Diversity of LEI0258 microsatellite locus in indigenous Ethiopian chickens

Bill & Melinda Gates Foundatio

Genetic polymorphism of beta-lactoglobulin in kenyan small east African goat breed using PCR-RFLP and sequencing

Refinement of coherence and economic gains is an essential target in Dairy industry. This can be achieved by increasing economic returns without increasing the size of the herd. Animal selection is the main method for improvement of livestock production around the world. The determination of candidate genes for economic traits holds a promising future as molecular markers for improving productivity in farm animals. Polymorphism in the beta-lactoglobulin gene has been successfully studied in many goat populations of the world. However, this has not been clarified yet in the local Kenyan goat breeds. The objectives of this study were to screen beta-lactoglobulin gene variants and to identify its polymorphism in Small east African goat breed using Polymorphic Chain Reaction and Restriction Fragment Length Polymorphism and sequencing techniques. A total of 60 goats were genotyped, 30 from each region (Samburu and Narok Counties). Genomic DNA was then isolated using Qiagen QiAmp blood mini kit. The amplified product was observed as 426 bp of exon 7 and the restriction digestion with SacII revealed two alleles, namely A and B and three genotypes, (AA, AB and BB) at the β-lactoglobulin gene locus. Allelic frequencies for goats found in Samburu and Narok were 0.233 and 0.133 respectively for A allele; 0.767 and 0.867 for B allele respectively , while genotypic frequencies were 0.1 and 0.0 for AA, 0.267 and 0.267 for AB, and 0.633 and 0.733 for BB respectively. In the pooled data for the small east African goat breed, the allelic frequencies were 0.183 and 0.817 for the A and B allele respectively, while genotypic frequencies were 0.05, 0.267 and 0.683 for the AA, AB and BB respectively. No deviations from the Hardy Weinberg equilibrium were observed. After PCR, a 426 base pairs sequence in exon 7 of 60 goat samples were sequenced and variation analyzed. Two point mutations corresponding to base substitutions were identified. The substitutions of G to A were found at both positions 6705 and 6751 as compared to the Capra hircus sequence (Accession number Z33881.1). Further studies on other beta-lactoglobulin gene regions as well as other milk protein genes are necessary to establish associations of all its variations and the effects of the variants in the indigenous goat breeds

Socio-economic characteristics and perceptions of cattle keepers and constraints to cattle production in western Kenya

A cross-sectional survey was done in two Districts in Western Kenya to determine the socio-economic characteristics and perceptions of the cattle types kept. This involved socio-economic profiles of households, herd structure, reasons for keeping specific types of cattle and production and marketing constraints together with desired policy interventions to address the constraints. A total of 210 farmers randomly selected were interviewed. The data was analysed using Statistical Analysis System program. The majority of farmers (84%) were males. The households surveyed had an average family size of 8 (± 4.7) members. The mean land holding was 7.8 acres, with 98% of them owning the land. Most of the farmers (64%) in the two districts were literate and were involved in farming (95%) as the primary livelihood. The majority (80%) of the households preferred keeping indigenous zebu cattle over the exotic cattle. The first three reasons for keeping zebu cattle were, in that order, work, especially ploughing (91%), milk (74%) and as a repository for wealth (32%), which accounted for about 62% of the respondents. Diseases (86%), inadequate and low quality feed (12%) and high cost of drugs (2%) were the major constraints to livestock productivity. The farmers also identified lack of market (48%), poor infrastructure (39%) and misuse by the middlemen traders (12%) as main marketing constraints. The survey showed that there is need for the effective implementation of policies on adequate financial aid and regulation of farm input prices to the farmers as well as improved livestock extension services to enhance the production of ruminant livestock

DNA species surveillance: Monitoring bushmeat poaching and trading in Kenya using partial cytochrome b gene

DNA species identification has applications in such areas as forensic science, systematics, conservation genetics and agriculture. One key anthropogenic activity threatening large wildlife fauna is illegal exploitation. In Kenya, species identification of raw and processed meat products remains a constraint to effective enforcement of illegal trade in game meat (bushmeat) and products. We tested the reliability of a 321 bp mitochondrial cytochrome b (cyt b) region as a species identification tool for application in wildlife forensics. Query sequences were generated from known specimens of 14 Eastern African wildlife species, 13 representing commonly poached ungulates, and three domesticated species. These were compared, using Basic Local Alignment Search Tool (BLAST) algorithm, with NCBI GenBank reference sequences for species identity. These query sequences were subsequently deposited on Genbank. They represent a contribution to a diagnostic internal East African Wildlife reference cyt b database. The test species comprised: Cape buffalo, bushbuck, Guenther’s dik-dik, common duiker, common eland, Grant’s gazelle, hartebeest, impala, lesser kudu, plains zebra, Thomson’s gazelle, common warthog, wildebeest, Maasai ostrich, cattle, goat and sheep. Additionally, cooked beef and pork samples were analyzed. The results show that, when conspecific sequences were available in the database, species discrimination was 100%. Phylogeny clustering of the species by maximum likelihood supported the species determination by BLAST.The second part of the study carried out a preliminary survey of the prevalence of illegal game meat sold in the dispersal area of Tsavo National Park, Kenya. Sixty two raw meat samples were randomly collected from small roadside retail outlets along the Nairobi-Mombasa highway (A109), a major transnational highway that transverses Tsavo National Park. The results indicate a 9.7% (n = 6) illegal game meat sale, comprising five Guenther’s dik-diks and a Beisa oryx. A 2 km radius hotspot, with 83% (n = 5) of the bushmeat sales was identified just south of Tsavo East National Park

Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa

In this study, swine fecal specimens (n = 251) collected from nursing and weaned piglets raised under smallholder production systems were screened for the presence of kobuviruses by RT-PCR. Porcine kobuviruses were detected in 13.1 % (33/251) of the samples. We demonstrated that porcine kobuvirus infections exist in indigenous pigs in Kenya and Uganda and that the prevalence was higher in young piglets than older pigs: nursing piglets (15 %), post-weaning (3-month-old) pigs (17 %), 4-month-old pigs (10 %). Genetic analysis of the partial RNA-dependent RNA polymerase (RdRp) region (690 nt) revealed that kobuviruses circulating in East Africa are diverse, sharing nucleotide sequence identities ranging from 89.7 to 99.1 % and 88 to 92.3 % among them and with known porcine kobuviruses, respectively. The nucleotide sequence identities between our kobuvirus strains and those of human, bovine and canine kobuviruses were 69.4-70.7 %, 73.1-74.4 % and 67-70.7 %, respectively. Additionally, upon sequencing selected samples that showed consistent 720-bp RT-PCR bands while using the same primer set, we detected porcine astroviruses in our samples belonging to type 2 and type 3 mamastroviruses. To our knowledge, this study reports the first detection and molecular analysis of both porcine kobuviruses and astroviruses in an African region. Further studies are required to determine the role of these viruses in gastrointestinal infections of pigs in this region and to determine the genetic diversity of the circulating strains to develop accurate diagnostic tools and implement appropriate control strategies

Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains

Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1-29.7%). This study revealed that age, management system and pig density significantly (p < 0.01) influenced the incidence of RVA infections, with housed_free-range management system and larger herd size showing higher risks for RVA infection. Partial (811-1604nt region) sequence of the VP4 gene of selected positive samples revealed that different genotypes (P[6], P[8] and P[13]) are circulating in the study area with P[8] being predominant. The P[6] strain shared nucleotide (nt) and amino acid (aa) sequence identity of 84.4-91.3% and 95.1-96.9%, respectively, with known porcine and human P[6] strains. The P[8] strains shared high nt and aa sequence identity with known human P[8] strains ranging from 95.6-100% and 92-100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6-91.7% and 89.3-96.4%, respectively, only with known porcine P[13] strains. No P[8] strains yielded RNA of sufficient quality/quantity for full genome sequencing. However analysis of the full genome constellation of the P[6], two P[13] and one untypeable strains revealed that the P[6] strain (Ke-003-5) genome constellation was G26-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, P[13] strains (Ug-049 and Ug-453) had G5-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 while the untypeable strain (Ug-218) had G5-P[?]-I5-R1-C1-M1-A8-N1-T1-E1-H?. In conclusion, P[6] and P[8] genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Further studies are required to determine the role of RVA in swine enteric disease burden and to determine the genetic/antigenic heterogeneity of the circulating strains for development of accurate diagnostic tools and to implement appropriate prophylaxis programs