Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens.

Information on the genetic architecture of the production traits of indigenous African chicken is limited. We performed a genome-wide association study using imputed Affymetrix Axiom® 600K SNP-chip genotypes on 1,113 chickens from three agroecological zones of Ghana. After quality control, a total of 382,240 SNPs remained. Variance components and heritabilities for some growth, carcass and internal organ traits were estimated. The genetic and phenotypic correlations among these traits were also estimated. The estimated heritabilities of body weight at week 22 (BW22), average daily gain (ADG), dressed weight, breast weight, thigh weight, wing weight, drumstick weight, and neck weight were high and ranged from 0.50 to 0.69. Estimates of heritabilities for head weight, shank weight, and gizzard weight were moderate (0.31-0.35) while those of liver weight, back weight, dressing percentage, and heart weight were low (0.13-0.21). The estimated heritabilities of dressed weight, breast weight, wing weight, drumstick weight, neck weight, shank weight, and gizzard weight, corrected for BW22, were moderate (0.29-0.38), while the remaining traits had low heritability estimates (0.13-0.21). A total of 58 1-Mb SNP windows on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 13, 18, and 33 each explained more than 1% of the genetic variance for at least one of these traits. These genomic regions contained many genes previously reported to have effects on growth, carcass, and internal organ traits of chickens, including EMX2, CALCUL1, ACVR1B, CACNB1, RB1, MLNR, FOXO1, NCARPG, LCORL, LAP3, LDB2, KPNA3, and CAB39L. The moderate to high heritability estimates and high positive genetic correlations suggest that BW22, ADG, dressed weight, breast weight, thigh weight, wing weight, drumstick weight, and neck weight could be improved through selective breeding.

Genetic Analyses of Response of Local Ghanaian Tanzanian Chicken Ecotypes to a Natural Challenge with Velogenic Newcastle Disease Virus.

Newcastle disease is a devastating poultry disease that often causes significant economic losses in poultry in the developing countries of Africa, Asia, as well as South and Central America. Velogenic Newcastle disease virus (NDV) outbreaks are associated with high mortalities, which can threaten household livelihoods, especially in the rural areas, and lead to loss of high-quality proteins in the form of meat and eggs, as well as household purchasing power. In this study, we exposed unvaccinated Ghanaian and Tanzanian chickens of six local ecotypes to velogenic NDV strains, measured NDV response traits, sequenced their DNA on a genotyping-by-sequencing platform, and performed variance component analyses. The collected phenotypes included: growth rates (pre- and post-exposure); lesion scores (gross lesion severity) in the trachea, proventriculus, intestine, and cecal tonsils; natural antibody levels; anti-NDV antibody levels at 7 days post exposure (dpe); tear and cloacal viral load at 2, 4, and 6 dpe; and survival time. Heritability estimates were low to moderate, ranging from 0.11 for average lesion scores to 0.36 for pre-exposure growth rate. Heritability estimates for survival time were 0.23 and 0.27 for the Tanzanian and Ghanaian ecotypes, respectively. Similar heritability estimates were observed when data were analyzed either separately or combined for the two countries. Survival time was genetically negatively correlated with lesion scores and with viral load. Results suggested that response to mesogenic or velogenic NDV of these local chicken ecotypes could be improved by selective breeding. Chickens that are more resilient to velogenic NDV can improve household livelihoods in developing countries.

Response of three local chicken ecotypes of Ghana to lentogenic and velogenic Newcastle disease virus challenge.

This study was carried out to assess the response of three Ghanaian local chicken ecotypes to LaSota (lentogenic) and virulent field strains of Newcastle disease virus (NDV). Local chickens sampled from the Interior Savannah (IS), Forest (FO) and Coastal Savannah (CS) agro-ecological zones were bred and their offspring were challenged with LaSota NDV at 4 weeks of age. The LaSota challenge was replicated four times with different chicken groups. A total of 1438 chicks comprising 509 Coastal Savannah, 518 Forest and 411 Interior Savannah ecotypes were used. Pre- and post-challenge anti-NDV antibody titre levels were determined via ELISA assays. A second trial was conducted by introducing sick birds infected with virulent NDV to a flock of immunologically naïve chickens at 4 weeks old. Body weights were measured pre- and post-infection. Sex of the chickens was determined using a molecular method. In both trials, there was no significant difference among ecotypes in body weight and growth rate. In the LaSota trial, anti-NDV antibody titre did not differ by ecotype or sex. However, there was a positive linear relationship between body weight and antibody titre. In the velogenic NDV trial, survivability and lesion scores were similar among the three ecotypes. This study confirms that a relatively high dose of LaSota (NDV) challenge has no undesirable effect on Ghanaian local chicken ecotypes. All three Ghanaian local chicken ecotypes were susceptible to velogenic NDV challenge. Resistance to NDV by Ghanaian local chickens appears to be determined more by the individual's genetic makeup than by their ecotype.

Comparison of early growth and survivability in indigenous guinea fowls from Northern Ghana.

Three guinea fowl populations from Northern Ghana were compared in terms of their body weight, growth rates, and survivability during the first 11 weeks of life. Keets (n = 865) were hatched from eggs collected from 32 sampling areas divided into eleven subpopulations within three populations in Northern Ghana. Together with an experimental flock maintained at Animal Research Institute (ARI flock), these birds were raised and appraised for weekly body weights, weekly growth rates, and survivability. Weekly body weights did not differ significantly (p > 0.05) among the three populations, although ARI flock were significantly heavier (p Ë‚ 0.05) compared to the main populations until the fourth week. In contrast, among the subpopulations, significant differences emerged in body weights from the second week and were more pronounced from the sixth week. Growth rates measured as weekly weight gains also differed significantly among subpopulations beyond the second week, although differences in growth rates were not significantly different among whole populations. The mean values for total feed intake, daily feed intake, and feed conversion ratio (FCR) did not vary significantly (p > 0.05) between the populations. Therefore, although the variations in body weight and growth rates were limited among the populations, there existed significant variations among subpopulations, creating opportunities to establish genetically divergent populations for growth rate and to improve early growth rates and body weights in local guinea fowls by selection. High survivability observed in the ARI flock compared to keets from the three populations of Northern Ghana was likely due to good breeder stock management practices despite their common ancestry.

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

Newcastle disease (ND) is a global threat to domestic poultry, especially in rural areas of Africa and Asia, where the loss of entire backyard local chicken flocks often threatens household food security and income. To investigate the genetics of Ghanaian local chicken ecotypes to Newcastle disease virus (NDV), in this study, three popular Ghanaian chicken ecotypes (regional populations) were challenged with a lentogenic NDV strain at 28 days of age. This study was conducted in parallel with a similar study that used three popular Tanzanian local chicken ecotypes and after two companion studies in the United States, using Hy-line Brown commercial laying birds. In addition to growth rate, NDV response traits were measured following infection, including anti-NDV antibody levels [pre-infection and 10 days post-infection (dpi)], and viral load (2 and 6 dpi). Genetic parameters were estimated, and two genome-wide association study analysis methods were used on data from 1,440 Ghanaian chickens that were genotyped on a chicken 600K Single Nucleotide Polymorphism (SNP) chip. Both Ghana and Tanzania NDV challenge studies revealed moderate to high (0.18 - 0.55) estimates of heritability for all traits, except viral clearance where the heritability estimate was not different from zero for the Tanzanian ecotypes. For the Ghana study, 12 quantitative trait loci (QTL) for growth and/or response to NDV from single-SNP analyses and 20 genomic regions that explained more than 1% of genetic variance using the Bayes B method were identified. Seven of these windows were also identified as having at least one significant SNP in the single SNP analyses for growth rate, anti-NDV antibody levels, and viral load at 2 and 6 dpi. An important gene for growth during stress, CHORDC1 associated with post-infection growth rate was identified as a positional candidate gene, as well as other immune related genes, including VAV2, IL12B, DUSP1, and IL17B. The QTL identified in the Ghana study did not overlap with those identified in the Tanzania study. However, both studies revealed QTL with genes vital for growth and immune response during NDV challenge. The Tanzania parallel study revealed an overlapping QTL on chromosome 24 for viral load at 6 dpi with the US NDV study in which birds were challenged with NDV under heat stress. This QTL region includes genes related to immune response, including TIRAP, ETS1, and KIRREL3. The moderate to high estimates of heritability and the identified QTL suggest that host response to NDV of local African chicken ecotypes can be improved through selective breeding to enhance increased NDV resistance and vaccine efficacy.

Age, genotype and sex effects on growth performance of local chickens kept under improved management in Ghana.

Characterisation of animal genetic resources has been recognised globally as an important step towards their sustainable use. Body weight data of local chickens (213 forest and 160 savannah chickens) and 183 French free-ranging SASSO T44 chickens kept under improved management were collected from hatch to 40 weeks of age and analysed to determine the effects of age, genotype and sex on their growth performance. At all ages, SASSO T44 chickens had significantly (P<0.05) higher weights (2.6-3.2 kg at 28 weeks) than the local chickens (1.2-1.7 kg at 28 weeks). The rate of growth at the earlier ages in the local genotypes (5.57-7.80 g/day) was lower than the range of 13.81-15.42 in SASSO T44 chickens. Except at hatch, savannah chickens were significantly heavier (P<0.05) than the forest chickens at all ages. Male chickens had significantly (P<0.05) superior growth rates than females across all genotypes except from the 20th to the 28th week. Growth trends in both sexes depicted linear increase in body weights; however, the rate of increase in body weights was higher in males as compared to females, thus showing clear sexual dimorphism. There were no significant (P>0.05) differences in the growth rates of SASSO T44 chickens and local genotypes at the later ages (20-28 weeks). Local chickens from the savannah zone had better growth rate than forest chickens. The significant effect of ecozone on the growth potential of local chickens is an indication that their productive potential could be improved through interventions in the environment such as provision of feed and some veterinary care.

Characterisation of local Ghanaian chickens: growth performance evaluation based on Richards growth model and genetic size scaling.

The Richards growth model was fitted to body weight-age data of local and SASSO T44 chickens to describe their growth performance. Males had higher (P < 0.05) asymptotic mature weights than females. Within the local chicken population, birds from the savannah zone had higher (P < 0.05) asymptotic mature weights compared to forest chicken which ironically had higher body weights at hatch. Male local chicken had lower maturing rates compared to the females. Female local chicken were superior to SASSO T44 females in terms of maturing rate. On the average, local chickens took relatively longer time (78.4-83.3 days) to reach the point of inflection than the SASSO T44 population (74.2-79.8 days). However, there were no significant differences (P > 0.05) in the age at inflection among local chicken populations. The shape parameter for SASSO T44 chicken (0.053-0.370) and maturation rate for local chicken (0.177-0.198) were the most critical parameters. Scaling the body weights into degree of maturity highlighted the degree to which genotypes matured over time. Female chickens had the highest (P < 0.05) degree of maturity at all ages. The local chicken populations were also metabolically older than SASSO T44 chickens. Results of this study provide an opportunity to develop breeding strategies for local chicken by modifying either management practices or their genetic makeup to positively affect their growth and productivity.

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers.

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco-zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations--a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F-statistics revealed negligible genetic differentiation (F(ST)) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south-north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.