accuracy of EBV, and reduced bias of EBV prediction for genotyped birds compared to the use of pedigree information only. A slight increase in accuracy of EBV was also observed for non-genotyped birds, but the bias of EBV prediction increased for non-genotyped birds.

CONCLUSIONS

The G × E interaction was strong for BW traits of broilers measured in environments B and C. The use of combined pedigree and genomic information increased population accuracy of EBV substantially for genotyped birds in the B environment compared to the use of pedigree information only.

Improvement of PD-4 (Aseel), an indigenous chicken, for growth and production traits

Backyard poultry production plays a vital role in providing animal protein at affordable and sustainable manner. Growth and production potential of indigenous chicken need to be improved through selective breeding to enhance the productivity of backyard farming. PD-4 birds (Aseel, indigenous breed) were subjected to selection for higher body weight over eight generations. Study investigated effect of selection on the performance of PD-4 birds with respect to economic traits. There was significant improvement in body weight and shank length at 8 weeks of age. Egg production up to 40 weeks had improved by 19.1 eggs. Egg weight at 28, 32, 36 and 40 weeks of age improved by 0.8, 1.3, 1.7 and 1.3 g respectively. Age at sexual maturity had declined by 14.2 days. There was no significant change in fertility and hatchability traits. Survivors’ egg production up to 72 weeks of age was 156.5±2.79 eggs while hen day and hen housed egg production were 144.9 and 137.5 eggs respectively. Egg weight consistently improved from 35.13 g at age at first egg to 48.07 g at 40 weeks and to 49.63 g at 72 weeks of age. The study demonstrated that indigenous chickens could be improved for body weight and egg production without affecting other economic traits and improved PD-4 variety has the potential to be used as improved dual purpose indigenous chicken variety for low input backyard poultry farming.

Genetic parameters and inbreeding effects for production traits of Thai native chickens

Objective

Estimate genetic parameters, the rate of inbreeding, and the effect of inbreeding on growth and egg production traits of a Thai native chicken breed Lueng Hang Kao Kabinburi housed under intensive management under a tropical climate.

Methods

Genetic parameters were estimated for weight measured at four weekly intervals from body weight at day 1 (BW1D) to body weight at 24 weeks (BW24) of age, as well as weight at first egg, age at first egg (AFE), egg weight at first egg, and total number of eggs (EN) produced during the first 17 weeks of lay using restricted maximum likelihood. Inbreeding depression was estimated using a linear regression of individual phenotype on inbreeding coefficient.

Results

Direct additive genetic effect was significant for all traits. Maternal genetic effect and permanent environmental hen effects were significant for all early growth traits, expect for BW24. For BW24, maternal genetic effect was also significant. Permanent environmental hen effect was significant for AFE. Direct heritabilities ranged from 0.10 to 0.47 for growth traits and ranged from 0.15 to 0.16 for egg production traits. Early growth traits had high genetic correlations between them. The EN was lowly negatively correlated with other traits. The average rate of inbreeding for the population was 0.09% per year. Overall, the inbreeding had no effect on body weight traits, except for BW1D. An increase in inbreeding coefficient by 1% reduced BWID by 0.09 g (0.29% of the mean).

Conclusion

Improvement in body weight gain can be achieved by selecting for early growth traits. Selection for higher body weight traits is expected to increase the weight of first egg. Due to low but unfavorable correlations with body weight traits, selection on EN needs to be combined with other traits via multi-trait index selection to improve body weight and EN simultaneously.

Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models

1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

Estimation of heritability and genetic correlation of body weight gain and growth curve parameters in Korean native chicken

Objective

This study estimated the genetic parameters for body weight gain and growth curve parameter traits in Korean native chicken (KNC).

Methods

A total of 585 F₁ chickens were used along with 88 of their F₀ birds. Body weights were measured every 2 weeks from hatching to 20 weeks of age to measure weight gain at 2-week intervals. For each individual, a logistic growth curve model was fitted to the longitudinal growth dataset to obtain three growth curve parameters (α, asymptotic final body weight; β, inflection point; and γ, constant scale that was proportional to the overall growth rate). Genetic parameters were estimated based on the linear-mixed model using a restricted maximum likelihood method.

Results

Heritability estimates of body weight gain traits were low to high (0.057 to 0.458). Heritability estimates for α, β, and γ were 0.211±0.08, 0.249±0.09, and 0.095±0.06, respectively. Both genetic and phenotypic correlations between weight gain traits ranged from −0.527 to 0.993. Genetic and phenotypic correlation between the growth curve parameters and weight gain traits ranged from −0.968 to 0.987.

Conclusion

Based on the results of this study population, we suggest that the KNC could be used for selective breeding between 6 and 8 weeks of age to enhance the overall genetic improvement of growth traits. After validation of these results in independent studies, these findings will be useful for further optimization of breeding programs for KNC.

Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes

Background

The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are hampered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability. In this study, we investigated the genetic architecture of antibody response to four major infectious diseases [infectious bursal disease (IBDV), Marek’s disease (MDV), fowl typhoid (SG), fowl cholera (PM)] and resistance to Eimeria and cestode parasitism, along with two production traits [body weight and body condition score (BCS)] in two distinct indigenous Ethiopian chicken ecotypes. We conducted variance component analyses, genome-wide association studies, and pathway and selective sweep analyses.

Results

The large majority of birds was found to have antibody titres for all pathogens and were infected with both parasites, suggesting almost universal exposure. We derived significant moderate to high heritabilities for IBDV, MDV and PM antibody titres, cestodes infestation, body weight and BCS. We identified single nucleotide polymorphisms (SNPs) with genome-wide significance for each trait. Based on these associations, we identified for each trait, pathways, networks and functional gene clusters that include plausible candidate genes. Selective sweep analyses revealed a locus on chromosome 18 associated with viral antibody titres and resistance to Eimeria parasitism that is within a positive selection signal. We found no significant genetic correlations between production, immune and disease traits, implying that selection for altered antibody response and/or disease resistance will not affect production.

Conclusions

We confirmed the presence of genetic variability and identified SNPs significantly associated with immune, disease and production traits in indigenous village chickens. Results underpin the feasibility of concomitant genetic improvement for enhanced antibody response, resistance to parasitism and productivity within and across indigenous chicken ecotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0252-7) contains supplementary material, which is available to authorized users.

Importance of Indigenous Breeds of Chicken for Rural Economy and Their Improvements for Higher Production Performance

Indigenous/native breeds of chickens are playing an important role in rural economies in most of the developing and underdeveloped countries. They play a major role for the rural poor and marginalised section of the people with respect to their subsidiary income and also provide them with nutritious chicken egg and meat for their own consumption. Performance of native fowl can be improved by change in husbandry, feeding, and better health cover. However, genetic improvement may be made either through selection and crossbreeding or by utilisation of both selection and crossbreeding. Improvement through selection may be time consuming but the improvement will be permanent. Through crossbreeding improvement may be faster but research has to aim for the production of native-type birds with higher production potential. In the present review efforts have been made to present the importance of native fowl to rural economy and their improvement for higher production performance.

Seleção para a produção de ovos em períodos parciais e acumulados em linhagem de frango de corte comercial

Objetivou-se com este estudo estimar parâmetros genéticos para produções parciais e acumuladas de ovos em uma linha fêmea de frangos de corte comercial. Foram considerados 10 períodos mensais entre 25 e 64 semanas, três períodos parciais de 25 a 32, 33 a 48 e 49 a 64 semanas, e três períodos acumulados de 25 até 30, 40 e 50 semanas de idade. Os componentes de covariância e parâmetros genéticos foram obtidos pelo método da máxima verossimilhança restrita, sob o modelo animal considerando o efeito fixo de incubação e os efeitos aleatórios genético aditivo e residual. As estimativas de herdabilidade variaram de 0,12 a 0,41. Evidenciou-se que os períodos anteriores e posteriores ao maior nível de produção apresentam maior variabilidade genética. As correlações genéticas entre os períodos de produção de ovos estudados variaram de -0,12 a 0,98. De modo geral, o padrão de variação foi semelhante entre as estratégias avaliadas, e todas foram geneticamente associadas com a produção total. Os resultados deste estudo mostraram que a melhoria da produção total é viável por meio de seleção de registros parciais. No entanto, caso se considere a eficiência relativa de seleção, o segundo mês e os períodos a partir da quadragésima semana de produção seriam os mais indicados.

High natural antibody titers of indigenous chickens are related with increased hazard in confinement

Natural antibody (NAb) levels and survival rates were evaluated in 4 breeds of laying hens in Ethiopia: indigenous, improved indigenous, exotic layer, and crossbred. Titers of NAb isotypes IgG and IgM binding keyhole limpet hemocyanin (KLH) in serum were measured at 20, 26, 35, and 45 wk age. Repeated-measure ANOVA showed that IgG and IgM levels vary with time within each breed (P < 0.05). Indigenous chickens had significantly (P < 0.05) higher NAb levels at all ages. The Cox proportional hazard analysis showed increased hazard with increased levels of NAbs in the exotic layers (P < 0.05). However, the reduced hazards with increased levels of NAbs were not significant in the improved indigenous and crossbred chickens. Indigenous chickens showed increased hazard with increasing levels of NAb (P > 0.05). We concluded that not only the NAb levels but also the effect of Nabs on survival vary between indigenous and improved breeds. The results indicate that NAb levels are associated with survival in elite (improved) breeds, but are associated with increased hazard in indigenous chickens.