Evaluation of breeding objectives for purebred and crossbred selection schemes for adoption in indigenous chicken breeding programmes

IBD sharing patterns as intra-breed admixture indicators in small ruminants

In this study, we investigated how IBD patterns shared between individuals of the same breed could be informative of its admixture level, with the underlying assumption that the most admixed breeds, i.e. the least genetically isolated, should have a much more fragmented genome. We considered 111 goat breeds (i.e. 2501 individuals) and 156 sheep breeds (i.e. 3304 individuals) from Europe, Africa and Asia, for which beadchip SNP genotypes had been performed. We inferred the breed's level of admixture from: (i) the proportion of the genome shared by breed's members (i.e. "genetic integrity level" assessed from ADMIXTURE software analyses), and (ii) the "AV index" (calculated from Reynolds' genetic distances), used as a proxy for the "genetic distinctiveness". In both goat and sheep datasets, the statistical analyses (comparison of means, Spearman correlations, LM and GAM models) revealed that the most genetically isolated breeds, also showed IBD profiles made up of more shared IBD segments, which were also longer. These results pave the way for further research that could lead to the development of admixture indicators, based on the characterization of intra-breed shared IBD segments, particularly effective as they would be independent of the knowledge of the whole genetic landscape in which the breeds evolve. Finally, by highlighting the fragmentation experienced by the genomes subjected to crossbreeding carried out over the last few generations, the study reminds us of the need to preserve local breeds and the integrity of their adaptive architectures that have been shaped over the centuries.

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.

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.

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.

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.

Widespread introgression in Chinese indigenous chicken breeds from commercial broiler

Chinese indigenous chickens (CICs) constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.