Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

Abstract

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18–0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes.

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance

“…Other studies have compared differences between the expression of key immune genes in these genetic lines after an NDV challenge in embryo (Schilling et al, 2018;Schilling et al, 2019) and at 3 weeks of age under heat stress conditions (Saelao et al, 2018). Also, genetic markers of interest have been identified in a commercial line (Rowland et al, 2018;Saelao et al, 2019) and African ecotypes (Walugembe et al, 2019) after infection with this same lentogenic strain. Data are being generated at a fast rate; new tools and types of analyses are needed to analyze the data in a more comprehensive way.…”

Genetic Basis of Response of Ghanaian Local Chickens to Infection With a Lentogenic Newcastle Disease Virus

“…This study was designed similar to a parallel study conducted in Tanzania as described by Walugembe et al (2019b). In brief, local breeder chickens were randomly sampled from three ecological zones of Ghana, namely Interior Savannah (IS), Coastal Savannah (CS), and Forest (FO) zones.…”

“…All chicks were raised under similar conditions with ad libitum access to feed and water. Chicks were challenged with a live attenuated type B1 LaSota lentogenic NDV strain at 28 days of age and evaluated for pre-and post-infection growth rate, antibody level in at 10 dpi, and viral load from tears at 2 and 6 dpi, as described by Walugembe et al (2019b).…”

“…Other studies have also reported genetic parameters for some NDV response traits in local chickens (Lwelamira et al, 2009;Lwelamira, 2012). As part of a large-scale study to understand the genetic basis of NDV response traits for local chicken ecotypes in Africa (under the Feed the Future Innovation Lab for Genomics to Improve Poultry), we recently reported estimates of genetic parameters and genome-wide association study (GWAS) results for response to lentogenic NDV infection in three Tanzanian local chicken ecotypes (Walugembe et al, 2019b). Here, we report results from a parallel study that was conducted with three Ghanaian local chicken ecotypes.…”

Phenotypic variability and population structure analysis of Tanzanian free-range local chickens

“…During quality control, SNP set with number of clusters ≥2, call rates ≥99% and minor allele frequency ≥ 0.05 were selected for downstream analyses. Other quality control metrics and imputation of missing genotypes are explained further in Walugembe et al [34]. A total of 396, 055 SNPs remained for further downstream analyses.…”