Livestock phenomics and genetic evaluation approaches in Africa: current state and future perspectives.

The African livestock sector plays a key role in improving the livelihoods of people through the supply of food, improved nutrition and consequently health. However, its impact on the economy of the people and contribution to national GDP is highly variable and generally below its potential. This study was conducted to assess the current state of livestock phenomics and genetic evaluation methods being used across the continent, the main challenges, and to demonstrate the effects of various genetic models on the accuracy and rate of genetic gain that could be achieved. An online survey of livestock experts, academics, scientists, national focal points for animal genetic resources, policymakers, extension agents and animal breeding industry was conducted in 38 African countries. The results revealed 1) limited national livestock identification and data recording systems, 2) limited data on livestock production and health traits and genomic information, 3) mass selection was the common method used for genetic improvement with very limited application of genetic and genomic-based selection and evaluation, 4) limited human capacity, infrastructure, and funding for livestock genetic improvement programmes, as well as enabling animal breeding policies. A joint genetic evaluation of Holstein-Friesian using pooled data from Kenya and South Africa was piloted. The pilot analysis yielded higher accuracy of prediction of breeding values, pointing to possibility of higher genetic gains that could be achieved and demonstrating the potential power of multi-country evaluations: Kenya benefited on the 305-days milk yield and the age at first calving and South Africa on the age at first calving and the first calving interval. The findings from this study will help in developing harmonized protocols for animal identification, livestock data recording, and genetic evaluations (both national and across-countries) as well as in designing subsequent capacity building and training programmes for animal breeders and livestock farmers in Africa. National governments need to put in place enabling policies, the necessary infrastructure and funding for national and across country collaborations for a joint genetic evaluation which will revolutionize the livestock genetic improvement in Africa.

Modeling genetic components of hatch of fertile in broiler breeders.

Reproductive efficiency such as fertility and hatch of fertile (HoF) are of economic importance and concern to breeding companies becaue of their effects on chick output. Similar to other traits of economic importance in poultry breeding, the rate of response for HoF is largely dependent on the use of an appropriate model for evaluating the trait. Therefore, the objectives of this study were to estimate genetic parameters from cumulative, repeatability, fixed regression, random regression, and multitrait models for HoF from a pure-line broiler breeder. The data available for this study consisted of weekly HoF records from 11,729 hens with a total pedigree record of 38,260. Estimates of heritability from the various models ranged from 0.04 to 0.22 with the highest estimate obtained from the cumulative model and the lowest from the repeatability model. Responses to selection estimated for the different models ranged from 0.03 to 0.08% gain per year of the phenotypic mean. In general, the cumulative and the repeatability models underestimated response to selection. The multitrait and random regression models gave similar results for response to selection at 0.08 percentage change in phenotypic mean. In conclusion, the cumulative model is not optimal for modeling HoF, and likewise, the repeatability model. The random regression and multitrait models should be considered instead as they offered a higher response to selection. However, if a multitrait analysis is to be considered, it is recommended to split up the production period in such a way as to avoid computational constraints due to overparameterization.

Genetic variation and potential for genetic improvement of cuticle deposition on chicken eggs.

BACKGROUND: The cuticle is an invisible glycosylated protein layer that covers the outside of the eggshell and forms a barrier to the transmission of microorganisms. Cuticle-specific staining and in situ absorbance measurements have been used to quantify cuticle deposition in several pure breeds of chicken. For brown eggs, a pre-stain and a post-stain absorbance measurement is required to correct for intrinsic absorption by the natural pigment. For white eggs, a post-stain absorbance measurement alone is sufficient to estimate cuticle deposition. The objective of the research was to estimate genetic parameters and provide data to promote adoption of the technique to increase cuticle deposition and reduce vertical transmission of microorganisms. RESULTS: For all pure breeds examined here, i.e. Rhode Island Red, two White Leghorns, White Rock and a broiler breed, the estimate of heritability for cuticle deposition from a meta-analysis was moderately high (0.38 ± 0.04). In the Rhode Island Red breed, the estimate of the genetic correlation between measurements recorded at early and late times during the egg-laying period was ~ 1. There was no negative genetic correlation between cuticle deposition and production traits. Estimates of the genetic correlation of cuticle deposition with shell color ranged from negative values or 0 in brown-egg layers to positive values in white- or tinted-egg layers. Using the intrinsic fluorescence of tryptophan in the cuticle proteins to quantify the amount of cuticle deposition failed because of complex quenching processes. Tryptophan fluorescence intensity at 330 nm was moderately heritable, but there was no evidence of a non-zero genetic correlation with cuticle deposition. This was complicated furthermore by a negative genetic correlation of fluorescence with color in brown eggs, due to the quenching of tryptophan fluorescence by energy transfer to protoporphyrin pigment. We also confirmed that removal of the cuticle increased reflection of ultraviolet wavelengths from the egg. CONCLUSIONS: These results provide additional evidence for the need to incorporate cuticle deposition into breeding programs of egg- and meat-type birds in order to reduce vertical and horizontal transmission of potentially pathogenic organisms and to help improve biosecurity in poultry.

Cuticle deposition improves the biosecurity of eggs through the laying cycle and can be measured on hatching eggs without compromising embryonic development.

The cuticle is part of the egg's natural defense and it can be improved by genetic selection. Prior to adoption of this measurement in breeding programs, questions that need to be addressed are whether improved cuticle deposition will result in a reduced risk of eggs becoming contaminated and whether selection for this trait will have any unintended consequences on the incubation process. Bacterial penetration experiments were carried out using eggs from a pedigree line of broiler breeders (BB) and Rhode Island Red (RIR) layers. Within the natural variation in cuticle deposition in each line, a good cuticle was shown to reduce an egg's susceptibility to penetration by Escherichia coli (BB, P = 0.023) and Salmonella typhimurium (RIR, P < 0.001). Deglycosylation of cuticle proteins had little effect on their antimicrobial activity. The effect of bird age on cuticle deposition was also examined. Shell color decreased with age as anticipated; however, we found no evidence that cuticle deposition decreases with age, at least up to 50 wk. A thicker cuticle could affect the water vapor conductance (WPC) of hatching eggs. The WPC of eggs was, therefore, measured on eggs selected from the top and tail of the cuticle distribution, this time in a Lohmann Selected Leghorn (LSL) pedigree line. Broiler breeder eggs were also tested. No evidence of a relationship between cuticle deposition and WPC was found for LSL or BB eggs. Cuticle deposition measurements require eggs to be stained. Here, we show that this has no adverse effect on embryo development at d 12 of incubation. Thus, we conclude that cuticle deposition is important in preventing bacterial penetration of eggs in genetically divergent breeds of chicken and that the measurement can be practically incorporated into breeding programs. This will contribute to improving the biosecurity of eggs by reducing vertical and horizontal transmission of potentially zoonotic and pathogenic organisms from parent to offspring.

Understanding avian egg cuticle formation in the oviduct: a study of its origin and deposition.

The cuticle is a unique invisible oviduct secretion that protects avian eggs from bacterial penetration through gas exchange pores. Despite its importance, experimental evidence is lacking for where, when, and what is responsible for its deposition. By using knowledge about the ovulatory cycle and oviposition, we have manipulated cuticle deposition to obtain evidence on these key points. Cuticle deposition was measured using staining and spectrophotometry. Experimental evidence supports the location of cuticle deposition to be the shell gland pouch (uterus), not the vagina, and the time of deposition to be within the final hour before oviposition. Oviposition induced by arginine vasotocin or prostaglandin, the penultimate and ultimate factors for the induction of oviposition, produces an egg with no cuticle; therefore, these factors are not responsible for cuticle secretion. Conversely, oviposition induced by GNRH, which mimics the normal events of ovulation and oviposition, results in a normal cuticle. There is no evidence that cuticle deposition differs at the end of a clutch and, therefore, there is no evidence that the ovulatory surge of progesterone affects cuticle deposition. Overall, the results demonstrate that the cuticle is a specific secretion and is not merely an extension of the organic matrix of the shell. Cuticle deposition was found to be reduced by an environmental stressor, and there is no codependence of the deposition of pigment and cuticle. Defining the basic facts surrounding cuticle deposition will help reduce contamination of hen's eggs and increase understanding of the strategies birds use to protect their eggs.

Inheritance of fertility in broiler chickens.

BACKGROUND: The fertility of a chicken's egg is a trait which depends on both the hen that lays the egg and on her mate. It is also known that fertility of an individual changes over the laying period. METHODS: Longitudinal models including both random genetic and permanent environmental effects of both the female and her male mate were used to model the proportion of fertile eggs in a pedigree broiler population over the ages 29-54 weeks. RESULTS: Both the male and the female contribute to variation in fertility. Estimates of heritability of weekly records were typically 7% for female and 10% for male contributions to fertility. Repeatability estimates ranged from 24 to 33%, respectively. The estimated genetic variance remained almost constant for both sexes over the laying period and the genetic correlations between different ages were close to 1.0. The permanent environment components increased substantially towards the end of the analyzed period, and correlations between permanent environment effects at different ages declined with increasing age difference The heritability of mean fertility over the whole laying period was estimated at 13% for females and 17% for males. A small positive correlation between genetic effects for male and female fertility was found. CONCLUSION: Opportunities to improve fertility in broiler stocks by selection on both sexes exist and should have an impact throughout the laying period.