Livestock Fish journal articles

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Bovine brucellosis: Prevalence, risk factors, economic cost and control options with particular reference to India – a review
(Journal Article, 2018-01) Deka, Ram Pratim; Magnusson, Ulf; Grace, Delia; Lindahl, Johanna F.
Background: Brucellosis is an economically important zoonotic disease with worldwide distribution, with low-income countries being more affected. The disease is endemic in India, a country that house the world’s largest cattle and buffalo population and produce the most milk in the world. Results: Prevalence of the disease in the country is reported as low as 1% to as high as 60% by different researchers but many of the published studies that reported higher prevalence were conducted in non-randomised samples. Based on this review, overall prevalence in the country is likely 12% or less. About 20 different risk factors are reported that contribute/predispose to occurrence of bovine brucellosis. The risk factors could be classified in four groups: host factors, farmer’s factors, managemental factors, and agro-ecological factors. Various studies reported high economic burden of the diseases in dairy animals but there is dearth of comprehensive and rigorous economic studies. Conclusions: In the absence of highly effective vaccines and because of difficulties in executing a segregation and slaughter policy of infected animals in countries like India, control of bovine brucellosis remains a challenge.
In the search for low-cost year-round feeds: Pen-level growth performance of local and crossbred Ugandan pigs fed forage- or silage-based diets versus commercial diet
(Journal Article, 2018-12-04) Carter, Natalie A.; Dewey, Catherine E.; Grace, Delia; Lukuyu, Ben A.; Smith, Eliza; Lange, Cornelis de
Smallholder pig farmers in East Africa report that lack of feed, seasonal feed shortages, quality and cost are key constraints to pig rearing. Commercially prepared pig diets are too expensive and people and pigs compete for food. Smallholder farmers typically feed nutritionally unbalanced diets, resulting in low average daily gain (ADG) and poor farmer profits. Our objective was to compare the ADG of Ugandan pigs fed forage- or silage-based or commercial diets. Ugandan weaner-grower pigs were randomly assigned to forage- or silage-based diets or commercial diet. Pigs were weighed every 3 weeks from 9 to 32 weeks of age. Pen-level ADG and feed conversion were compared across diets using multiple linear regression. The ADG of pigs fed forage- or silage-based diets was lower than those fed commercial diets between 9 and 24 weeks of age (p < 0.05). Between 28 and 32 weeks, pigs fed forage-based diets had lower ADG than those on other diets (p < 0.05). Least squares mean ADG (g/pig/day) for pigs fed forage- or silage-based diets or commercial diet were 36, and 52, and 294 respectively at 9–15 weeks; 163, 212, 329 at 15–19 weeks; 112, 362, 574 at 20–24 weeks and 694, 994, and 1233 at 28 to 32 weeks of age. It was concluded that forage- and silage-based diets are unsuitable for small, newly weaned pigs. Feeding forage- or silage-based diets to finishing pigs is more suitable. Forage- and silage based diets are year-round low-cost pig-feeding strategies that will improve the growth performance of East African pigs, thereby increasing pig farmer income and food security.
Detection of Tilapia Lake Virus in Egyptian fish farms experiencing high mortalities in 2015
(Journal Article, 2017-12) Nicholson, P.; Fathi, M.A.; Fischer, A.; Mohan, C.; Schieck, Elise G.; Mishra, N.; Heinimann, A.; Frey, J.; Wieland, Barbara; Jores, Joerg
Currently, tilapia are the second most important group of farmed fish worldwide, wherein Nile tilapia (Oreochromis niloticus) is the foremost cultured species (FAO 2005). In 2014, the global tilapia production was valued at 4.5 million tons and is expected to surge to 7.3 million tons by 2030 (FAO 2014). Specifically, Egypt represents over 90% of the commercial Arab aquaculture production and currently ranks second to China with regard to global tilapia output (FAO 2005). Since 2013, an increasing number of tilapia farms in Egypt have been experiencing high summer morbidity and mortality rates (WorldFish 2015). Such disease outbreaks are a major constraint to the aquaculture trade and have devastating economic and social consequences (Aly, 2013). Tilapia have become such an important global food source, not only because they are an inexpensive source of protein but also due to their favourable culturing characteristics such as, their mode of reproduction, omnivorous diet, fast growth, tolerance for high-density aquaculture and because they are relatively resistant to poor water quality and disease (FAO 2005). Despite this, various bacteria, fungi, protozoa and viruses have been associated with disease in tilapia aquaculture (FAO 2005). There have been many reports implicating bacteria in tilapia diseases and in particular, bacterial infections caused by Aeromonas or Streptococcus species. For example, A. hydrophila and A. veronii are the causative agents of Motile Aeromonas Septicaemia (Aly, 2013; FAO 2005). Far less has been reported regarding viruses causing diseases in tilapia (Bigarre et al., 2009; Mcgrogan, Ostland, Byrne, & Ferguson, 1998; Shlapobersky et al., 2010), especially in Egyptian farms (Aly, 2013). However, a new virus called Tilapia Lake Virus (TiLV) has been implicated in recent mass tilapia losses in Israel and Ecuador (Bacharach et al., 2016; Del-Pozo et al., 2016; Eyngor et al., 2014; Ferguson et al., 2014). Oddly, the virus seems to manifests itself as a problem of the brain in Israel (Bacharach et al., 2016; Eyngor et al., 2014), while it targets the liver of fish in Ecuador (Del-Pozo et al., 2016; Ferguson et al., 2014) and Colombia (Kembou Tsofack et al., 2017). Our aim was to detect potential pathogens in diseased tilapia that might account for the high summer mortalities observed in Egyptian fish farms. To this end, diseased fish were examined from eight farms in different areas of the Nile delta. Here, we report the detection of Aeromonas species and, for the first time, the presence of TiLV in Egyptian tilapia aquaculture. In September 2015, we visited eight commercial farms experiencing the so-called summer mortality spanning a large area of the Nile Delta (Figure 1). We randomly sampled 13–40 fish per farm and examined them macroscopically to determine disease prevalence (Table 1 and Table S1). External clinical examinations considered haemorrhagic patches, detached scales, open wounds, dark discoloration and fin rot as signs of disease. Two diseased fish per farm were dissected, and tissues from the head kidney were collected in Universal Transport Medium tubes (UTM™, Copan, Italy) and kept at 4°C during transportation before being stored at −80°C. Additionally, the head kidney, spleen and liver tissues were swabbed using Amies Agar Gel (with charcoal) swabs (Copan, Italy). As controls, 20 healthy tilapia were examined from WorldFish in Abbassa and two were dissected and processed as outlined above. A. veronii A. hydrophilia A. veronii A. ichthiosmia A. enteropelogenes A. veronii A. enteropelogenes A. jandaei A. veronii A. ichthiosmia A. enteropelogenes A. hydrophilia The presence of TiLV was tested using a PCR protocol published elsewhere (Eyngor et al., 2014). Briefly, 20–60 mg of head kidney tissue was homogenized in 1 ml TRIzol reagent (Thermo Fisher Scientific, USA) using Lysing Matrix B and D (MP Biomedicals, USA,) in a MP FastPrep-24 sample preparation system (MP Biomedicals) for 2 × 40 s, with cooling in between, at a speed of 6.5 m/s. Thereafter, the TRIzol reagent protocol was followed, with the exception that 1-Bromo-3-chloropropane (Sigma Life Sciences, USA) was used instead of chloroform. About 10 ng of purified RNA was used in a one-step RT-PCR reaction using the Thermo Scientific Verso 1-Step RT-PCR ReddyMix Kit (Thermo Fisher Scientific). The virus was detected in four farms (Figure 1, Table 1 and Figure S1) using a diagnostic RT-PCR amplifying a 250-bp fragment of segment 3 (Eyngor et al., 2014). Additionally, primers in coding regions from segments 4 (S4_F-AGCAGCAGCAGGAGAAAGAG and S4_R-ACCGTCCTGTTTCTGAATGG) and 9 (S9_F-TTGGTGATGTCACGATGGATA and S9_R-AGTTCTATCGCCAGCCATGT) were designed using the available genome sequence of TiLV isolate Til-4-2011 (GenBank accessions numbers KU751817 and KU751822). We were able to amplify a 358-bp and a 351-bp fragment from segment 4 and segment 9, respectively, from three of the five virus isolates. All amplicons, including the 250-bp amplicons derived from segment 3, were Sanger sequenced (microsynth.ch) and assembled. The trimmed sequences (segment 3 = 249 bp, segment 4 = 263 bp, segment 9 = 252 bp) were used for a comparative analysis against the sequences of the Israeli and Ecuadorian TiLV. Egyptian TiLV sequences were deposited in GenBank under accession numbers KY817381–KY817390. Nucleotide sequences were aligned using muscle (Edgar, RC. 2004 NAR). When comparing all sequences, segments 3, 4 and 9 had 18, 16 and 2 SNPs, respectively. This led to two non-synonymous substitutions for sequences derived from segments 3 and 4. The amino acid changes in segment 3 distinguished the Egyptian isolates from the Israeli and Ecuadorian isolates, while the ones in segment 4 were unique to either the Ecuadorian isolate or to the Egyptian isolate from farm 5. Segment 9 sequences were identical for all viruses investigated at protein level (Table 2). The TiLV from Ecuador showed 98% nucleotide identity to the Israeli strain (Bacharach et al., 2016; Del-Pozo et al., 2016; Eyngor et al., 2014), while the Egyptian TiLV isolates showed only 93% identity to the Israeli strain when comparing sequences from segments 3, 4 and 9. We built phylogenetic trees for each segment using phyML (Guindon et al., 2010). All trees were congruent pointing towards the absence of reassortment (Figure 2). The Egyptian isolates cluster together with high bootstrap support. Surprisingly, the Israeli isolate is closer to the Ecuadorian isolate than to the Egyptian isolates. Additionally, we investigated the presence of bacterial fish pathogens using swabs which were stored at 4°C until they were spread onto tryptic soy agar containing 5% sheep blood (BD, USA) and incubated aerobically at 30°C for 48 h. Single colonies were subcultured and used to identify the bacteria present in our fish samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) using a Microflex LT instrument (Bruker Daltonics GmbH, Germany) with FlexControl (version 3.0) software (Bruker Daltonics) for the automatic acquisition of mass spectra in the linear positive mode within a range of 2–29 kDa (Bizzini, Durussel, Bille, Greub, & Prod'hom, 2010). We did not detect any Streptococcus species, but we found Aeromonas species in every farm (Table 1). Our aim was to identify candidate pathogens potentially responsible for the recent summer mortalities reported from Egyptian tilapia aquaculture (Worldfish, 2015). We visited eight commercial farms, covering different regions of the Nile delta and observed morbidities ranging from 43% to 100%. In every farm, we identified Aeromonas species which have been detected in Egyptian tilapia farming for many decades and have been linked to previous severe disease outbreaks (Aly, 2013). The new finding in trying to account for the recent Egyptian tilapia mortalities is the discovery of TiLV in 50% of the farms investigated. Notably, the application of a recently published Nested Reverse Transcription-PCR (Kembou Tsofack et al., 2017) probably would have resulted in a higher detection rate of TiLV. So far, TiLV has been implicated in mass tilapia deaths occurring also during the hot seasons in Israel and Ecuador. It is a segmented negative sense RNA virus that appears to be a real threat to global tilapia aquaculture. The absence of re-assortment and the closer similarity of Israeli to Ecuadorian isolates than to geographically closer Egyptian isolates could be due to anthropogenic influence via movement of feeds, live fish or water. Given our data, we cannot conclusively state that the emergence of this virus in Egyptian tilapia aquaculture is solely responsible for their summer mortalities, but it is a significant finding. Therefore, a prompt investigation into the prevalence of this virus in further regions of the Nile delta and how the Egyptian TiLV, which is divergent from the Ecuadorian and Israeli strain, manifests itself in Nile tilapia is required. Additional Future studies should investigate the effect of co-infections of pathogenic Aeromonas species with TiLV. Moreover, abiotic factors, such as water quality and temperature, should be investigated with respect to their effect on tilapia susceptibility to TiLV. Crucially, future work must focus on implementing existing diagnostic methods (Kembou Tsofack et al., 2017) into disease control policies. The development and application of an efficient vaccine would be the most effective disease control measure, but this endeavour requires more time. We are grateful to everybody involved in the sampling of tilapia in Egypt for this study. This work was supported by the CGIAR research programme Livestock and Fish, the University of Bern, and the Egyptian General Authority for Fish Resources Development. We thank Felix Drexler for his comments on the manuscript. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Dairy farm households, processor linkages and household income: The case of dairy hub linkages in East Africa
(Journal Article, 2016-12-01) Rao, E.J.O.; Omondi, Immaculate A.; Karimov, A.A.; Baltenweck, Isabelle
In this study we have analysed the effects of household linkages to milk market via dairy hubs currently implemented under the East African Dairy Development project. Our analyses show that participation in dairy hubs increases dairy revenues by USD 1,022 on average. Impacts are higher for households participating in hubs supplying exclusively to processors (USD 1,673) relative to ones supplying hubs that pursue mixed-linkage approach. Moreover, participation in dairy hubs also yields significant effect on household income. Appropriate measures should be undertaken to widen the reach of such processor linkages while also safeguarding existing gains, more so as the processing sector becomes more concentrated.
Measurement of the aboveground biomass of some rangeland species using a digital non-destructive technique
(Journal Article, 2016-07-02) Tarhouni, M.; Salem, F.B.; Tlili, A.; Belgacem, A.O.; Neffati, M.; Louhaichi, Mounir
Plant biomass is usually assumed to be positively correlated with canopy cover. Measurements of canopy cover can now be easily and precisely made through image processing of high-resolution digital photography. This study aims to determine rapid, accurate and non-destructive ecological measurements of the aboveground biomass of selected plant species of the dry rangelands of southern Tunisia. The digital vegetation charting technique was used to estimate the canopy cover of three plant species: Artemisia herba-alba Asso., Rhanterium suaveolens Desf. and Stipa tenacissima L. Biomass of the selected species was also determined to develop regression models and correlation equations with the relative canopy cover. The main result was a strong correlation between canopy cover and dry biomass: coefficients of determination of 0.46 and 0.96 for A. herba-alba during the springs of 2014 and 2015, respectively; and correspondingly 0.9 and 0.97 for R. suaveolens and 0.69 and 0.97 for S. tenacissima. This digital charting technique offers a non-destructive, accurate and rapid means for monitoring and assessment of rangeland productivity dynamics as well as an efficient tool for developing range management strategies in dry areas.
Complete genome sequences of virulent Mycoplasma capricolum subsp. capripneumoniae strains F38 and ILRI181
(Journal Article, 2014-10-30) Falquet, Laurent; Liljander, Anne M.; Schieck, Elise G.; Gluecks, Ilona V.; Frey, J.; Jores, Joerg
Contagious caprine pleuropneumonia (CCPP) caused by Mycoplasma capricolum subsp. capripneumoniae is a severe epidemic affecting mainly domestic Caprinae species but also affects wild Caprinae species. M. capricolum subsp. capripneumoniae belongs to the “Mycoplasma mycoides cluster.” The disease features prominently in East Africa, in particular Kenya, Tanzania, and Ethiopia. CCPP also endangers wildlife and thus affects not only basic nutritional resources of large populations but also expensively built-up game resorts in affected countries. Here, we report the complete sequences of two M. capricolum subsp. capripneumoniae strains: the type strain F38 and strain ILRI181 isolated druing a recent outbreak in Kenya. Both genomes have a G+C content of 24% with sizes of 1,016,760 bp and 1,017,183 bp for strains F38 and ILRI181, respectively.
Approaches to vaccination against Theileria parva and Theileria annulata
(Journal Article, 2016-12) Nene, Vishvanath M.; Morrison, W. Ivan
Despite having different cell tropism, the pathogenesis and immunobiology of the diseases caused by Theileria parva and Theileria annulata are remarkably similar. Live vaccines have been available for both parasites for over 40 years, but although they provide strong protection, practical disadvantages have limited their widespread application. Efforts to develop alternative vaccines using defined parasite antigens have focused on the sporozoite and intracellular schizont stages of the parasites. Experimental vaccination studies using viral vectors expressing T. parva schizont antigens and T. parva and T. annulata sporozoite antigens incorporated in adjuvant have, in each case, demonstrated protection against parasite challenge in a proportion of vaccinated animals. Current work is investigating alternative antigen delivery systems in an attempt to improve the levels of protection. The genome architecture and protein-coding capacity of T. parva and T. annulata are remarkably similar. The major sporozoite surface antigen in both species and most of the schizont antigens are encoded by orthologous genes. The former have been shown to induce species cross-reactive neutralizing antibodies, and comparison of the schizont antigen orthologues has demonstrated that some of them display high levels of sequence conservation. Hence, advances in development of subunit vaccines against one parasite species are likely to be readily applicable to the other.
Dairy production systems and the adoption of genetic and breeding technologies in Tanzania, Kenya, India and Nicaragua
(Journal Article, 2016-12) Ojango, Julie M.K.; Wasike, C.B.; Enahoro, Dolapo K.; Okeyo Mwai, Ally
Development of the livestock industry and its role in poverty alleviation in developing countries depends on how adaptive the production systems are to changing global environmental and economic trends. This paper characterizes dairy production systems in India, Tanzania, Kenya and Nicaragua, and describes the genetic and breeding technologies that hold promise for the advancement of global development goals. The dairy value chain has been prioritized for development under the CGIAR research programme on Livestock and Fish in Tanzania (East Africa), India (South Asia) and Nicaragua (Latin America), while ILRI is involved in research on dairy development in Kenya. In all the countries, a large number of smallholder farmers operating mixed crop–livestock production systems play a significant role in dairy production. In Tanzania, Kenya and Nicaragua, milk is predominantly produced by cattle of genotypes that differ both across countries and among production systems within the same country. In India, buffaloes contribute to a larger proportion of the national milk than cattle. Information on productivity per animal and on optimal genotypes to utilize within the smallholder production systems of all the countries is however limited. Crossbreeding and artificial insemination were identified as the most widely utilized breeding and reproductive technologies. Only in Kenya is there a national organization conducting livestock recording and monitoring productivity, however, the proportion of the dairy cattle population enrolled in the recording system is small (<2.5 percent). In all the countries, enhanced and adequately planned use of breeding and reproductive technologies, complemented with the relevant infrastructure, is needed to sustainably increase dairy productivity. The capacities of actors in the dairy value chain need to be developed in order to properly implement and manage improvements.
Microsatellite based genetic diversity and mitochondrial DNA D-Loop variation in economically important goat breeds of Pakistan
(Journal Article, 2017-03) Naqv, A.N.; Bukhari, J.F.; Vahidi, S.M.F.; Yuri T. Utsunomiya; García, J.F.; Babar, M.E.; Han Jianlin; Pichler, R.; Periasamy, K.
The present study was undertaken to analyze the genetic diversity of five economically important goat breeds of Pakistan, Beetal, Kaghani, Teddy, Nachi and Pahari. Fifteen microsatellite loci recommended by ISAG/FAO guidelines were investigated for measures of genetic variability, differentiation and population structure. The genetic variability in terms of allelic diversity and heterozygosity were moderate. The estimated inbreeding coefficient was low in all the investigated goat breeds and not significant. Overall, the populations were less diverse than Eurasian goat breeds, but did not exhibit signs of loss of diversity. Analysis of molecular variance (AMOVA) showed breed differences accounted for 5.42% of total genetic variation indicating low to moderate genetic differentiation among the investigated goat breeds. The genetic structure analysis revealed Teddy, Pahari, and Nachi as distinct breeds, while Beetal and Kaghani form a single genetic group distinct from the other three goats. The mitochondrial DNA control region sequences showed a total of 60 distinct haplotypes belonging to two major maternal lineages A and B1 with a frequency of 76.9% and 23.1% respectively. Comparison of mtDNA sequences from Pakistani, Indian and Iranian goats indicated distinct evolutionary history for Teddy, Beetal, Nachi and Pahari goats different from that of Indian and Iranian goats.
Gendered intra-household contributions to low-input dairy in Senegal
(Journal Article, 2016) Walugembe, M.; Tebug, Stanly Fon; Tapio, M.; Missohou, Ayao; Juga, J.; Marshall, Karen; Rothschild, Max F.
A survey was conducted in two sites of Senegal to determine the intra-household gender roles in the Senegal dairy cattle systems. Two surveys, baseline and longitudinal were conducted and the main survey respondents were the households heads. Households were grouped into two levels (higher or lower) of market orientation using the longitudinal household milk production data. Baseline survey results revealed that adult males (> 15 years of age) were responsible for the costs and decision making of most of the dairy related activities though less so when production was quite low. Adult males, hired males (> 15 years of age), and any other household members, except the female gender were the main labor source for the dairy activities. When comparing who received income from milk sales, income from lower market orientated households went to females for a larger proportion of households, than in higher market orientated households.
Comparative study of Indigenous pig production in Vietnam and Sri Lanka
(Journal Article, 2016-10-31) Silva, Gamamada Liyanage Lalanie Pradeepa; Thuy, L.T.; Abeykoon, N.D.; Hanh, N.T.H.; Bett, R.C.; Okeyo Mwai, Ally; Ibrahim, Mohamed N.M.
Smallholder pig farming is an important livelihood source in many rural communities of countries in Asia region such as Vietnam and Sri Lanka. The indigenous pig population is diminishing over the years and it requires a better attention for conservation and sustainable utilization. The objectives of this study were to identify the pig farming system characteristics and investigate the effect of these characteristics on keeping pigs for livelihood in Vietnam and Sri Lanka. A total of 725 households were surveyed including 264 keeping pigs and 461 without pigs. Farming system characteristics were analyzed by descriptive statistics. The effect of farming system characteristics on keeping pigs for livelihood was determined by logistic regression models (Models I and II). The results revealed that majority of famers (>80) kept indigenous pigs as an income source in both countries. Free range pig rearing system with low cost feeding (mainly the kitchen waste) was predominant in Sri Lanka whereas confined pigs and providing commercial concentrates was mainly practiced in Vietnam. The average herd size was significantly (p<0.05) different in Vietnam (8) and in Sri Lanka (4). Age at first farrowing, farrowing intervals and number of piglets per farrow were higher in Vietnam than in Sri Lanka. The results of model-I showed that family size, availability of piped water, keeping other livestock than pigs, watering pigs adlibitum, positively influenced keeping pigs for home consumption, whereas feeding kitchen waste, availability of water connection in working condition and livestock income negatively influenced for the same attribute. The results of model-II revealed that availability of river water and livestock income have positive impacts while availability of piped water and watering pigs adlibitum have negative impacts on keeping pigs as a income source. These findings will be useful in formulating policies to conserve the gene pool of indigenous pigs and facilitate the indigenous pig production. Increasing indigenous pig production will contribute in considerable level to ensure the food security and income generation of rural families.
Description of production system and on-farm phenotypic characterization of Central Highland and Woyto-Guji goat breeds in Ethiopia
(Journal Article, 2016-06) Zergaw, N.; Dessie, Tadelle; Kebede, K.
The study examines phenotypic characterization of Central Highland and Woyto-Guji goat breeds at Meta Robi and Konso districts of Ethiopia. Purposive and random sampling techniques were employed to select sample villages and respondent. For administration of semi-structured questionnaire and phenotypic characterization, a total of 240 households and 601 adult animals, respectively, were selected. The average goat flock size (31.25 ± 22.46) owned per household of Konso was significantly (P < 0.01) higher than Meta Robi (12.73 ± 8). In Konso, natural pasture was the most frequently mentioned feed source during wet season, while hay was the most important feed source during dry season. On the other hand, in Meta Robi, natural pasture was the most frequently mentioned feed source during wet and dry seasons. Coat colour type, horn shape, ear orientation, wattle and beard were found to differ highly significantly (P < 0.001) among the two goat breeds. Goat breed had a significant effect (P < 0.001) on body weight and other body measurements except pelvic width (P > 0.05). The least-square means of body weight, body length, height at wither, chest girth, chest width, ramp length, horn length, ear length and pelvic width of Central Highland female goats were 29.5 ± 0.2 kg, 62.2 ± 0.2 cm, 67.5 ± 0.2 cm, 72.9 ± 0.2 cm, 13.4 ± 0.1 cm, 19.7 ± 0.1 cm, 12.8 ± 0.2 cm, 14.6 ± 0.1 cm and 13.5 ± 0.1 cm, respectively. The corresponding values for Woyto-Guji female goats were 24.8 ± 0.3 kg, 57.4 ± 0.2 cm, 61.9 ± 0.2 cm, 68.3 ± 0.2 cm, 12.1 ± 0.1 cm, 17.3 ± 0.1 cm, 10 ± 0.2 cm, 13 ± 0.1 cm and 13.4 ± 0.1 cm, respectively. The observed variations in production system and morphological traits among the sample populations coupled with their adaptive traits would indeed justify the need for designing breed improvement programme for both breeds.
Use of body linear measurements to estimate liveweight of crossbred dairy cattle in smallholder farms in Kenya
(Journal Article, 2016-12) Lukuyu, Margaret N.; Gibson, John P.; Savage, D.B.; Duncan, Alan J.; Mujibi, F.D.N.; Okeyo Mwai, Ally
Body linear measurements, and specifically heart girth (HG), have been shown to be useful predictors of cattle liveweight. To test the accuracy of body linear measurements for predicting liveweight, crossbred dairy cattle of different genotypes were measured and weighed. A total of 352 mature cows and 100 heifers were weighed using an electronic weighing scale and measurements of HG, body length, height at withers were taken using an ordinary measuring tape and body condition scored (BCS) using a five-point scale. The animals were grouped according to genotype and age. Genotype classification was undertaken from farmer recall and by visual appraisal as 40–60, 61–80 or 81–100 % exotic (non-indigenous). Age classification was simply as mature cows or heifers. Liveweight of the animals ranged from 102 to 433 kg. Liveweight was strongly correlated with HG (r = 0.84) and body condition scores (r = 0.70) and moderately correlated with body length (r = 0.64) and height at withers (0.61). Regressing LW on HG measurements gave statistically significant (P < 0.01) equations with R2 ranging from of 0.53 to 0.78 and residual standard deviation ranging from 18.11 to 40.50 kg. The overall model developed (adjusted R2 = 0.71) had a prediction error of 26 kg (or 11 % of the mean) and predicted LW of over 95 % of crossbred dairy cattle in the range of 100–450 kg, regardless of age and breed group. Including BCS in the model slightly improved the model fit but not the prediction error. It was concluded that the model can be useful in making general management decisions in smallholder farms
Complete genome sequence of Mycoplasma mycoides subsp. mycoides T1/44, a vaccine strain against contagious bovine pleuropneumonia
(Journal Article, 2016-04-28) Gourgues, G.; Barre, A.; Beaudoing, E.; Weber, J.; Magdelenat, G.; Barbe, V.; Schieck, Elise G.; Jores, Joerg; Vashee, S.; Blanchard, Alain; Lartigue, C.; Sirand-Pugnet, P.
Mycoplasma mycoides subsp. mycoides is the etiologic agent of contagious bovine pleuropneumonia. We report here the complete genome sequence of the strain T1/44, which is widely used as a live vaccine in Africa.
Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas
(Journal Article, 2016-07-22) Gorkhali, N.A.; Kunzhe Dong; Min Yang; Shen Song; Kader, A.; Shrestha, B.S.; Xiaohong He; Qian-Jun Zhao; Yabin Pu; Xiangchen Li; Kijas, J.; Weijun, Guan; Han Jianlin; Lin Jiang; Yuehui Ma
Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas.
Live weight, conformation, carcass traits and economic values of ram lambs of Red Maasai and Dorper sheep and their crosses
(Journal Article, 2017-01) Zonabend König, Emelie; Ojango, Julie M.K.; Audho, James O.; Mirkena, T.; Strandberg, E.; Okeyo Mwai, Ally; Philipsson, J.
Meat production is the most important trait in the breeding objectives of sheep production in East Africa. The aim of this study was to investigate breed differences in live weight, conformation, carcass traits and economic values for meat production among Red Maasai and Dorper sheep and their crosses. In total, 88 ram lambs, which were reared at the ILRI experimental station, Kapiti plains Estate in Central Kenya, were used for the study. The lambs were slaughtered at Kenya Meat Commission (KMC) at about 1 year of age. Prior to slaughter, the lambs were weighed, measured and assessed by experienced evaluators, and at the abattoir carcass traits were recorded. Large breed differences were found for most traits. Dorper lambs were heavier at delivery for slaughter and had better carcass grade but lower dressing percentage and fat levels than Red Maasai. Crossbreds were generally better than the parental breeds. Evaluators were willing to pay more for the Dorper lambs for slaughter although carcass weights later were shown not to be higher than for Red Maasai. Evaluators undervalued Red Maasai lambs by 8–13 % compared to Dorper lambs according to the prices quoted per kilogramme live or carcass weight by KMC. Live weight was better than any other live measure in predicting carcass weight. Due to the overall higher ranking of the crossbred lambs for meat production, Dorper may be useful as a terminal sire breed for crossing with Red Maasai ewes.
Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
(Journal Article, 2016-11) Vasoya, D.; Law, A.; Motta, P.; Mingyan Yu; Muwonge, A.; Cook, Elizabeth A.J.; Xiaoying Li; Bryson, K.; MacCallam, A.; Sitt, Tatjana; Toye, Philip G.; Bronsvoort, B.M. de C.; Watson, Mick; Morrison, W. Ivan; Connelley, T.
The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
Expression profiling and functional characterization of miR-192 throughout sheep skeletal muscle development
(Journal Article, 2016-07-25) Qian-Jun Zhao; Ye Kang; Hong-Yang Wang; Weijun, Guan; Xiang-Chen Li; Lin Jiang; Xiao-Hong He; Yabin Pu; Han Jianlin; Yue-Hui Ma
MicroRNAs (miRNAs) are evolutionarily conserved, small, non-coding RNAs that have emerged as key regulators of myogenesis. Here, we examined the miRNA expression profiles of developing sheep skeletal muscle using a deep sequencing approach. We detected 2,396 miRNAs in the sheep skeletal muscle tissues. Of these, miR-192 was found to be up-regulated in prenatal skeletal muscle, but was down-regulated postnatally. MiR-192 expression also decreased during the myogenic differentiation of sheep satellite cells (SCs). MiR-192 overexpression significantly attenuated SCs myogenic differentiation but promoted SCs proliferation, whereas miR-192 inhibition enhanced SCs differentiation but suppressed SCs proliferation. We found that miR-192 targeted retinoblastoma 1 (RB1), a known regulator of myogenesis. Furthermore, knockdown of RB1 in cultured cells significantly inhibited SCs myogenic differentiation but accelerated SCs proliferation, confirming the role of RB1 in myogenesis. Taken together, our findings enrich the ovine miRNA database, and outline the miRNA transcriptome of sheep during skeletal muscle development. Moreover, we show that miR-192 affects SCs proliferation and myogenic differentiation via down-regulation of RB1.
The complete mitochondrial genome of Mong Cai pig (Susscrofa) in Vietnam
(Journal Article, 2016-01-01) Thuy Nhien Thi Tran; Pan Ni; Jianhai Chen; Thuy Thi Le; Kemp, Stephen J.; Han Jianlin; Haiyan Wang; Zhao, Shuhong
The Mong Cai pig is an indigenous breed and popularly raised as maternal line in northern Vietnam. In this study, the complete mitochondrial genome sequence of the Mong Cai pig is reported. The total length of this mitochondrial genome is 16 632bp, including 1 non-coding control region (D-loop region), two ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. The phylogenetic tree of 162 pig complete mitogenomes reveals a very close relationship between Mong Cai pig in Vietnam and Bama miniature pig in southern China. This complete mitochondrial genome sequence of Mong Cai pig is useful to further genetic studies on adaptation and performance.
Variation in the straw traits of morphological fractions of faba bean (Vicia faba L.) and implications for selecting for food-feed varieties
(Journal Article, 2016-12) Alkhtib, A.; Wamatu, Jane; Wegi, T.; Rischkowsky, Barbara A.
Five varieties of faba beans, 4 improved and released variety and one local variety, were investigated for varietal variation in straw yield, nutritive value of straw morphological fractions and grain yield. Samples of the whole plant biomass were collected and separated into grain and straw. The straw was further divided into leaves, stems and pods. Straw samples were analyzed for their chemical composition, in vitro organic matter digestibility (IVOMD) and metabolizable energy (ME). The potential utility index (PUI) was employed to rank the varieties. The results demonstrated significant varietal variation in grain yield, straw yield and proportions of botanical fractions of straw. The improved varieties were superior to the local variety in grain yield, straw yield and PUI. The local variety had the highest proportion of stem and lowest proportion of leaf and pods. Significant varietal variations (P < 0.001) were detected in dry matter (DM), organic matter (OM), ash, IVOMD, ME but not in crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL) of whole straw. The leaves showed the highest IVOMD and content of crude protein, while pods were highest in ME. Canonical correlation analysis showed significant (P < 0.001) correlations between the nutritive value of whole straw and nutritive value and proportions of its botanical fractions. Grain and straw yields were positively, strongly and significantly (P < 0.001) correlated. Weak correlations were detected between grain yield and straw quality traits. Ranking the varieties differed when grain yield, straw quality scores and PUI were considered. However the weak correlation existed between grain yield and straw quality, including straw quality index or PUI to select food-feed varieties of faba bean is still necessary. These findings indicate the possibility of selecting faba bean varieties which combine superior grain and straw traits.

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