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High‐throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well‐structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on‐farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community‐based breeding programs in the South‐West of Burkina Faso. The three populations were pure Baoulé (called Lobi locally) in sedentary production systems, Baoulé x Zebu crossbreds in sedentary systems and Zebu × Baoulé crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoulé group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent–offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoulé animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community‐based breeding program will make use of genomic information about admixture levels.

Los corrales elevados (RP) han sido promovidos en las regiones tropicales de México como un sistema de alojamiento que mejora el comportamiento productivo de los corderos en crecimiento y han mostrado una gran aceptación entre los productores, tanto para corderos machos como en hembras; sin embargo, han sido poco estudiados y se han usado sin enriquecimiento ambiental en los sistemas intensivos. Por lo tanto, el objetivo de este estudio fue comparar el comportamiento productivo de corderos en crecimiento tanto machos como hembras alojados en RP y a nivel del suelo (GL) usando viruta como material de cama. Se usaron 32 corderos, 15 machos y 17 hembras, con un promedio de peso vivo y edad inicial de 10,54 ± 1,89 kg y 66,54 ± 22,43 días, respectivamente. Los datos fueron analizados empleando análisis de varianza, incluyendo como efectos fijos el tipo de alojamiento (RP y GL) y el sexo (machos y hembras) y las variables dependiente ganancia diaria de peso (DWG), el consumo de alimento (DMI), la conversión alimenticia (FC) y el peso vivo final (FBW). El tipo de alojamiento no tuvo efecto sobre DWG, DMI, FC y FBW (P > 0,05). Los machos presentaron mejores valores en todos los indicadores productivos que las hembras (excepto en FC). Bajo las condiciones de este estudio, el comportamiento productivo de corderos en crecimiento alojados ya sea en RP o en GL fue similar.

A morphometric characterization study was conducted using purebred Baoulé cattle and two crossbreds’ populations in the southwestern region of Burkina-Faso. A total of 421 cattle, including 266 crossbreds from the department of Kampti and Loropeni and 155 purebred Baoulé, from the department of Bouroum-Bouroum were measured for quantitative and qualitative traits. The quantitative traits were analyzed by fitting the linear model including genotype-location, sex, age and all two-way interactions. The chi square test was performed for qualitative traits. The results provide evidence for difference between purebred and crossbred populations, and among crossbreds for all traits. The genotype-location effect showed that facial length, distance between horn tips, ear length and chest width differed between purebred and crossbred populations. For qualitative traits, coat color and horn shape showed large variation between Baoulé and crossbreds. These results will serve as basis for further characterization, conservation and improvement strategies for purebred and crossbred populations.

Community-based breeding programs (CBBPs) for small ruminants have been suggested as alternatives to centralised, government-controlled breeding schemes which have been implemented in many developing countries. An innovative methodological framework on how to design, implement and sustain CBBPs was tested in three sites in Ethiopia: Bonga, Horro and Menz. In these CBBPs, the main selection trait identified through participatory approaches was 6-month weight in all three sites. In Horro and Bonga, where resources such as feed and water permitted larger litter sizes, twinning rate was included. Ten-year (2009 to 2018) performance data from the breeding programs were analysed using Average Information Restricted Maximum Likelihood method (AI-REML). Additionally, the socioeconomic impact of CBBPs was assessed. Results indicated that 6-month weight increased over the years in all breeds. In Bonga, the average increase was 0.21 ± 0.018 kg/year, followed by 0.18 ± 0.007 and 0.11 ± 0.003 kg/year in Horro and Menz, respectively. This was quite substantial in an on-farm situation. The birth weight of lambs did not improve over the years in Bonga and Horro sheep but significant increases occurred in Menz. Considering that there was no direct selection on birth weight in the community flock, the increased weights observed in Menz could be due to correlated responses, but this was not the case in Bonga and Horro. The genetic trend for prolificacy over the years in both Bonga and Horro flocks was positive and significant (P < 0.01). This increase in litter size, combined with the increased 6-month body weight, increased income by 20% and farm-level meat consumption from slaughter of one sheep per year to three. The results show that CBBPs are technically feasible, result in measurable genetic gains in performance traits and impact the livelihoods of farmers.

Simple Summary Alpaca breeding takes place in the most entrenched areas of the Andes, where the conditions to implement genetic improvement programs are very difficult. Likewise, taking phenotypic records is limited in its ability to predict genetic merit accurately. For this reason, genomic information is shown as an alternative that helps to predict the genetic values of fiber traits more precisely. This study showed how genomic information increased precision by 2.623% for the fiber diameter, 6.442% for the standard deviation of the fiber diameter, and 1.471% for the percentage of medullation compared to traditional methods for predicting genetic merit, suggesting that adding genomic data in prediction models could be beneficial for alpaca breeding programs in the future. Abstract Improving textile characteristics is the main objective of alpaca breeding. A recently developed SNP chip for alpacas could potentially be used to implement genomic selection and accelerate genetic progress. Therefore, this study aimed to compare the increase in prediction accuracy of three important fiber traits: fiber diameter (FD), standard deviation of fiber diameter (SD), and percentage of medullation (PM) in Huacaya alpacas. The data contains a total pedigree of 12,431 animals, 24,169 records for FD and SD, and 8386 records for PM and 60,624 SNP markers for each of the 431 genotyped animals of the Pacomarca Genetic Center. Prediction accuracy of breeding values was compared between a classical BLUP and a single-step Genomic BLUP (ssGBLUP). Deregressed phenotypes were predicted. The accuracies of the genetic and genomic values were calculated using the correlation between the predicted breeding values and the deregressed values of 100 randomly selected animals from the genotyped ones. Fifty replicates were carried out. Accuracies with ssGBLUP improved by 2.623%, 6.442%, and 1.471% on average for FD, SD, and PM, respectively, compared to the BLUP method. The increase in accuracy was relevant, suggesting that adding genomic data could benefit alpaca breeding programs.

The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.

Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2–50% while “local” blood contributed 69.2% (36.9–95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.

Gastrointestinal nematodes (GIN) remain one of the main health and production constraints of sheep globally. Considering alternatives to anthelmintics in control of GIN of sheep has become important mainly due to development of anthelmintic resistance. In this study, we used a questionnaire survey in combination with participatory epidemiology methods, ranking and scoring, with the objectives of (1) understanding local sheep disease problems related to GIN in community-based breeding programs (CBBP) in Bonga and Horro of Ethiopia, compared to neighboring communities not involved in CBBP, and (2) assessing current practices and preferences in control of GIN of sheep in both types of communities. The most important disease conditions of sheep in Bonga CBBP with weighed ranks of 1 to 3 were coenurosis, diarrhea and coughing. The corresponding sheep disease conditions in Horro CBBP were coughing, diarrhea and bottle jaw. Diarrhea and bottle jaw presumably are related to gastrointestinal nematodes. Ethnoveterinary medicinal plants are widely used in Bonga while the knowledge is at risk of loss in Horro. Respondents in non CBBP and CBBP communities did not differ (p > 0.05) regarding most of the plant species used frequently in control of GIN in Bonga. There was significant difference (p

Burkina Faso livestock is made up of two main cattle population, namely Zebuine and Taurine. Transhumance and settlement of Zebu cattle breeders in tsetse challenged areas lead to cross-breeding Zebu and Taurine. Introgression of the Zebu cattle may have changed the structure of the trypanotolerant Lobi/Baoule breed. The objective of the present study was to appreciate the introgression of Zebu genes into Baoule population by assessing the structure and the genetic diversity of cattle populations across the tsetse belt in Burkina Faso. Therefore, 450 blood samples were taken for genotyping in 29 villages of 3 main regions where Baoule, Baoule×Zebu and Zebu populations are found. Twenty five loci of 22 autosomes have been genotyped. The mean of observed alleles per locus was 12.44±4.31 while the mean of expected alleles was 4.67±1.48. The heterozygosity ranged from 0.34 to 0.76 and 0.36 to 0.87, respectively for observed and expected heterozygosity across loci. The average heterozygosity across population was 0.73±0.10. The mean estimates of F-statistics were FIS = 0.117±0.019, FIT = 0.158±0.019 and FST = 0.047±0.005. The phylogenetic tree showed the Baoule South-West segregating apart from the other populations, Baoule×Zebu being an intermediate genetic group between Baoule South-West and Zebu North populations. The Baoule West could not be differentiated from crosses. The Baoule breed seems to be impacted by the introgression of Zebu genes to its biotope and pure Baoule seems to be confined to the South-West with very few pure individuals in the West. Key words: Burkina Faso, Zebu, Baoule×Zebu, Baoule, introgression, microsatellite.

In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.

This study aimed to estimate genetic parameters for four guinea pig lines of a crossbreeding scheme. Two paternal lines are selected for growth rate (P1) and feed conversion rate (P2), whereas two maternal lines are selected for growth rate of litter (M1) and litter size at birth (M2). The heritabilities and genetic correlations were estimated with animal linear models employing multivariate analyses with REML. The heritabilities for birth weight (BW) were 0.21±0.02 and 0.23±0.03 for P1 and P2, respectively, and for weaning weight (WW), the heritability was 0.28±0.03 for P2. The estimates for weight at 60 days of age (W60) were 0.34±0.01 and 0.47±0.04 for P1 and P2, respectively, and for partial feed conversion rate was 0.46±0.03 for P2. Heritabilities for litter weight at birth (LW) were 0.09±0.03 and 0.10±0.03 for P1 and M1, respectively. For litter weight at 10 days of age (LW10), the heritability was 0.15±0.03 for M1. Heritabilities for litter size (LS) were 0.17±0.03, 0.20±0.03 and 0.11±0.03, and for number of pups born alive (BA) were 0.09±0.03, 0.14±0.03 and 0.09±0.03 for P1, M1 and M2, respectively. Similarly, high genetic correlations were found between BW, WW and W60 and between LW, LS, LW10 and BA. The genetic correlation between BW direct and maternal was moderately negative (− 0.24 ± 0.10) for P1. These results show the genetic status for all four guinea pig lines, which is essential for the further improvement of the currently implemented breeding programme and also indicate an opportunity for genetic improvement.

Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.

A comprehensive dynamic simulation model was developed to describe a community-based breeding program for the Menz sheep population of Ethiopia. Selection of male and female animals based on their own and maternal performance was simulated. The breeding goal traits were 6-mo weight, preweaning survival, and fertility rate. The model input data were obtained from the flock book, questionnaires, and references. The simulation model used a mix of deterministic and stochastic procedures to model the complex system. In the baseline scenario, the proportion of selected male and female animals varied between 20 and 30% and between 70 and 80%, respectively. A reasonable annual genetic gain was predicted for the breeding goal traits at the village level. For 6-mo weight and preweaning survival rate, the annual genetic gain varied from 0.213 to 0.214 kg and 0.255 to 0.256%, respectively. For fertility rate, an annual genetic gain of 0.063% was obtained. The predicted rate of inbreeding per year was between 0.094 and 0.116%. Furthermore, a scenario analysis was conducted by varying the proportions of selected animals. Annual genetic gains of 0.230 kg, 0.277%, and 0.069% were obtained for 6-mo weight, preweaning survival rate, and fertility rate, respectively, when the proportion of selected male and female animals decreased by 10%. The annual genetic gains decreased to 0.198 kg, 0.236%, and 0.059%, respectively, when the selection proportion of male and female animals increased by 10%. The lowest rate of inbreeding per year, ranging from 0.065 to 0.079%, was achieved when the selection proportion of selected male and female animals increased. The model is relevant for the step-by-step evaluation of more than one round of selection. It is flexible and usage driven. The model is a valuable tool to design different population structures and can be easily expanded to adopt different breeding strategies. Hence, the system dynamics modeling approach is a potential tool to describe complex breeding programs.

Made available in DSpace on 2019-10-06T15:49:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Genetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors (age) associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model. Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH > 2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH > 2Mb, and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding. Division of Livestock Sciences Department of Sustainable Agricultural Systems University of Natural Resources and Life Sciences Department of Animal Science Faculty of Agriculture Lilongwe University of Agriculture and Natural Resources Animal Genomics and Improvement Laboratory United States Department of Agriculture Agriculture Research Service National Livestock Resources Research Institute Department of Agriculture Kyambogo University School of Agricultural and Veterinarian Sciences Jaboticabal São Paulo State University (UNESP) Department of Animal Science Faculty of Agriculture University of Zagreb School of Agricultural and Veterinarian Sciences Jaboticabal São Paulo State University (UNESP)

The effect of two housing systems during the fattening period on productive performance of lambs from different hair-type sheep breeds in southeastern Mexico was evaluated. Effects of housing system (raised-slatted floor cages (RFC) vs. floor pens (FP)), year (2009, 2012 and 2013) and season of the year (rainy vs. dry) on average daily gain (ADG), weights adjusted to 60 (P60) and 90 (P90) days post-weaning were evaluated. Data from 1213 lambs collected on the farm over a period of three years were analysed. The ADG, P60 and P90 were affected (P

The objective of this review paper is to examine whether or not sheep crossbreeding is a feasible option to improve indigenous sheep breeds in developing countries using Ethiopian case as example. The paper reviewed and discussed the history of exotic breed introduction, research, and development efforts in crossbreeding and performance of crossbreds under on-station and on-farm management. Earlier, the choice of breed for crossbreeding overlooked interests and preferences of farmers mainly for physical appearance. More recently the introduction of Awassi sheep considered their preference. Performance evaluation results from the on-station and on-farm (mainly based on Awassi pilot crossbreeding villages) showed that crossbreds often outperformed their local contemporaries. Thus comparisons of pure local sheep and crossbreds among those breeds produced in some areas indicated a good outcome of this type of crossbreeding. However, the performance of crossbred sheep varied by location and depended on management and exotic inheritance levels. For most programs, no comprehensive data were available to do on-farm comparisons of herd productivity and cost-benefits or to evaluate the sustainability of the programs. Regardless of location, farmers participating in crossbreeding often showed keen interest in crossbreeding, mainly due to the fast growth, larger body size of crossbreds resulting in higher market prices as compared to their local sheep breeds. Ram multiplication and dissemination from the government farms were found inefficient. The predominant practice of a ubiquitous dissemination and selling of breeding rams to individual farmer dilute the efforts of crossbreeding and prevents generating the benefits expected from crossbreeding programs. Furthermore, indiscriminate crossbreeding without prior analysis of suitability of crossbreds for a given production environment and without clear breeding objectives presents a potential threat to better adapted indigenous breeds. Crossbreeding programs require strong research and development support from public service and non-governmental institutions for sustainable design, optimization, and implementation in clearly defined production environments. Key words: Awassi, developing countries, Dorper, on-farm performance, smallholder farmer.

Received: 2016-07-14 | Accepted: 2016-07-28 | Available online: 2017-03-31 http://dx.doi.org/10.15414/afz.2017.20.01.10–12 This study was carried out to estimate the inbreeding levels in Abergelle, Gumuz, Keffa and Woytoguji goats in Ethiopia from genomic information. A total of 161 animals (53 Abergelle, 39 Gumuz, 31 Keffa and 38 Woytoguji) were genotyped using the Illumina 50K SNP chip. Runs of homozygosity were computed at cut-offs of 1MB, 2MB, 4MB, 8MB and 16MB, using cgaTOH Analysis & Clustering Suite, Version 1.0.1. The estimated levels of inbreeding based on runs of homozygosity greater than 1MB were 0.0210, 0.0209, 0.0502 and 0.0199 for Abergelle, Gumuz, Keffa and Woytoguji, respectively. The results suggest that inbreeding levels are low in the four breeds, although relatively higher in the Keffa breed than in the other three breeds. Suitable strategies may need to be implemented for reducing inbreeding when designing breeding programmes for the Keffa goats. This study was carried out to estimate the inbreeding levels in Abergelle, Gumuz, Keffa and Woytoguji goats in Ethiopia from genomic information. A total of 161 animals (53 Abergelle, 39 Gumuz, 31 Keffa and 38 Woytoguji) were genotyped using the Illumina 50K SNP chip. Runs of homozygosity were computed at cut-offs of 1MB, 2MB, 4MB, 8MB and 16MB, using cgaTOH Analysis & Clustering Suite, Version 1.0.1. The estimated levels of inbreeding based on runs of homozygosity greater than 1MB were 0.0210, 0.0209, 0.0502 and 0.0199 for Abergelle, Gumuz, Keffa and Woytoguji, respectively. The results suggest that inbreeding levels are low in the four breeds, although relatively higher in the Keffa breed than in the other three breeds. Suitable strategies may need to be implemented for reducing inbreeding when designing breeding programmes for the Keffa goats. Keywords: goats, genome, inbreeding, runs of homozygosity References FALCONER, D.S. and MACKAY, T.F.C. (1996) Introduction to quantitative genetics . 4th ed. London: Longman FERENCAKOVIC, M., et al. (2011) Runs of Homozygosity Reveal Genome-wide Autozygosity in the Austrian Fleckvieh Cattle. Agriculturae Conspectus Scientificus, vol . 76, pp. 325–329. FERENCAKOVIC, et al.(2013) Estimates of autozygosity derived from runs of homozygosity: Empirical evidence from selected cattle populations. Journal of Animal Breeding and Genetics , vol. 130, pp. 286–293. doi: http://dx.doi.org/10.1111/jbg.12012 PURCELL, S., et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics , vol. 81, pp. 559–575. doi: http://dx.doi.org/10.1086/519795 PURFIELD, D.C., et al. (2012) Runs of homozygosity and population history in cattle. BMC Genetics , vol. 13, no. 70. 1 p. doi: http://dx.doi.org/0.1186/1471-2156-13-70 TEFERA, M. (2013) Atlas biogeography and biodiversity of indigenous wild mammals of Ethiopia . Alemaya: Haramaya University. ZHANG, L., et al. (2013) cgaTOH: Extended Approach for Identifying Tracts of Homozygosity. PLoS One, vol. 8, no. 1. doi: http://dx.doi.org/0.1371/journal.pone.0057772

Understanding characteristics of production systems and identification of specific preferred traits related to breeding objectives is a first important step to the successful implementation of any breeding program. This study was conducted in the South West of Burkina Faso, the traditional habitat of trypanotolerant Baoule cattle, to identify farmers’ trait preferences and breeding practices. Following a synthesis of information from stakeholders, a structural questionnaire was designed and administered to 194 heads of households. Cattle herd structure was investigated via herd survey on 101 farms to record breed, age, status, weight and linear body measurements of animals. Own herd ranking method was used in addition to identify the most important criteria for selecting breeding cows. The importance of each criterion was estimated by computing the index of ranking. Regarding breeds and herd mobility, sedentary pure Baoule, sedentary mixed breed, and transhumant Zebu and crossbred systems were defined. Average cattle herd size was 51.23±55.72 heads and was significantly (P˂0.05) highest in the transhumant Zebu and crossbred system. Herd structure showed that cows were the most frequent age-sex-class in all the production systems. A high proportion of all farmers reported purposefully selecting their breeding animals but only 36.67% of them in pure Baoule system select their breeding females. Breeding bulls were selected from young males in the own herd and they were selected significantly (P˂0.05) later in pure Baoule system. The majority of transhumant farmers reported castration of not selected males while only 33% of farmers in pure Baoule system reported that. The most important common criteria for selection among the production systems were adult size for both males and females, including calf growth for females. Production systems were heterogeneous on the other preferred traits. Based on these findings, implementation of breeding programs involving farmers and their specific characteristics and practices can contribute to improve and conserve local cattle breeds in this area. Community-based breeding programs for pure Baoule and crossbreds aiming to improve body size and trypanotolerance are being implemented.

Improved Awassi sheep from Israel has been used for the improvement of the productivity of Ethiopian short-fat tailed Menz and Wollo sheep breeds through crossbreeding. High density (~50,000) single nucleotide polymorphism (SNP) markers distributed along the ovine genome were analyzed for Menz (n = =34), Wollo (n = =18), local Awassi (n = =24) and improved Awassi (n = =23) sheep breeds to assess genetic diversity and population structure. Proportion of polymorphism was highest for local Awassi (96.2%) followed by the Ethiopian breeds (91.7 to 93.0%). Lowest proportion of polymorphic SNP was found in improved Awassi (84.3%). Expected heterozygosity was high (0.37) for local Awassi followed by the local Ethiopian breeds (0.35 and 0.36) and the improved Awassi (0.35). Highest genetic differentiation measured as fixation index (FST) appeared between local Ethiopian breeds and improved Awassi (FST ~ 0.14) while the two Ethiopian breeds were closely related (FST=0.004). Surprisingly, local Awassi sheep differentiated from improved Awassi at a higher level (FST = 0.09) than it differentiated from Wollo (FST = 0.058) and Menz (FST = 0.065). Principal component, model based structure and neighbor net analysis revealed clustering of populations according to their geographic location and breed development history. Strong selection pressure on the Awassi sheep resulted in significant differentiation from local Awassi, less within population variation, excess monomorphic loci and high level of runs of homozygosity (ROH) based genomic inbreeding. The high level of differentiation between local Ethiopian and improved Awassi supported the use of improved Awassi sheep to improve Menz and Wollo sheep breeds. However, importation of Awassi sheep and mating should consider strategies of controlling the level of inbreeding.

A study was conducted in the Himalayan mixed conifer forests to generate estimates of cattle carrying capacity of logged sites, using consumable forage dry matter and nutrient content. Field samples were collected from four major understory vegetation types dominated by Yushania microphylla (ground cover proportions of 100% and 50%), Rubus nepalensis, Synotis alata and Sambucus adnata. The amount of dry matter, total digestible nutrient and digestible crude protein removed by cattle grazing was highest for the vegetation with 100% Y. microphylla. Vegetation with S. adnata, S. alata and R. nepalensis provided low consumable dry matter yield and nutrient content per hectare area. For vegetation with 100% Y. microphylla, based on consumable dry matter, total digestible nutrients and digestible crude protein, the cattle carrying capacities were estimated at 4.17, 2.27 and 1.27 Livestock Units per Year (LUY) per hectare, respectively. Vegetation with 50% Y. microphylla provided about one LUY per hectare both in terms of consumable DM and nutrient content. Vegetation with S. alata also provided nutritional carrying capacity of about one LUY per hectare but the carrying capacity in terms of consumable dry matter was lower than one LUY per hectare. Cattle carrying capacity, both in terms of dry matter and nutrient content was lower than one LUY per hectare for vegetation with S. adnata and R. nepalensis. We concluded that, depending on the type of understory vegetation, carrying capacity differs within hemlock-dominated mixed conifer forest in the Eastern Himalaya. Forage utilization was higher for S. alata, S. adnata and R. nepalensis vegetation, suggesting the need for vigilance to avoid overgrazing in these vegetation types. The study indicates the opportunity to select appropriate carrying capacities allowing optimum cattle density and providing the required level of nutrition, while avoiding over-grazing. We recommend our estimates to be used as guide to better understand the carrying capacity of logged sites in the Himalayan conifer forest.

Survival analysis applying proportional hazards models was used to investigate genetic and non-genetic factors affecting ewe longevity and lamb survival of sheep in Ethiopia. Data were obtained from an on-station closed nucleus breeding program of Menz sheep and an on-farm Awassi×Menz sheep crossbreeding project. A total of 695 ewes and 1890 lambs born from the nucleus population of Menz sheep were used for the analysis of ewe productive life and lamb survival to yearling age respectively. In addition, 5530 lamb records of purebred local and crossbreds with proportions of ~25–50% Awassi, collected from three locations were used for the analysis of lamb survival from birth to weaning age. The effects of year, ewe parity and litter weight at weaning were significant (p

Argentina’s annual camelidfibre production is estimated at 60 000 kg for llama (Lama glama), somewhat more than 2 000 kg for gua-naco (Lama guanicoe) and about 845 kg for vicuña (Vicugna vicugna). The potential for increasing these amounts is huge consideringthat barely 30 percent of llamas are shorn and considering the size of the wild camelid population in the country. A compilation ofpublished and unpublished work confirms that almost 50 percent of the llamas are single-coated, about 40 percent have whitefleecesand that averagefibre diameter is about 22 μm in the main llama production area. In general, there is a wide variation infleece weightsandfibre quality between and within herds. However, a llamafleece classing and pricing system is not yet in place to motivate imple-mentation of such programmes. Guanaco and vicuñafleeces are double-coated but thefine undercoat represents more than 80 percent ofthefleece weight. The proportion of downfibre remaining after mechanical dehairing is only 50 percent in guanacos and 70 percent invicuñas. The guanaco undercoatfibre diameter is about 16 μm and vicuñafibre diameter is typically between 13 and 14 μm. Bothfibresare relatively short. Research is needed to establish optimum shearing season and shearing frequency that results infibre qualitydemanded for handcraft and industry in each of the three species. La producción anual defibras de camélidos en la Argentina se estima en 60.000 kg de llama (Lama glama), algo más de 2 000 kg deguanaco (Lama guanicoe) y unos 845 kg de vicuña (Vicugna vicugna). El potencial para aumentar esas cifras es enorme considerandoque apenas el 30% de las llamas son esquiladas y considerando el tamaño de las poblaciones de camélidos silvestres de ese país. En unarecopilación de trabajos publicados y trabajos inéditos se confirma que casi el 50% de las llamas tienen vellones de simple capa, el 40%de los vellones son blancos y que el promedio de diámetro defibras es menor a 22 μm. En general se observa una gran variabilidad enpesos de vellón y en caracteres cualitativos de lasfibras entre y dentro de tropas. Sin embargo todavía no hay un sistema de clasificacióncon precios diferenciales que motive al productor a implementar tales programas de mejora. Los vellones de guanacos y de vicuñas sonde doble capa aunque la capa interior representa más del 80% del peso de vellón. El descerdado mecánico deja solo un 50% defibrasfinas de guanaco y 70% defibrasfinas de vicuñas. El diámetro defibras de la capa interior de los guanacos es de aproximadamente16 μm y el de vicuñas está entre 13 y 14 μm. Ambasfibras son relativamente cortas. Es necesario estudiar en los tres camélidos laépoca y la frecuencia de esquila que resulten enfibra de la calidad demandada por artesanos e industria. Fil: Mueller, Joaquin Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; Argentina Fil: Rigalt, Francisco Antonio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Catamarca; Argentina Fil: Lamas, Hugo Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Abra Pampa; Argentina Fil: Sacchero, Diego Mariano. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; Argentina Fil: Cancino, Andrea Karina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; Argentina Fil: Wurzinger, Maria. University of Natural Resources and Applied Life Sciences. Department of Sustainable Agricultural Systems. Division of Livestock Sciences; Austria

Background Understanding the relationship between genetic admixture and performances is crucial for the success of crossbreeding programs. Use of small sets of ancestry informative markers (AIMs) is a cost effective option to estimate the levels of admixture in situations where pedigree recording is difficult. In this study we select AIMs from Ovine 50KSNP data (SNP – single nucleotide polymorphism) and validate their ability in estimating the contributions of parental breeds to get information about optimum admixture levels for smallholders. Results We estimated admixture levels using ADMIXTURE software based on 74 AIMs selected from Ovine 50KSNP data. Awassi x Ethiopian fat-tailed crossbred sheep populations kept in government farms and farmer villages in different districts were included in the study. Mean Awassi levels estimated based on the selected AIMs were close to the Awassi levels obtained from pedigree information. Estimates from the 74 SNPs were compared to subsets of 65, 55, 45, 35, 25 and 15 SNPs selected based on both top and bottom fixation index (FST) rank using Spearman’s rank correlation (r = 0.862–0.996). A t-test comparison revealed that all SNP subsets had produced similar (P > 0.05) estimates with the 74 SNPs, except for the bottom 15 SNPs (P

We investigated whether species richness, diversity and density of understory herbaceous plants differed along logging (gap) and grazing (primarily by cattle) disturbance gradients, and sought to identify drivers of richness, diversity and density of understory vegetation of logged sites. A factorial experiment was conducted in the mixed conifer forest of Gidakom in Western Bhutan. Levels of the logging treatment included small (0.15 – 0.24 ha), medium (0.25 – 0.35 ha) and large (0.36 – 1.31 ha) gaps. The grazing treatment included grazed (primarily by cattle) and ungrazed (where herbivores were excluded by a fence) plots nested within each gap. Data were collected from 12 gaps (4 replicates at each level of logging) using the point intercept method. Shannon Weaver Diversity and Margalef’s indices were used to estimate species diversity and describe species richness, respectively. Soil samples were analyzed for pH and nutrients. The interaction effect of logging and grazing was significant (p≤0.001) only on species diversity. Relative to ungrazed areas, species diversity was significantly higher (0.01≤p≤0.05) in medium grazed gaps. Under grazed conditions, soil P was negatively correlated with gap size and species diversity. While species diversity was positively correlated (0.01≤p≤0.05) with soil N in grazed plots species richness was positively correlated (0.001≤p≤0.01) with soil N in ungrazed plots. Relative density of Yushania microphylla and Carex nubigena were higher under ungrazed conditions. Our study suggests that the combined effect of cattle grazing and logging results in higher species diversity of understory vegetation in medium and grazed gaps in mixed conifer forests of Bhutan,whereas increase or decrease in relative density of major species is determined primarily by the independent effects of grazing and logging. From management perspective, forest managers must refrain from creating large gaps to avoid loss of nutrients (mainly P and N), which may eventually affect tree regeneration. Managers intending to maintain understory vegetation diversity must consider the combined effects of grazing and logging, ensuring low to moderate grazing pressure.

A community-based sheep breeding program has been implemented in the highlands of Ethiopia to improve the body weight of Menz sheep. It is important to evaluate the potential consequences of such a breeding strategy on herd dynamics. For this purpose, a dynamic, stochastic herd model was built. The model adopts a system dynamics methodology to study the effect of genetic improvement of body weight on herd dynamics and profitability. The length of the time horizon was 240 months (20 years). The first 120 months served as a baseline scenario, where the fattening of culled breeding rams was practiced. For the second 120 months genetic selection of body weight was introduced considering two scenarios: culled ram and lamb fattening. Results from the model showed a gradual decrease in sheep population size while body weight of the animals improved. The model keeps heavier animals in smaller flocks to match the herd dry matter demand with the available resources. The simulation also demonstrates that breeding for heavier body weight was considerably more profitable than the baseline scenario; and lamb fattening was more profitable than culled ram fattening, as the current practice. Furthermore, voluntary culling may be used to balance herd size with available feed resources. The introduction of a more intensive system that provides more feed resources by resourceful smallholders can be used to achieve higher income without reducing flock size. Further work is however needed to evaluate the model introduced here against field results.

Trypanosomosis is an important disease affecting humans as well as animals. It remains a big constraint to livestock productions in tropical areas. The objective of this study was to assess the importance of trypanosomosis among cattle diseases in Burkina Faso, mainly in tsetse-challenged areas, and to capture information on how farmers apply available methods for controlling the disease. A survey has been carried out in 29 villages of Burkina Faso in three regions (north, southwest, and west regions). One hundred and thirty-four cattle breeders were interviewed individually with a questionnaire. The results indicate that among the 16 diseases mentioned by cattle breeders, trypanosomosis is the most important one in tsetse-challenged areas. Overall, 76.12 % of the breeders mentioned it as the most important disease, while 54.55 % of the farmers in the southwest region and 70.91 % of the farmers in the west region ranked it as a priority disease. Chemoprophylaxis/chemotherapy is widely used as a control method. Isometamidium chloride and diminazene aceturate were used by 53.49 and 46.52 % of the responders, respectively. Among farmers, 85.55 % ranked diminazene aceturate as the less efficient while 14.45 % ranked isometamidium chloride as the most efficient trypanocid. Trypanocidal drug quality and drug resistance were raised as a major concern by 30.77 and 50 % of the respondents, respectively. According to them, zebu cattle are more susceptible to trypanosomosis than taurine Baoule cattle and their crosses with zebu, emphasizing that crossing susceptible breeds with trypanotolerant ones, could be used as part of an integrated control strategy.

A bio-economic model was adapted to estimate economic values for important traits of two Ethiopian indigenous sheep breeds, the Menz and Horro breeds. To do so, a meat sheep herd for fattening lambs and rearing young replacement sheep was simulated. Traits included in the analysis were: daily gain (fattening trait), live weight of ewes, length of productive life, lambing interval, litter size, stillbirths and lamb survival (functional traits). To avoid double counting, the economic value for each trait was derived while keeping all other traits constant. Economic values were obtained per ewe place, year, and genetic standard deviation. For the Menz breed, economic values in € per genetic standard deviation were 0.63 (daily gain), −0.77 (mature ewe live weight), −0.97 (length of productive life), 1.57 (lambing interval), 0.98 (litter size), 0.41 (stillbirths) and 2.20 (lamb survival). Economic values (in €) of 1.35 (daily gain), −1.26 (mature ewe live weight), −1.15 (length of productive life), 1.98 (lambing interval), 3.67 (litter size), 0.56 (stillbirth) and 3.25 (lamb survival) were derived for the Horro breed. Negative economic values for length of productive life and mature ewe live weight were estimated for both breeds. After setting the economic values of length of productive life and mature ewe live weight to zero, the economic values (in %) for the ratio of the trait complexes fattening: functional traits were 11:89 and 12.5:87.5 for Menz and Horro, respectively. Economic values for litter size, lambing interval and lamb survival traits were sensitive to changes in price for breeding rams in both breeds.

The Bahima ethnic group have been crossbreeding autochthonous Ankole with Holstein-Friesian cattle. Separate herds (pure Ankole and crossbreds) are common. A survey was conducted to characterize pasture utilization and management in the Ankole region to gain a better understanding of current and emerging practices. Herds are largely grazed by continuous stocking although there are efforts to establish paddocks. Factors considered for pasture allocation to cattle genotypes were high-quality feed, limited shrubs/weeds and close proximity to homestead for 80, 80 and 30% of farmers, respectively. Cross-bred cattle were kept on medium/high-quality, and Ankole cattle on medium/low-quality pastures. Pastures for cross-bred cattle yielded 0·17 t ha−1 more dry matter than pastures allocated to Ankole cattle. Crude protein (CP) content of Ankole pasture was significantly (P

Summary Based on the results of participatory approaches to define traits in the breeding objectives, four scenarios of ram selection and ram use were compared via deterministic modelling of breeding plans for community-based sheep breeding programmes in four diverse agro-ecological regions of Ethiopia. The regions (and production systems) were Afar (pastoral/agro-pastoral), Bonga and Horro (both mixed crop-livestock) and Menz (sheep-barley). The schemes or scenarios differed in terms of selection intensity and duration of ram use. The predicted genetic gains per year in yearling weight (kilograms) were comparable across the schemes but differed among the breeds and ranged from 0.399 to 0.440 in Afar, 0.813 to 0.894 in Bonga, 0.850 to 0.940 in Horro, and 0.616 to 0.699 in Menz. The genetic gains per year in number of lambs born per ewe bred ranged from 0.009 to 0.010 in both Bonga and Horro. The predicted genetic gain in the proportion of lambs weaned per ewe joined was nearly comparable in all breeds ranging from 0.008 to 0.011. The genetic gain per year in milk yield of Afar breed was in the order of 0.018 to 0.020 kg, while the genetic gain per generation for greasy fleece weight (kg) ranged from 0.016 to 0.024 in Menz. Generally, strong selection and shorter duration of ram use for breeding were the preferred options. The expected genetic gains are satisfactory but largely rely on accurate and continuous pedigree and performance recording.

High altitude pulmonary hypertension is common in cattle at high altitude areas. The extent of proneness, epidemiology, and genetics of the disease is not, however, known in Ethiopia where a large proportion of the area is at altitudes above 2700 m. To learn about adaptive characteristics of cattle towards altitude, a study of physiological adaptation, measured via pulmonary artery pressure (PAP) score from 218, hematological parameters from 672, and arterial oxygen saturation predicted by pulse oximeter from 241 animals was conducted in North Western Ethiopia. Local breeds and their crosses with Holstein Friesian and Jersey were investigated. Results showed that all PAP scores (21 to 47 mm Hg) fall under low to moderate risks. No sign of pulmonary hypertension was observed among all the cattle genotypes. Crosses of the local cattle with Holstein Friesian and Jersey were not more prone to the disease than local cattle. A statistically significant (P 0.05) in % SaO2. We report a new clinically relevant range of oxygen saturation, ≥ 68%, for the high altitude cattle which is far below the threshold value usually assumed for temperate cattle, > 80%. Hematological values of the studied genotypes lie within normal ranges set for temperate breeds despite suffering from heavy parasitic infestation. The significantly greater (P

The current study evaluated the effect of glutamate supply on the onset of puberty and possible links to changes in serum concentrations of insulin [INS], glucose [GLU] and triiodothyronine [T3]. The study was conducted from June to November in prepuberal female goats (n=18; 3 mo. old, 7/8 Saanen-Alpine, 1/8 Criollo, 26° north) randomly assigned to two experimental groups (i) excitatory amino acids group (group AA, n=10; 16.52±1.04kg LW, 3.4±0.12 body condition score [BCS], receiving an intravenous infusion of 7mgkg-1 live weight [LW] of l-glutamate, twice a week, and (ii) control group (group CC, n=8; 16.1±1.04kg LW, 3.1±0.12 BCS) receiving saline. Blood samples were obtained twice a week, for assessing progesterone [P4], as well as in a monthly basis to evaluate INS and T3 by RIA. Mean final LW and BCS were 23.2±0.72kg, 3.53±0.10units, without differences between groups. The AA group depicted an earlier onset of puberty (6.9±0.3 compared to 7.5±0.4 mo.; P0.05, respectively). Serum T3 concentrations, however, were greater in AA goats (1.55±0.03 compared to 1.39±0.04ngmL-1). In addition, a treatment x time interaction occurred (P0.05) for glucose concentrations across time occurred between treatments. Results indicate that, in prepuberal goats, glutamate acts as a cue for sexual maturation in a glucose-independent pathway, while both T3 and INS seem to act as metabolic modulators for the establishment of puberty in goats. Actions of INS and T3 are mediated directly on hypothalamic centers regulating the pulsatile release of GnRH or indirectly by peripheral cues reflecting INS-T3 actions on somatic development remains to be determined. © 2011 Elsevier B.V.

El objetivo de este estudio fue caracterizar las estrategias de alimentación existentes y las principales fuentes de alimentación utilizadas en dos diferentes sistemas de producción caprina en el altiplano mexicano durante la temporada de seca. Se recolectaron plantas forrajeras importantes en los pastizales, éstas fueron analizadas para conocer su contenido de nutrientes. En encuestas y talleres participativos, los granjeros proporcionaron información sobres sus sistemas de producción. Se recopilaron análisis químicos de 43 plantas forrajeras durante la temporada de seca, estos análisis en su mayoría mostraron escasos contenidos de nutrientes. Algunas leguminosas y compuestas tuvieron un valor razonable de alimentación, pero podrían contener mecanismos de defensa los cuales limitan su uso potencial. Mejorar o incluso mantener la productividad del sistema de producción actual depende fuertemente del mejoramiento de la base nutricional, sobre todo durante la temporada de seca que es cuando las plantas forrajeras escasean. Enfoques recientes, como el cultivo de ciertas plantas forrajeras, las cuales también contribuyen a la reducción de la erosión y la pérdida del suelo, deberían ser desarrollados e implementados. La información proporcionada por los granjeros muestra que los dos sistemas de producción estudiados en el presente artículo difieren: Por una parte, los granjeros se basan principalmente en los métodos agrícolas tradicionales, y por la otra, los granjeros están continuamente en busca de nuevas opciones agrícolas con fuerte apoyo técnico de un proyecto externo.

High feed-cost constraints are currently threatening the livelihoods of farmers fattening lambs in developing Middle Eastern countries. Reduced-cost feeds and adequate management alternatives are needed for more efficient lamb-fattening systems. Therefore lamb fattening performances of different Awassi sheep genotypes, on different diets and fattening environments, were therefore evaluated. Two trials were conducted. The first trial was conducted on-farm in northern Syria to assess the fattening performance of Syrian Awassi, and Turkish × Syrian Awassi crossbred lambs, and the suitability of 2 cost-reducing feeding diets compared to the traditional spring fattening diet of grazing green barley with supplementation (C): intensive feeding based only on concentrate and barley straw (D1) and semi-intensive grazing on vetch (Vicia sativa) with minor supplementation using the same D1-mix (D2). Lambs of both genotypes did not significantly differ in weight gain in the 49-day fattening period. There were no significant differences in weight gains among C, D1 and D2 diets: 14.4, 15.3 and 15.9 kg/lamb, respectively. The D2 diet reduced feeding costs by 20% and promoted high growth, notwithstanding its beneficial soil effects. The second trial was conducted on-station at the International Center for Agricultural Research in the Dry Areas (ICARDA), Syria, to assess the fattening performance of lambs of the above 2 genotypes in addition to Turkish × (Turkish × Syrian) crossbred lambs, both in indoor and outdoor conditions. Paralleling the first trial, live weight gains of the 3 genotypes did not differ significantly. Fattening lambs under a more favorable and healthier outdoor environment using a simple shed, avoiding negative effects of lack of ventilation and high temperature, produced significantly more live weight gain (5.8 kg) per lamb than indoors. No differences in smell, taste, juiciness and tenderness were found among genotypes in the second trial, confirming no negative effects of using these diets in the first trial, reported elsewhere. There were no statistical differences in smell, taste, juiciness and tenderness, in the meat with the distinct diets or the fattening (indoor/outdoor) environments. Both trials showed that whereas no gains could be expected by using the Turkish genotype for fattening, vetch grazing and molasses are suitable options for reducing high feed costs and could be safely used by farmers without compromising meat quality. Raising animals in a more favorable and healthier environment outdoors under a simple shed can also translate into substantial revenue in large batches of fattened lambs with considerable benefit for fattening systems.

This review summarizes available information on genetics of adaptation in major livestock species focusing on small ruminants. Adaptation to humans and consequences of domestication on predator aversion, mechanisms of adaptation to available feed and water resources, severe climates and genetic evidence of disease tolerance or resistance have been presented. The latter focuses on gastrointestinal parasites and bacterial diseases. The resource allocation by the animal to production and fitness traits under both optimal and sub-optimal conditions has a genetic background. Such information would help in identifying the most appropriate and adapted genotypes capable of coping with the environmental challenges posed by the production systems or, wherever possible, in adapting the environments to the requirements of the animals.

Summary Establishment of the hypothalamic-hypophyseal-gonadal function is dependent on the highly controlled and dynamic interactions between regulatory signals from the brain, pituitary and gonads, all of them leading to the attainment of reproductive capacity, where a coordinated and timely activation of GnRH neurons must occur. The GnRH neurons extend their neurosecretory axons to the hypothalamus where GnRH is released into the pituitary portal vessels to elicit the secretion of LH and FSH, which in turn, will promote gonadal development and support reproductive physiology. Genetic studies have demonstrated that disabling mutations and targeted deletions of the G-protein-coupled receptor (GPR54) generated hypogonadotropic hypogonadism. This link between GPR54 and reproduction, generated attention to the natural ligands of the GPR54 receptor, known as kisspeptins, which are translational products of the hypothalamic gene KiSS1. Recent advances in kisspeptin research have defined a major role of this molecule in controlling the onset of the reproductive function observed at puberty. The aim of this review is to highlight the basic endocrine and genetic concepts involved in the establishment of the hypothalamic-hypophyseal-gonadal axis function which promotes the onset of the reproductive function during puberty. The review highlights what is currently known about the kisspeptin-GPR54 signalling system in the activation of the GnRH neurons.

The aim of this study was to assess the grazing, social and comfort behaviour of the indigenous purebred Ankole cattle breed and crossbred (Holstein × Ankole) animals under typical management conditions in south western Uganda. Twelve focal animals in each of four groups (two groups per genotype) were observed regarding their grazing, social and comfort behaviour on pasture. No significant differences in grazing behaviour patterns (eating, walking, standing) were found between the genotypes. Resting occurred only very rarely in both genotypes. Walking distances of Ankole and Ankole × Holstein crosses were also similar. There was no difference in the occurrence of agonistic interactions between the two genotypes. However, Ankole cattle engaged in more non-agonistic social interactions than their crossbred counterparts. Individual distances were lower in Ankole heifers and more herd mates were found within a radius of 5 m around the Ankole animals. The most important comfort behaviour pattern in both genotypes was self-licking, which occurred to similar frequency in Ankole and crossbred heifer groups. Crossbred animals scratched themselves and rubbed on objects more often than Ankole heifers. Although Ankole cattle and their Holstein crosses did not differ in grazing, distances walked and agonistic behaviours, the significant differences between the two genotypes in herd cohesion and comfort behaviour may pose challenges on the management of crossbred animals under extensive open grazing conditions as present in south western Uganda. Thus, apart from (re)productive performance traits, behavioural traits of both genotypes may also be taken into account for breeding decisions and management under current production conditions.

The Jabali mountain goats inhabit the extremly unfriendly and harsh environment of western Syria, where they are kept by different ethnic groups, namely, the Alawits, Druses and Bedouins. The Jabali goat is a black goat, with dropping ears and a curved head; both sexes have horns. A survey was conducted in two different sites, namely, Al-Ghab in Hama district and in As-Sweida district. Forty-three household interviews were carried out to document the current production system. The system can be characterised as a low-input, mixed crop–livestock system. Goat keeping is only of minor importance to the household income compared to crop production or off-farm activities, but provide food in the form of milk, dairy products and meat for the family. Animals are kept on natural pasture most of the year; feed is only supplemented during winter. Farmers emphasise milk production. Milk products like ghee, Shinglish or Jameed are produced for home consumption and for sale. Major constraints mentioned by farmers are government policies for the conservation of forests, feed shortage and limited access to markets because of bad infrastructure and low market prices for their products. The fact that young people migrate to urban areas or work off-farm is seen as potential problem in the near future.

Ankole cattle are well known for their massive white horns and red coat colour. These characteristics are attributed to centuries of cultural breeding practices. Two experiments with traditional cattle keepers were carried out at a governmental Ankole nucleus farm in south-western Uganda to identify phenotypic characteristics as well as production and fitness traits which are important indigenous selection criteria. Forty one body measurements each were taken from 15 bulls and 35 cows and phenotypic characteristics were described in detail. In the first experiment 12 groups of 6 to 8 cattle keepers were invited to rank several groups of 4–5 animals according to their preference for a breeding bull or cow based on phenotype alone. In the second experiment the ranking was based on phenotype and a hypothetical life history that was randomly assigned to each animal on each day of experiment. The history included milk yield (on own performance for cows and that of the dam for bulls), fertility of the animal and its sire as well as events of East Coast Fever. For analysis, Generalized Multinomial Logit Models were fitted. To compare different models the likelihood-based pseudo R square measure was used. The results indicate that, in the selection of cows, performance and fitness traits are emphasized by the cattle keepers while in the selection of bulls, the phenotypic appearance of the animal plays an important role. Individual fertility followed by milk performance are the main criteria for selecting cows, resistance to East Coast Fever was of highest importance in bulls. In both sexes a dark red coat colour was highly rated. The study indicates that the methodology of preference ranking combining phenotype and a hypothetical life history may provide insight into indigenous selection criteria of stock owners elsewhere.

Breeding objectives always involve consideration of multiple traits, even in situations where output of a single trait is dominant. We review literature dealing with formal definition of breeding objectives. Involvement of farmers in the process of setting up breeding objectives is also considered. In the optimal selection index, the relative importance of a trait is scaled by its economic value, derived as marginal profit related to a change in expression of defined size. Normative approaches to derive economic values use partial derivatives of a profit equation with respect to the traits involved or model the bio-economic system with various techniques. The theory is well developed and includes consideration of non-linear profit functions and traits with an intermediate optimum. It is frequently applied in animal breeding. In dairy cattle breeding, a major change of focus from traits related to output (i.e., milk yield) to traits related to cost of input (health, fertility, feed efficiency) has taken place recently. Plant breeders find the concept of deriving relative economic weights of traits difficult to apply and often replace the optimal index by restricted or desired gains indices. A change of paradigms similar to that in cattle breeding seems advisable. Participatory approaches to evaluate the relative importance of traits are more frequently applied in plant breeding than in animal breeding. We review two studies, dealing with methods of acquiring information about selection criteria of farmers planting maize in the Ethiopian highlands and of pastoralists keeping cattle in Uganda, in detail.

A survey in Burundi, Rwanda, Tanzania and Uganda was conducted in order to determine the different production systems under which Ankole cattle are currently kept. Additionally, selection criteria of livestock keepers were documented. In Burundi, Rwanda and parts of Uganda, livestock keepers are sedentary and herds are small, whereas in the other areas Ankole cattle are kept in large herds, some of them still under a (semi-)nomadic system. Milk is the main product in all areas, and is partly for home consumption and partly for sale. Although the production systems vary in many aspects, the selection criteria for cows are similar. Productive traits such as milk yield, fertility and body size were ranked highly. For bulls, the trait 'growth' was ranked highly in all study areas. Phenotypic features (coat colour, horn shape and size) and ancestral information are more important in bulls than in cows. The only adaptive trait mentioned by livestock keepers was disease resistance. In areas of land scarcity (Burundi, Rwanda, western Uganda), a clear trend from pure Ankole cattle towards cross-bred animals can be observed.

Llamas display a great variability of fibre traits that determine the quality of the fleece as raw material for textiles. Little research has been conducted on the extent of this variability, although it is important for optimal use of natural resources in the Andean region. Fibre samples of 1869 llamas were analysed with the optical fibre diameter analyser (OFDA). The following traits were considered: Mean fibre diameter (MFD), standard deviation (SD), diameter of fine fibre (DFF), proportion of fine fibre (PFF), proportion of kemp (PK) and proportion of medullated fibre (PMF). The effects of type of llama, age, sex and coat colour were studied. The type of llama influences all traits /

The present study was carried out in the High Andes of the Department Cochabamba, Bolivia. Two types of llamas were found in the study area: Th'ampullis with higher fleece yields and fitting a fibre type; Kh'aras used as pack animals and fitting a meat-type. Growth curves for height at withers (HW), body length (BL), chest circumference (CC), abdomen circumference (AC) and body weight (BW) were described with the non-linear Brody function. The differences between sexes or types, except in the case of BW, were small. Equations for predicting body weight from different body measurements that could be easily obtained under field conditions were calculated. Reasonable fits were obtained with the inclusion of chest circumference and body length or chest circumference alone. Heritabilities and genetic correlations were estimated using animal model procedures based on mother–offspring relationships. Heritabilitiy estimates were 0.36, 0.27, 0.15, 0.09 and 0.11 for BW, HW, CC, BL and AC, genetic correlations ranged from 0.55 to 0.94.

Identification of breeding objective traits pertinent to specific production environments with the involvement of target beneficiaries is crucial to the success of a breed improvement program. A choice experiment was conducted in four locations representing different production systems and agro-ecologies that are habitat to four indigenous sheep breeds (Afar, Bonga, Horro and Menz) of Ethiopia with the objective of identifying farmers’/pastoralists’ preferences for sheep breeding traits. Following a synthesis of secondary information and diagnostic surveys, two communities per location consisting of 60 households each having at least four breeding ewes were identified. Producers’ priority attributes used in the choice sets were identified through in-depth production system studies conducted from December 2007 to March 2008. On the basis of prior information, four to seven attributes were used to design choice sets with different profiles in order to capture results that mimic real life of the different communities. The attributes and levels chosen for the sheep profile were as follows: body size (large/small), coat color (brown/white/black), tail type (good/bad) for both rams and ewes; horn (polled/horned) and libido (active/poor) for rams; and lambing interval (three lambings in 2 years/two lambings in 2 years time), mothering ability (good mother/bad mother), twinning rate (twin bearer/single bearer) and milk yield (two cups per milking/one cup per milking) for ewes. A fractional factorial design was implemented to construct the alternatives included in the choice sets. The design resulted in a randomized selection of 48 sheep profiles (24 sets) for both sexes, which were grouped into four blocks with six choice sets each. An individual respondent was presented with one of the four blocks to make his/her choices. Results indicate that producers’ trait preferences were heterogeneous except for body size in rams and mothering ability in ewes where nearly homogeneous preferences were investigated. In the pastoral production system, attention was given to coat color of both breeding rams and ewes, favoring brown and white colors over black. Ram libido influenced producers’ decisions in Bonga, Horro and Menz areas. The influence of milk yield and twinning on respondents’ decision making was high in Afar and Horro, respectively. Breeders in all areas attempt to combine production and reproduction traits as well as they can in order to maximize benefits from their sheep. The elicited measurable objective traits were used to design alternative community-based sheep breeding plans for the four indigenous sheep breeds in their production environments that have been implemented since.

Increased feed costs affect the livelihoods of dairy sheep farmers in the Middle East. Farmers endure high risks with large fluctuations in the price of grain used as animal feed, which is further affected by drought and declining range productivity. Using agricultural by-products and treated straw or vetch grazing for supplementing sheep diets would provide resource-poor dairy farmers with increased options to reduce feed costs, but the effects of such feeds on the quality of yogurt (the main product) need to be better understood. Two experiments were conducted to evaluate these effects. The first trial evaluated alternative diets using locally available feedstuffs, including agricultural by-products, compared with traditional diets used by dairy sheep farmers, and was conducted on-station at the International Center for Agricultural Research in Dry Areas (ICARDA, Tel Hadya, Aleppo, Syria). Milking Awassi ewes (n=56) were used to test 6 alternative diets against a traditional control diet containing barley, wheat bran, and barley straw. The 6 alternative diets contained 4 or more of the following ingredients: barley, sugar beet pulp, molasses, cotton seed cake, wheat bran, urea-treated wheat straw, and barley straw. Ewes on one of the alternative diets grazed vetch pasture, whereas ewes on the control diet and the 5 alternative diets grazed native range pasture. The milk fat content was higher in diets containing urea-treated straw. Yogurt firmness and adhesiveness were significantly lower in energy-rich diets (e.g., the control diet) and in the diets rich in soluble sugar (molasses). The effects of diet on yogurt color and on citric and succinic acid contents were significant. A yogurt produced from the milk of the group grazing on vetch was the most yellowish in color, which is appealing to Syrian consumers. The content of citric acid tended to be higher in yogurts produced from diets containing molasses. The second trial was conducted on 3 farms in northern Syria to assess an alternative diet (1 of the 6 tested in the first trial) on 15 milking ewes compared with the farmer's traditional diet (control). The alternative diet increased yogurt firmness and adhesiveness by 7 to 9% and 10 to 16%, respectively. The use of nonconventional feeds available in the region enhances yogurt quality, may reduce requirements for expensive grains, and thus, increase farmers' livelihoods by targeting expanding markets with better quality products.

The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall F ST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.

La finalización intensiva de corderos en corrales elevados con piso de rejilla permite que los animales se mantengan en un ambiente sano, con menos carga parasitaria, protección de los depredadores, reducción en el gasto energético y un mejor microclima, sin embargo, poco se conoce sobre el comportamiento productivo de los corderos bajo este sistema de producción. La identificación de los factores que influyen sobre el comportamiento productivo de los corderos en este tipo de alojamiento es crucial para mejorar su productividad. El objetivo de este estudio fue determinar los efectos de granja, año y época del año sobre algunas variables productivas de corderos finalizados en corrales elevados con piso de rejilla en el trópico subhúmedo de México. Se analizaron 882 datos de la ganancia diaria de peso post-destete (GDP), del peso corporal final (PCF) y del periodo de finalización (DE) de corderos machos de cuatro granjas (granja A, n = 166; granja B, n = 122; granja C, n = 350; granja D, n = 244). El modelo estadístico incluyo los efectos fijos de la granja (A, B, C y D), de la época del año (lluvia y seca) y del año (2010, 2011, 2012 y 2013) sobre GDP, PCF y DE. El modelo incluyó el peso corporal inicial como covariable. Las medias generales para GDP, PCF y DE fueron 263 g, 35 kg y 77 días, respectivamente. La granja afectó (P

Made available in DSpace on 2018-12-11T17:22:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-08-22 Background: Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods: ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results: In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions: Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps. Division of Livestock Sciences (NUWI) University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33 Lilongwe University of Agriculture and Natural Resources, P. O. Box 219 School of Agricultural and Veterinarian Sciences Jaboticabal Department of Preventive Veterinary Medicine and Animal Reproduction São Paulo State University (UNESP) National Livestock Resources Research Institute, P.O Box 96 Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences, Box 7023 Department of Animal Science Faculty of Agriculture University of Zagreb, Svetošimunska cesta 25 School of Veterinary Medicine Araçatuba Department of Support Production and Animal Health São Paulo State University (UNESP) Animal Genomics and Improvement Laboratory School of Agricultural and Veterinarian Sciences Jaboticabal Department of Preventive Veterinary Medicine and Animal Reproduction São Paulo State University (UNESP) School of Veterinary Medicine Araçatuba Department of Support Production and Animal Health São Paulo State University (UNESP)