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

Genetic Analysis of Egg Production Traits in Luhua Chickens: Insights from a Multi-Trait Animal Model and a Genome-Wide Association Study

Egg production plays a pivotal role in the economic viability of hens. To analyze the genetic rules of egg production, a total of 3151 Luhua chickens were selected, the egg production traits including egg weight at first laying (Start-EW), egg weight at 43 weeks (EW-43), egg number at 43 weeks (EN-43), and total egg number (EN-All) were recorded. Then, the effects of related factors on egg production traits were explored, using a multi-trait animal model for genetic parameter estimation and a genome-wide association study (GWAS). The results showed that body weight at first egg (BWFE), body weight at 43 weeks (BW-43), age at first egg (AFE), and seasons had significant effects on the egg production traits. Start-EW and EW-43 had moderate heritability of 0.30 and 0.21, while EN-43 and EN-All had low heritability of 0.13 and 0.16, respectively. Start-EW exhibited a robust positive correlation with EW-43, while Start-EW was negatively correlated with EN-43 and EN-All. Furthermore, gene ontology (GO) results indicated that Annexin A2 (ANXA2) and Frizzled family receptor 7 (FZD7) related to EW-43, Cyclin D1 (CCND1) and A2B adenosine receptor (ADORA2B) related to EN-All, and have been found to be mainly involved in metabolism and growth processes, and deserve more attention and further study. This study contributes to accelerating genetic progress in improving low heritability egg production traits in layers, especially in Luhua chickens.

Heat stress effects on the genetics of growth traits in Thai native chickens (Pradu Hang dum)

OBJECTIVE

The objective of this study was to investigate the effect of heat stress on the growth traits and genetic parameters of Thai native chickens.

METHODS

A total of 16,487 records for growth traits of Thai native chickens between 2017 and 2022 were used in this study. Data included the body weight at birth, body weight at 4, 8, and 12 weeks of age (BW0, BW4, BW8, BW12), average daily gain during 0 to 4, 4 to 8, and 8 to 12 weeks of age (ADG0-4, ADG4-8, ADG8-12), absolute growth rate at birth, at 4, 8, and 12 weeks of age (AGR0, AGR4, AGR8, AGR12). The repeatability test day model used the reaction-norm procedure to analyze the threshold point of heat stress, rate of decline of growth traits, and genetic parameters.

RESULTS

At temperature and humidity index (THI) of 76, Thai native chickens began to lose their growth traits, which was the onset of heat stress in this study. The estimated heritability, genetic correlation between animal and heat stress effect, and correlations between the intercept and slope of the permanent environmental effects were 0.27, -0.85, and -0.83 for BW, 0.17, -0.81, and -0.95 for ADG, 0.25, -0.61, and -0.83 for AGR, respectively. Male chickens are more affected by heat stress than female chickens with a greater reduction of BW, ADG, and AGR, values equal to -9.30, -0.23, -15.21 (in males) and -6.04, -0.21, -10.10 (in females) gram per 1 level increase of THI from the THI of 76.

CONCLUSION

The influence of thermal stress had a strong effect on the decline in growth traits and genetic parameters in Thai native chickens. This study indicated that genetic models used in conjunction with THI data are an effective method for the analysis and assessment of the effects of heat stress on the growth traits and genetics of native chickens.

Elucidation of the genetic determination of clutch traits in Chinese local chickens of the Laiwu Black breed

BACKGROUND

Egg laying rate (LR) is associated with a clutch, which is defined as consecutive days of oviposition. The clutch trait can be used as a selection indicator to improve egg production in poultry breeding. However, little is known about the genetic basis of clutch traits. In this study, our aim was to estimate genetic parameters and identify quantitative trait single nucleotide polymorphisms for clutch traits in 399 purebred Laiwu Black chickens (a native Chinese breed) using a genome-wide association study (GWAS).

METHODS

In this work, after estimating the genetic parameters of age at first egg, body weight at first egg, LR, longest clutch until 52 week of age, first week when the longest clutch starts, last week when the longest clutch ends, number of clutches, and longest number of days without egg-laying until 52 week of age, we identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with clutch traits in Laiwu Black chickens. The restricted maximum likelihood method was used to estimate genetic parameters of clutch pattern in 399 Laiwu Black hens, using the GCTA software.

RESULTS

The results showed that SNP-based heritability estimates of clutch traits ranged from 0.06 to 0.59. Genotyping data were obtained from whole genome re-sequencing data. After quality control, a total of 10,810,544 SNPs remained to be analyzed. The GWAS revealed that 421 significant SNPs responsible for clutch traits were scattered on chicken chromosomes 1-14, 17-19, 21-25, 28 and Z. Among the annotated genes, NELL2, SMYD9, SPTLC2, SMYD3 and PLCL1 were the most promising candidates for clutch traits in Laiwu Black chickens.

CONCLUSION

The findings of this research provide critical insight into the genetic basis of clutch traits. These results contribute to the identification of candidate genes and variants. Genes and SNPs potentially provide new avenues for further research and would help to establish a framework for new methods of genomic prediction, and increase the accuracy of estimated genetic merit for egg production and clutch traits.

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.

Comparative study and relationship analysis between purine content, uric acid, superoxide dismutase, and growth traits in purebred and crossbred Thai native chickens

The objective was to compare and analyze the relationship between growth, purine content, uric acid, and superoxide dismutase (SOD) in purebred and crossbred Thai native chickens. A total of 300 Thai native chickens were divided into 3 groups. Group 1 was purebred Thai native chickens (100%TN), Group 2 was 50% Thai native chickens (50%TN), and Group 3 was 25% Thai native chickens (25%TN). Data included the body weight (BW), average daily gain (ADG), and breast circumference (BrC). At 6, 8, and 10 weeks of age, 10 chickens from each group were randomly euthanized to collect breast meat, liver, and blood samples to analyze the purine content consisting of total purine, adenine, guanine, xanthine, and hypoxanthine, and uric acid, in breast meat and liver and SOD in blood. A general linear model, Pearson correlation and principal component analysis were used to analyze the significant differences and relationship between variables. The results showed the 25%TN group had the highest growth traits at every age, while the 100%TN group had the lowest (p < 0.05). Consistent with the analysis results of purine values, purine content and uric acid in breast meat and liver and SOD in blood decreased with age (p < 0.05). The correlations between purine content (total purine, adenine, guanine, xanthine, and hypoxanthine) and growth traits (BW, ADG, and BrC) ranged from moderate negative to moderate positive (-0.542 to 0.253)(p < 0.05). The correlations between uric acid and growth traits (0.348-0.760) and SOD and growth traits (0.132-0.516) were low to moderate positive with significant differences (p < 0.05). The principal component plot, which highlighted three principal components (PC 1, PC 2, and PC 3), explained 86.44 and 86.53% of the total information in breast meat and liver for selecting animals for optimal balance of the variation in the growth traits, purine content, uric acid, and SOD. Although purebred Thai native chickens showed the lowest growth traits, purine content, uric acid, and SOD were also lowest compared to crossbred Thai native chickens. Therefore, the development of genetics in Thai native chickens to produce healthy food could be possible.

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.

Estimation of genetic parameters of eggshell translucency and production traits in different genotypes of laying hens

The translucency of eggshells is a ubiquitous appearance problem caused by moisture translocation and the accumulation of egg contents into the eggshell ultrastructure. Previous studies have mainly investigated the causes of eggshell translucency from nutritional and environmental perspectives. However, little is known of the effect of genetics the causes of eggshell translucency on hen production performance. To evaluate the genetic parameters of eggshell translucency and other production performance indicators, we performed an experiment on 3 pure hen lines: 624 Dwarf Layer-White, 1,612 Rhode Island Red, and 813 Rhode Island Red-White. We collected eggs from each hen over 5 d and measured eggshell translucent level (TL) using the grading method. Additionally we measured indicators of each hen during the laying period, including age at laying of the first egg (AFE), body weight at laying of the first egg (BWFE), weight of the first egg (FEW), body weight at 40 wk (BW40), egg weight at 40 wk (EW40), egg production up to 40 wk of age (EN), and calculated the genetic parameters among the indicators. The results showed that the estimated heritability of TL in the 3 genotypes were 0.30, 0.24, and 0.20, respectively, suggesting a low or moderate level of heritability. We found a positive correlation between TL and AFE, with genetic correlation coefficients 0.19 to 0.41, and negative genetic correlation between TL and EN, with correlation coefficient -0.36 to -0.19. Additionally, we observed positive correlation exists between AFE and FEW, BWFE and FEW, and BW40 and EW40; and negative correlation between AFE and EN in the 3 pure lines. These results enriched the research on heritability of eggshell translucency in different hen breeds and demonstrated moderate or low heritability of the indicator. Furthermore, eggshell translucency was negatively affected by AFE and EN. Our results provide a valuable reference for predicting selection response of eggshell translucency and production performance in brood hens, and locating the genes regulating eggshell translucency.

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.

Direct and maternal genetic effects for preinflection point growth traits and humoral immunity in quail

Early growth traits in quails are considered as the growth performances before the inflection point which are genetically different from body weights (BW) at later stages. Moreover, in addition to growth performance, humoral immunity is moderately heritable and is considered in some breeding programs. However, estimating the direct genetic, particularly the maternal genetic correlations between growth and immunity in quail, are not studied sufficiently, which were the aims of the present study. The quails' BW were recorded at hatch (BW0) to 25 d of age with a 5-d interval and body weight gains (BWG) were measured as average growth performance of the birds in a 5-d period. Antibody titer against Newcastle disease virus (IgN) was measured through the hemagglutination inhibition (HI) test. For titration of anti-SRBC antibodies (IgY and IgM), a hemagglutination microtiter assay was used. In general, growth records in 4,181 birds and humoral immune responses in 1,023 birds were assigned to the study. The genetic parameters were estimated by single-trait analysis via Gibb's sampling. After finding the best model for each trait, multi-trait analysis was done to estimate the direct and maternal genetic correlations. Direct heritabilities (h²) were estimated to be moderate for BW (0.481-0.551) and BWG (0.524-0.557), while h² for immune responses were low (0.035-0.079). Maternal environmental effect (c²) was only significant for BW0, BW5, and BWG0-5. Maternal heritabilities (m²) for BW and BWG were all lower than corresponding h², ranging from 0.072 (BW25) to 0.098 (BW0). The m² for IgN (0.098) was more than 2.5 times greater than h² (0.040) for this trait. Direct (r_a) and maternal (r_m) genetic correlations between IgN-BW, IgY-BW, and IgY-BWG were negative, while ra and rm for IgM-BW, IgN-BWG, and IgM-BWG were positive. The r_a between humoral immune responses were low to moderate and rm was significant only for IgY-IgM (0.339). Given positive genetic correlations in BWG-IgN and BWG-IgM as well as positive genetic correlations between both IgN and IgM with IgY, it is suggested that including the BWG in the breeding programs would directly result in the improvement of the birds' growth performance. It would also contribute indirectly to the improvement of the birds' humoral immune responses.

Combining Abilities, Heterosis, Growth Performance, and Carcass Characteristics in a Diallel Cross from Black-Bone Chickens and Thai Native Chickens

The purpose of this study was to determine the combining abilities and heterosis for the growth performance and carcass characteristics in crosses between Hmong black-bone (HB), Chinese black-bone (CB), and Thai native (TN) chickens using a mating system diallel crossing. Nine crossbred chickens including HB × HB, CB × CB, TN × TN, HB × TN, TN × HB, CB × HB, HB × CB, TN × CB, and CB × TN, were tested. The total data were 699 recorded at the beginning of the experiment to 595 recorded in weeks 14 of age. Body weight (BW), average daily gain (ADG), feed conversion ratio (FCR), and survival rate (SUR) were recorded. Heterosis and combining ability regarding general combining ability (GCA), specific combining ability (SCA), and reciprocal combining ability (RCA) were estimated. The study found that CB had the greatest BW and ADG at all weeks (p < 0.05) except for hatch, while those of HB were the lowest. The highest GCA was found in CB; meanwhile, GCA was significantly negative in HB of all ages. Crossing between TN × CB had the greatest BW from 8 weeks of age, which was related to positive SCA and RCA values. However, the RCA value of TN × CB was lower than the SCA value of CB × TN. The yield percentages of the carcass in CB (87.00%) were higher than those in TN (85.05%) and HB (82.91%) (p < 0.05). The highest breast and thigh meat lightness (L*) values were obtained in TN (p < 0.05), while those of CB and HB were not different (p > 0.05). In the crossbreed, the yield percentage of the carcass was highest in TN × CB (89.65%) and CB × TN (88.55%) (p > 0.05) and was lowest in TN × HB (71.91%) (p < 0.05). The meat and skin color of the breast and thigh parts in the crossbreed had the lowest lightness in HB × CB (27.91 to 38.23) (p < 0.05), while those of TN × CB and CB × TN were insignificant (p > 0.05). In conclusion, crossing between the TN sires and CB dams has the preferable potential to develop crossbred Thai native chickens for commercial use based on their high growth performance.

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 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.

Genetics and breeding of a black-bone and blue eggshell chicken line. 2. Laying patterns and egg production in two consecutive generations

The BG line was originated from the cross between 2 Chinese indigenous breeds, Dongxiang blue eggshell, and Jiangshan black-bone, and has been bred to combine dark heavy black-bone body and high production of blue-shell eggs, into single dual-purpose line. Full-pedigree hens from 2 generations, G4 (n = 441) and G5 (n = 464), were reared in the same single-cage laying facility in 2019–2020 and 2020–2021, respectively. Starting from the first egg of each hen, its daily egg production was recorded until 300 days-of-age. Up to 7 "no-egg" days were considered normal laying breaks between clutches, whereas laying cessation of 8 or more days was considered Pause, and the laying pattern of each hen was assigned either with Pause or No-Pause. The other traits included PsDays: number of Pause days; AFE: age at first egg; EN300: eggs laid until 300 d; %L300: total laying rate (EN300/[300-AFE]); %Lnet: net laying rate (EN300/[300-AFE-PsDays]); ClLng: average clutch length; EW200 and EW300: average egg weight around 200 d and 300 d. Estimates of heritability (h²) of each trait, and phenotypic and genetic correlation between traits, were calculated in each generation using the animal model. Heritability estimates were calculated also by regressing the means of full-sib G5 hens on their G4 parents' means. Mean overall laying rate of all G4 hens was low (%L300 = 57%) because 53% of them had Pause in their laying pattern. In G5, incidence of Pause was higher (75%) due to a 3-wk cold stress, with mean %L300 = 54%. However, significant estimates of heritability and genetic correlations suggest that selection for low PsDays will reduce the incidence of Pause in BG hens and elevate the line's mean laying rate towards %L300 = 70%, as the No-Pause hens in G5. PsDays-free laying rate (%Lnet) was found to be highly correlated with the significantly heritable (h²≈0.4) clutch length (ClLng). Selection index combining the genetically independent low PsDays and high ClLng is expected to maximize egg production improvement in the BG line, and in similar populations derived from indigenous breeds.

Polymorphism analysis and expression profile of the estrogen receptor 2 gene in Leizhou black duck

Our previous study on the ovarian transcriptomic analysis in Leizhou black duck revealed that the ESR2 gene was involved in hormone regulation in reproduction and the estrogen signaling pathway related to reproductive performance was enriched. This suggested that ESR2 may have a functional role in the reproductive performance of the Leizhou black duck. Thus, this study aimed at evaluating the polymorphism of the ESR2 gene and its association with egg-laying traits and the distribution pattern of ESR2 mRNA in laying and non-laying Leizhou black ducks. In this study, genomic DNA was extracted from blood samples of 101 Leizhou black ducks to identify single nucleotide polymorphisms (SNPs) of the ESR2 gene to elucidate molecular markers highly associated with egg-laying traits. Four each of laying and non-laying Leizhou black ducks were selected to collect different tissues to analyze the ESR2 gene expression. A total of 23 SNPs were identified and association analysis of the single SNP sites showed that SNPs g.56805646 T>C and exon 3-20G>A were significantly (P < 0.05) associated with egg weight. Ducks with CT and AG genotypes had significantly higher (P < 0.05) egg weights than their respective other genotypes. Haplotype association analysis of g.56805646 T>C and exon 3-20G>A showed that the haplotypes were significantly associated with egg weight. Higher egg weight was seen in individuals with H3H4 haplotypes. In the hypothalamus-pituitary-gonadal (HPG) axis, the results of qRT/PCR showed that ESR2 mRNA was significantly (P < 0.05) expressed in the ovaries of both duck groups than in the hypothalamus and pituitary. In the oviduct, ESR2 was significantly (P < 0.05) higher in the infundibulum and magnum of laying and non-laying ducks respectively. This study provides a molecular marker for selecting Leizhou black ducks for egg production. In addition, it offers theoretical knowledge for studying the related biological functions of the ESR2 gene at the cellular level.

Genetic Effect and Growth Curve Parameter Estimation under Heat Stress in Slow-Growing Thai Native Chickens

Heat stress is becoming a major problem because it limits growth in poultry production, especially in tropical areas. The development of genetic lines of Thai native chickens (TNC) which can tolerate the tropical climate with the least compromise on growth performance is therefore necessary. This research aims to analyze the appropriate growth curve function and to estimate the effect of heat stress on the genetic absolute growth rate (AGR) in TNC and Thai synthetic chickens (TSC). The data comprised 35,355 records for body weight from hatching to slaughtering weight of 7241 TNC and 10,220 records of 2022 TSC. The best-fitting growth curve was investigated from three nonlinear regression models (von Bertalanffy, Gompertz, and logistic) and used to analyze the individual AGR. In addition, a repeatability test-day model on the temperature-humidity index (THI) function was used to estimate the genetic parameters for heat stress. The Gompertz function produced the lowest mean squared error (MSE) and Akaike information criterion (AIC) and highest the pseudo-coefficient of determination (Pseudo-R²) in both chicken breeds. The growth rates in TSC were higher than TNC; the growth rates of males were greater than females, but the age at inflection point in females was lower than in males in both chicken breeds. The THI threshold started at 76. The heritability of the AGR was 0.23 and 0.18 in TNC and TSC, respectively. The additive variance and permanent environmental variance of the heat stress effect increased sharply after the THI of 76. The growth rate decreased more severely in TSC than TNC. In conclusion, the Gompertz function can be applied with the THI to evaluate genetic performance for heat tolerance and increase growth performance in slow-growing chicken.

How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock

Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.

Detection of loci exhibiting pleiotropic effects on body weight and egg number in female broilers

The objective of the present study was to discover the genetic variants, functional candidate genes, biological processes and molecular functions underlying the negative genetic correlation observed between body weight (BW) and egg number (EN) traits in female broilers. To this end, first a bivariate genome-wide association and second stepwise conditional-joint analyses were performed using 2586 female broilers and 240 k autosomal SNPs. The aforementioned analyses resulted in a total number of 49 independent cross-phenotype (CP) significant SNPs with 35 independent markers showing antagonistic action i.e., positive effects on one trait and negative effects on the other trait. A number of 33 independent CP SNPs were located within 26 and 14 protein coding and long non-coding RNA genes, respectively. Furthermore, 26 independent markers were situated within 44 reported QTLs, most of them related to growth traits. Investigation of the functional role of protein coding genes via pathway and gene ontology analyses highlighted four candidates (CPEB3, ACVR1, MAST2 and CACNA1H) as most plausible pleiotropic genes for the traits under study. Three candidates (CPEB3, MAST2 and CACNA1H) were associated with antagonistic pleiotropy, while ACVR1 with synergistic pleiotropic action. Current results provide a novel insight into the biological mechanism of the genetic trade-off between growth and reproduction, in broilers.

Thai Native Chicken as a Potential Functional Meat Source Rich in Anserine, Anserine/Carnosine, and Antioxidant Substances

This study identified anserine and anserine/carnosine in chicken breast of Thai native chicken (TNC; 100% Thai native), Thai synthetic chicken (TSC; 50% Thai native), and Thai native crossbred chicken (TNC crossbred; 25% Thai native) compared with commercial broiler chicken (BR; 0% Thai native) using nuclear magnetic resonance (NMR) spectroscopy and the effect on antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl assay (DPPH). We conducted experiments with a completely randomized design and explored principal components analysis (PCA) and orthogonal projection to latent structure-discriminant analysis (OPLS-DA) to identify the distinguishing metabolites and relative concentrations from 1H NMR spectra among the groups. The relative concentrations and antioxidant properties among the groups were analyzed by analysis of variance (ANOVA) using the general linear model (GLM). This study revealed seven metabolites alanine, inositol monophosphate (IMP), inosine, and anserine/carnosine, lactate, anserine, and creatine. Lactate, anserine, and creatine were major components. In terms of PCA, the plots can distinguish BR from other groups. OPLS-DA revealed that anserine and anserine/carnosine in the chicken breast were significantly higher in TNC, TSC, and TNC crossbred than BR according to their relative concentrations and antioxidant properties (p < 0.01). Therefore, TNCs and their crossbreeds might have the potential to be functional meat sources.

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.

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.

Luzhong mutton sheep: inbreeding and selection signatures

Intense artificial selection has been imposed to Luzhong mutton sheep population in the past years. Improvements on growth and reproductive performance are two breeding goals in the present herd. Although some progresses were phenotypically observed possibly due to inbreeding induced by strong selection in terms of these traits, the genomic evaluation was poorly understood. Therefore, a high-density SNP array was used to characterize the pattern of runs of homozygosity (ROH), estimate inbreeding and inbreeding depressions on early growth performance and litter size based upon ROH, and scan positive selection signatures of recent population. Consequently, a low inbreeding level was observed which had negative effects on litter size, but not on early growth performance. And 160 genes were under selection, of which some were reported to be linked to several traits of sheep including body weight, litter size, carcass and meat quality, milk yield and composition, fiber quality and health, and the top genes were associated with growth (growth hormone [GH]- growth hormone receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding measures was highlighted, but purging selection was proposed to alleviate the inbreeding depression on litter size, providing some genomic insights to breeding management of Luzhong mutton sheep.

Genetic parameters and direct and maternal effects for important traits in late-feathering Qingyuan partridge hens in China

Qingyuan partridge chicken is an important indigenous chicken in China. In its breeding schemes, chickens are usually selected at the age of 105-day-old for five traits, including body weight (BW), shank length (SL), shank girth (SG), comb height (CH) and feather maturity (FM). At present, genetic parameters of the aforementioned traits have still not been studied in Qingyuan partridge chickens. The objectives of this study were the following: (1) to investigate whether the optimal statistical models of these traits need to consider maternal genetic and permanent environmental effects in late-feathering Qingyuan partridge hens, and (2) to estimate genetic parameters for these traits based on the optimal models. The numbers of records for BW, SL, SG, CH and FM were 13,721, 13,671, 13,670, 13,669 and 13,672, respectively. Variance components were estimated using average information-restricted maximum likelihood method, and the optimal model was determined based on Bayesian information criterion. More specifically, the optimal model for BW considered maternal genetic and permanent environmental effects in addition to direct additive genetic effect; SL, SG and FM considered direct and maternal genetic effects; and CH considered direct and maternal genetic effects, and the covariance between them. The direct heritabilities of these traits estimated using the optimal models were 0.21 ± 0.04, 0.30 ± 0.05, 0.40 ± 0.05, 0.59 ± 0.09 and 0.09 ± 0.04, respectively; the maternal heritabilities were 0.01 ± 0.04, 0.05 ± 0.05, 0.04 ± 0.05, 0.09 ± 0.09 and 0.03 ± 0.04, respectively. Maternal genetic effect evidently played an important part in FM and maternal heritability accounted for 30 per cent of total heritability. Furthermore, the direct and maternal genetic effects for CH were estimated to be negatively and moderately correlated (-0.51 ± 0.11). For all traits, neglecting existent maternal effects biased the estimation of direct heritability. Therefore, to implement optimum breeding strategies for improvement of these traits in Qingyuan partridge hens, maternal effects should be taken into consideration.

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.