Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences.

The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima's D (-2.320) and Fu's Fs (-51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.

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.

Challenges and opportunities of smallholder pig production systems in Rwanda.

To decipher the dynamics, challenges, and opportunities of smallholder pig farming in Rwanda, a household survey was conducted in ten districts of the country. A total of 900 households selected randomly across four provinces and one city, 12 districts, 28 sectors, and villages were interviewed using a pretested printed questionnaire. Most of the respondents were heads of household: 70.9% for western, 63.5% in eastern, 54.1% in northern, and 52.5% in southern province, and their mean age was 46.7 years and had widely varying education levels. Crossbred pig genotypes were the most preferred due to their high growth rate and produce large litters compared to local pigs, as well as their high resistance to disease, and can better utilize low-quality feeds compared to pure exotic pigs. Piglets and sows were the biggest populations on most farms. Production of piglets for sale was the main purpose of rearing pigs in 63.7% of the farms. Natural mating was almost (99.1%) exclusive on all farms, implying that artificial insemination is yet to take root in Rwanda. Weeds were reported to be the main feed resource used particularly in wet season, while cereal grain mashes and concentrates were used by very few farmers due to high costs. Dominant challenges related to limited pig and pork markets, high taxation, limited extension services, and disease outbreak were highlighted. The most common diseases affecting pigs were swine erysipelas and internal parasites. Access to veterinary services by the households was limited especially in northern province (20%) leading to wrong diagnosis. Capacity building and provision of access to quality animal health services as well as setting up of markets were proposed as strategies to improve pig production by smallholders in Rwanda and grab a share of the lucrative pork market in the region.

Uganda chicken genetic resources: I. phenotypic and production characteristics.

The extent of diversity in the indigenous chicken breeds of Uganda was assessed for their potential utilisation in breeding programmes. A total of 293 indigenous-chicken-keeping households in villages across 35 districts forming 12 sub-regions of the four regions were randomly sampled for 586 mature chickens of both sexes. While only 20.8% of households were headed by women, 40.6% of indigenous chicken keepers were women. The production objectives mainly focused on chickens as sources of income from sales and household food. The chickens were predominantly managed in a scavenging (94.2%) feeding system in a mainly (96.9%) mixed crop-livestock system. The average flock size was 19.80 ± 1.21 chickens with 3.83 ± 0.29 laying hens, each producing an average of 13.41 ± 0.20 eggs/clutch and 40.3 ± 0.6 eggs/annum of 5.20 ± 0.03-month egg production age. Normal-feather strains predominated (>90%), with scattered incidences of naked neck, frizzles, polydactyl, and ptilopody traits in both sexes. Dark (49.0% hen; 43.8% cock) and white (38.3% hen; 42.4% cock) skin colours were most common among the chickens compared to yellow skin. However, yellow-coloured shanks were proportionally the most observed (41% cock; 29% hen). Orange and brown iris (eye) colours were the most common in both sexes. The hens commonly had small round earlobes with varying colours, while cocks had large oval-shaped, mainly red (70%) earlobes. The single-comb type was dominant in both sexes, with wattles almost universally present. Frizzle and polydactyl allele frequencies were significantly lower (p < 0.05) than the expected Mendelian proportions, indicating a possible state of endangerment. Meanwhile, the estimated allele frequencies of ptilopody, tufted-crest, and rose comb alleles in the population were similar (p > 0.05) to the expected Mendelian frequencies. However, these strains did not show any significant (p > 0.05) influence on the body weight or the linear morphometric estimates except for being marginally higher than the normal strains. The phenotypic correlations of body weight and morphometric traits ranged from 0.457 to 0.668 and 0.292 to 0.454 in cocks and hens, respectively. These findings provide hints about the prospects for improved performance with modifications in the production environment. The wide phenotypic diversity would support management efforts for their sustainable utilisation and preservation.

Varying dietary levels of wheat pollard and wheat bran in growing pigs: effect on growth and carcass traits.

To study the effect of increasing levels of wheat pollard as a replacement for wheat bran on growth and carcass characteristics of growing pigs, 64 crossbred (Landrace × Large white Yorkshire) pigs were fed with diets in which wheat pollard was added back to wheat bran in ratios of 15, 30, 45 and 60 %. The pigs were divided into groups of four, balanced for sex, ancestry and body weight. They were then allotted to the dietary treatments in a completely randomised design with four replications. The trial lasted 4 months and data were collected on feed intake and weight gain. A digestibility trial was carried out on eight male pigs per treatment during the growth period. At the end of the growth period, two pigs per replicate in each treatment (n = 32) were slaughtered for determination of carcass characteristics. There were significant differences in the rate of gain and efficiency of feed utilisation among treatments. Diet significantly affected weights of the liver, lungs and small intestine (P < 0.05). The availability of nutrients was not a limiting factor for the growing pigs and that substituting wheat bran by wheat pollard at 60 % improved the pig's average daily gain and feed efficiency.

Performance of growing pigs fed diets based on by-products of maize and wheat processing.

Forty-eight crossbred Landrace × Large white pigs with an average body weight of 8.5 ± 0.4 kg and aged 2 months were used to evaluate performance and carcass characteristics of pigs fed two diets in which bran from maize or wheat was used as the energy source. A third diet based on whole maize grain was used as a control. Animals in groups of four, balanced for litter, sex and weight were allotted to dietary treatments in a completely randomised design with four replications. Data were collected on feed intake and weight gain for a period of 4 months. A digestibility trial was carried at the end of the feeding trial using two male pigs per treatment while six pigs per treatment were randomly selected for slaughter to determine carcass characteristics. Daily gain averaged 0.23, 0.31 and 0.13 kg/day, for pigs fed maize bran, wheat bran and whole maize diets, respectively. Average feed intake and final body weight were significantly (P < 0.05) affected by diets. Digestibility of dry matter, crude fibre and calcium were higher (P < 0.05) for pigs fed maize bran while crude protein digestibility was highest (P < 0.05) for the pigs fed wheat bran. There were significant differences (P < 0.05) between the diets in carcass yield, ham, head, trotters and heart weights and also for rib weight, rib eye muscle and other tissues. This study indicates that comparable performance of growing pigs fed cereal bran and full-grain diets are real.

Pastoralists' indigenous selection criteria and other breeding practices of the long-horned Ankole cattle in Uganda.

The criteria for identification, selection and kinship assignment of Ankole cattle and their roles to pastoralists were studied on 248 farms in Kiboga, Mbarara, Mpigi and Sembabule districts of Uganda using a questionnaire, administered during one-to-one interviews. Farms were randomly sampled along transects originating from the headquarters of each of the 19 sub-counties studied. We found that male Ankole cattle are reared for income from sales, meat for home use and ceremonies, aesthetic value and to maintain cultural heritage. Female cattle are mainly kept for milk production, income from sales, heritage and aesthetics, and in few cases, for home use as meat. Other functions included savings, manure and butter production. All cattle are named at birth with coat colour or pattern being the main identification criterion; hence, it is also useful in assigning kinship. Selection criteria for males are more stringent than for females. On most farms, all females are kept for further breeding and are only culled in cases of poor reproductive health. Primary emphasis in selecting males is on the performance of ancestors in milk and reproductive traits, and then on the qualities of the bull itself. Bulls are selected mainly focusing on a big body frame and size, horns that are white, large and curved upward and a plain dark red "ruhogo" coat colour. The results of this study show that pastoralists have a rich body of indigenous knowledge on this breed, and this should effectively be incorporated into planned selective improvement schemes of the Ankole cattle breed.