Genetic evaluation of test-day milk yields from smallholder dairy production systems in Kenya using genomic relationships.

Efforts to improve dairy production in smallholder farming systems of East Africa over the past decade have had limited impact because of the lack of records on performance to guide targeted breeding programs. Estimates of genetic parameters in these systems are lacking. Using data generated through a project ("Germplasm for Dairy Development in East Africa") in Kenya and a genomic relationship matrix from genotypic records, we examined the potential impact of different models handling contemporary groups or herd effects on estimates of genetic parameters using a fixed regression model (FRM) for test-day (TD) milk yields, and the covariance structure for TD milk yield at various stages of lactation for animals using a random regression model (RRM). Models in which herd groups were defined using production levels derived from the data fitted the data better than those in which herds were grouped depending on management practices or were random. Lactation curves obtained for animals under different production categories did not display the typical peak yield characteristic of improved dairy systems in developed countries. Heritability estimates for TD milk yields using the FRM varied greatly with the definition of contemporary herd groups, ranging from 0.05 ± 0.03 to 0.27 ± 0.05 (mean ± standard error). The analysis using the RRM fitted the data better than the FRM. The heritability estimates for specific TD yields obtained by the RRM were higher than those obtained by the FRM. Genetic correlations between TD yields were high and positive for measures within short consecutive intervals but decreased as the intervals between TD increased beyond 60 d and became negative with intervals of more than 5 mo. The magnitude of the genetic correlation estimates among TD records indicates that using TD milk records beyond a 60-d interval as repeated measures of the same trait for genetic evaluation of animals on smallholder farms would not be optimal. Although each individual smallholder farmer retains only a few animals, using the genomic relationship between animals to link the large number of farmers operating under specified environments provides a sufficiently large herd-group for which a breeding program could be developed.

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers.

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F(1) hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

Livestock keeper perceptions of four indigenous cattle breeds in tsetse infested areas of Ethiopia.

Four cattle breeds indigenous to western and south-western Ethiopia--Abigar, Gurage, Horro and Sheko--were included in a study of the perceptions of smallholder cattle keepers regarding cattle management, production levels and constraints for production. A semi-structured questionnaire was used and 60 cattle keepers from each of the four areas were interviewed. Diseases were reported as the main constraint to cattle production by a majority of livestock keepers in all areas except in the Sheko area, where over-stocking was the main constraint. Among diseases, trypanosomosis was the main livestock disease according to more than half of Gurage, Horro and Sheko keepers, whereas anthrax was most important in the Abigar area. Gurage had highest age at first calving, longest calving interval and also the lowest milk production, whereas Sheko and Abigar had the most favorable characteristics both for milk production (600-700 kg) and fertility (age at first mating 3-3.5 years and above 8 calves/cow). Cattle keepers in the Sheko area reported relatively less problems with cattle diseases compared to the other areas, especially regarding trypanosomosis. Abigar showed a different disease pattern than the other breeds and may also have advantages as regards trypanotolerance.

Serum enzymes levels and influencing factors in three indigenous Ethiopian goat breeds.

Serum enzymes were studied in 163 apparently healthy goats from three indigenous goat breeds of Ethiopia. The effect of breed, age, sex and season on alanine aminotransferase (ALT) / glutamic pyruvic transaminase (GPT), aspartate aminotransferase (AST) / glutamic oxalacetic transaminases (GOT), alkaline phosphatase (ALP) and acid phosphatase (AcP) levels was assessed. The mean serum enzymes levels of the indigenous Arsi-Bale, Central Highland and Long-eared Somali goat breeds ranged from 14.0-20.2 iu L(-1) for ALT/GPT, from 43.2-49.3 iu L(-1) for AST/GOT, from 83.7-98.8 iu L(-1) for ALP, and from 2.99-4.23 iu L(-1) for AcP, were within the normal range for goats elsewhere. Breed had significant influence on AST/GOT values. Sex had significant effect on ALT/GPT for Arsi-Bale goats with higher values in males than females. Age was significant on all serum enzymes studied in the Arsi-Bale goats and on ALP in the Central Highland goats. Season had significant influence on all serum enzymes except for ALT/GPT in the Arsi-Bale goats. The serum enzyme levels of these indigenous goat breeds can be used as normal reference values for Ethiopian goat breeds adapted to similar agro-ecology and production system.

A field trial of production and financial consequences of helminthosis control in sheep production in Ethiopia.

We used a partial-budget analysis to evaluate profitability of different management strategies of three genotypes of sheep in a 2 x 2 x 3 factorial experiment conducted at Debre Berhan research station in the central highlands of Ethiopia. This involved two anthelmintic-treatment levels (treated vs. non-treated), two supplementary nutrition levels (protein-energy supplementation yes/no) and three genotypes: indigenous Menz (n=40), 50% Awassi x 50% Menz crosses (n=38) and 75% Awassi x 25% Menz crosses (n=31). All sheep were exposed to natural sub-clinical helminthosis challenge. Supplemented sheep were offered a concentrate mix daily on an individual basis. Anthelmintic-treated sheep were drenched with fenbendazole against nematodes and with triclabendazole against trematodes. Data were collected during the experimental period (for 10 months from approximately 1 year of age) on feed intake, live weight, eggs per gram (EPG) of faeces, packed-cell volume (PCV), wool weight, and adult-worm burden. Actual market input and output prices were recorded. Supplemented sheep had significantly higher marginal profit (MP) per sheep than non-supplemented sheep (ETB 33 vs. 4). Likewise, anthelmintic treated sheep performed significantly better than their non-treated contemporaries (MP=ETB 28 vs. 8). The 75% Awassi crosses were least profitable.

Effects of non-genetic factors on responses to gastro-intestinal nematode infections in Ethiopian sheep.

The effects of non-genetic factors on responses to gastrointestinal nematode infections were examined in artificially infected indigenous Horro and Menz lambs in the central highlands of Ethiopia. The experiment involved lambs of two sexes, infection and monitoring regimens (3 levels), dam parity (4 levels) and birth types (2 levels). A total of 152 weaner lambs (103 Menz and 49 Horro) were used. Endoparasite challenge involved three infection periods (primary, secondary and tertiary) each separated by an anthelmintic treatment. Data were collected on faecal egg counts (FEC), packed cell volume (PCV), worm count, and weight gain. Female lambs were found to harbor lower numbers of T. colubriformis counts and had lower (p < 0.01) FEC in tertiary infection compared to males. Younger animals were more susceptible to the nematode infections than older animals as measured by all the parameters studied (p < 0.01). Twins had higher FEC in both secondary and tertiary infections compared to singles. Lambs born to dams of first parity had higher PCV and lower FEC values during the tertiary infection compared to other parities. These results would be used as basic information in designing a more rational control strategy and should also help to advise on better management care for less resistant sheep.

The small east african shorthorn zebu cows in Kenya. I: linear body measurements.

Assessment of genetic diversity is a prerequisite for the management and conservation of animal genetic resources. Appropriate design of breeding programmes is therefore impossible for breeds that have not been adequately characterized either phenotypically and/or genetically. Phenotypic characteristics are important in breed identification and classification in ways that farming communities can relate with. This study phenotypically characterized two breeds of zebu cattle in Kenya. A total of 12 measurements (face length, ear length, horn length, heart girth, height at withers, chest depth, body length, height at rump, pelvis width, corpus length, pin bone width and tail length) were collected on 373 Maasai and 277 Kamba zebu kept by traditional farmers in south-east Kenya. The data were classified on the basis of breed group, age group, sex and coat colour pattern. Breed group, age group and sex significantly influenced all measurements. Coat colour pattern significantly influenced only height at withers, corpus length, ear length and tail length. Except for horn and ear length, all the other measurements were significantly higher for the Maasai zebu. Additionally, the Maasai zebu was taller than it was long. The opposite was true for the Kamba zebu. The Maasai and Kamba zebus can be classified as medium-sized breeds; however, great variations exist in their body sizes within and between the breeds.

Genetic diversity and differentiation of Mongolian and Russian yak populations.

In this study we examined the genetic diversity of yak populations in the northernmost part of their current global distribution. Five Mongolian and one Russian yak populations as well as one Chinese yak population from the Qinghai-Tibetan Plateau, the putative centre of yak domestication, were analysed with 15 microsatellite loci to determine the level of genetic variation within populations as well as the genetic differentiation and relationship between populations. A total of 116 microsatellite alleles were identified. The mean number of alleles per locus (MNA) across populations was 7.73 +/- 1.98 and the mean expected heterozygosity (HE) was 0.696 +/- 0.026. The relative magnitude of gene differentiation (F(ST)) among populations was 4.1%, and all genetic differentiations (F(ST)) between populations were significant (p < 0.001). A significant inbreeding effect (F(IS)) was detected in the Hovsgol yak (p < 0.01). There was no indication of a recent bottleneck in any of the populations studied. The results showed that yak populations in Mongolia and Russia have maintained high genetic diversity within populations and a low, although significant, genetic differentiation between populations. Both phylogenetic and principal component analyses support a close genetic relationship between the Gobi Altai, south Gobi and north Hangai populations, and between the Hovsgol and Buryatia populations respectively. Our results indicate that these yak populations should be considered as distinct genetic entities in respect of conservation and breeding programmes.

Risk factors for mortality associated with respiratory disease among Menz and Horro sheep in Ethiopia.

A retrospective case-control study was conducted on 6718 sheep of two breeds (2772 Horro and 3946 Menz) on risk factors for mortality associated with respiratory disease (MARD) in Ethiopia, based on data collected between October 1993 and December 1997. Potential risk factors examined were breed, gender, age, month, and air temperatures.Fifty-four per cent of total deaths in the flock could be attributed to respiratory disease and the annual MARD rate ranged between 6.3 and 19.0%. There was significant breed (P<0.0001) and gender (P<0.0001) difference in MARD. The Horro breed had a higher (P<0.0001) annual MARD than the Menz breed (16.5+/-0.18 vs. 12.4+/-0.15%). A higher (P<0.0001) proportion of males suffered than females (15.1+/-0.23% vs. 13.8+/-0.13%). Age was also an important risk factor for MARD: there was a strong polynomial relationship (R(2)=0.91, P<0.0001) between MARD and age; the risk of being young if a sheep was a MARD case was high. MARD was high between October and March but relatively low between the months of April and September. There was a significant (P<0.05) negative cubic relationship (R(2)=0.49) between monthly MARD and monthly average minimum air temperatures. There was also a significant (P<0.01) positive exponential relationship (R(2)=0.61) between monthly MARD and average monthly daily deviation between maximum and minimum air temperatures. Timely health and management interventions focusing on these factors are necessary to alleviate losses from MARD. Understanding variations in MARD risk within a population can enhance early response to potential outbreaks, reducing losses.

Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification.

The genetic diversity and relationships amongst the dromedary (Camelus dromedarius) populations are poorly documented. Four recognized Kenyan dromedary breeds (Somali, Turkana, Rendille, Gabbra) and dromedary from Pakistan and the Arabian Peninsula (Saudi Arabia, United Arab Emirates) were studied using 14 microsatellite loci. Phylogenetic analysis showed that Kenyan dromedaries are distinct from Arabian and Pakistani populations. Expected heterozygosity and allelic diversity values indicate that Kenyan dromedaries are less diverse than non-Kenyan populations. With the exception of the Somali population, the Kenyan dromedaries are poorly differentiated (average FST=0.009), with only one to two loci separating the Gabbra, Rendille and Turkana populations studied (P < 0.05). Individual assignments were performed using the maximum likelihood method. A correct breed assignment of only 39-48% was observed for the Kenyan dromedaries, using an allocation stringency of a log of the odds ratio >2. Our results do not support the present classification of the indigenous Kenyan dromedary into four distinct breeds based on socio-geographical criteria. Instead, our results point to just two separate genetic entities, the Somali and a group including the Gabbra, Rendille and Turkana populations.

Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites.

Hybridization between wild and domestic bovine species occurs worldwide either spontaneously or by organized crossing. We have analysed hybridization of banteng (Bos javanicus) and zebu (Bos indicus) in south-east Asian cattle using mitochondrial DNA (PCR-RFLP and sequencing), AFLP, satellite fragment length polymorphisms (SFLP or PCR-RFLP of satellite DNA) and microsatellite genotyping. The Indonesian Madura zebu breed is reputed to be of hybrid zebu-banteng origin, but this has never been documented and Bali cattle are considered to be a domesticated form of banteng. The banteng mitochondrial type was found in all animals sampled on the isle of Bali, Indonesia, but only in 35% of the animals from a Malaysian Bali-cattle population. The Madura animals also carried mitochondrial DNA of either zebu and banteng origin. In both populations, zebu introgression was confirmed by AFLP and SFLP. Microsatellite analysis of the Malaysian Bali population revealed for 12 out of 15 loci screened, Bali-cattle-specific alleles, several of which were also found in wild banteng animals. The tools we have described are suitable for the detection of species in introgression studies, which are essential for the genetic description of local breeds and the preservation of their economic and cultural value.

Patterns of growth and partitioning of fat depots in tropical fat-tailed Menz and Horro sheep breeds.

A total of 147 Menz and Horro lambs of both sexes were serially slaughtered and dissected at five different stages of growth to define the pattern of growth and partitioning of fat among body depots in indigenous Ethiopian Menz and Horro sheep breeds. The GLM procedure of SAS and allometric growth equation were used to assess the effects of various factors on the growth of body depots and to estimate its growth relative to total carcass fat (TCF) and empty body weight (EBW), respectively. Results obtained showed that the growth of carcass fat (CF), non-carcass fat (NCF) and tail fat (TF) is significantly affected by the genotype (P<0.001) and stages of growth (P<0.001) of lambs. Except for CF, the growth of both NCF and TF were also significantly affected (P<0.001 and P<0.05) by the sex and the season in which the lambs were born. Of the two breeds, the Menz sheep deposited more fat into the carcass and less into the non-carcass depots as compared to the Horro sheep and ewe lambs in both breeds deposited more fat intra-abdominally than the ram lambs. The highest allometric growth coefficient was obtained for TF (1.2-2.1 relatively to TCF and EBW) and the lowest for NCF (0.8-1.3 relative to TCF and EBW) indicating that the former is a late developing while the later is an early maturing depot in the tropical fat-tailed Menz and Horro sheep breeds.