SummaryThis paper reviews experiences with cross-breeding for milk production in the tropics. Data were compiled from 23 different studies evaluating the performance of different grades of cross-bred animals as well as local breeds. Relative performance of indigenous breeds compared with different grades of cross-breeds was calculated for three climatic zones. Traits considered were milk yield per lactation, age at first calving, services per conception, lifetime milk yield and total number of lactations completed. At 50 percent Bos taurus blood, lactation milk yields were 2.6, 2.4 and 2.2 times higher than those of local cattle in the highland, tropical wet and dry, and semi-arid climatic zones, respectively; lactation lengths increased by 1.2, 1.2 and 1.9 months in the above-mentioned climatic zones, respectively; there was a reduction in calving interval by 0.8 times and in age at first calving by 0.9 times. Similarly, cross-breds with 50 percent B. taurus genes had 1.8 times higher lifetime milk yields and a 1.2 times higher number of total lactations. Although cross-breeding faces a number of challenges such as better infrastructure, higher demand for health care, there are many advantages of using it. These are higher production per animal, higher income for the families and provision of high-value food. It is therefore likely to continue to be an important livestock improvement tool in the tropics in the future, where farmers can provide sufficient management for maintaining animals with higher input requirements and access to the milk market can be secured.Keywords: Cattle, cross-breeding, milk production, tropics ResumenEste artículo hace un repaso por las experiencias obtenidas con el cruzamiento de razas para la producción de leche en los trópicos. Se recopilaron datos de 23 estudios diferentes que evaluaron los rendimientos de animales con distinto grado de cruce así como de animales de razas autóctonas. Se compararon los rendimientos de las razas autóctonas con los de animales con distinto grado de cruce para tres zonas climáticas. Las características consideradas fueron el rendimiento lechero por lactación, la edad al primer parto, el número de servicios por concepción, la producción lechera total a lo largo de la vida del animal y el número total de lactaciones completadas. Con un 50 por ciento de sangre Bos taurus, los rendimientos lecheros por lactación fueron 2,6, 2,4 y 2,2 veces mayores que los del ganado bovino autóctono en las zonas climáticas de las Tierras Altas, Tropical Húmeda y Seca y Semiárida, respectivamente; la duración de la lactación se incrementó en 1,2, 1,2 y 1,9 meses en las zonas climáticas anteriormente mencionadas, respectivamente; el intervalo entre partos y la edad al primer parto se redujeron, respectivamente, 0,8 y 0,9 veces. Asimismo, los animales cruzados con una genética 50 por ciento Bos taurus tuvieron rendimientos lecheros, para la totalidad de su vida productiva, 1,8 veces mayores y un número total de lactaciones 1,2 veces mayor. Si bien el cruzamiento implica afr...

BackgroundRuns 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.MethodsROH 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.ResultsIn 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.ConclusionsOur findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0414-x) contains supplementary material, which is available to authorized users.

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 (F G ) 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 (F ROH ) and for ROH longer than 2 Mb (F ROH > 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 F ROH , F ROH > 2Mb , and F G , 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.

Gastro-intestinal nematode (GIN) infections are the leading cause of production losses in commercial goat farms worldwide. This study determined the level of gastro-intestinal nematodes (GIN) infection and identified the common GIN parasites in commercial goat production in Central Uganda. Faecal egg counts and morphological larval identification in coprocultures were used to estimate the burden of common GIN of goats in Central Uganda. Egg shedding was detected in 43% of the goats. Worm burdens were highest (498 -713 epg) in goats 3-5 and 8-9 months old. Goats of 6-8 and older than 9 months showed relatively lower egg counts (254-491epg). Haemonchus (56%), Oesophagostomum (33%) and strongyloides species (11%) were the only nematode species identified on coprocultures.

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 crossbred cattle yielded 0AE17 t ha )1 more dry matter than pastures allocated to Ankole cattle. Crude protein (CP) content of Ankole pasture was significantly (P < 0AE05) lower than CP of cross-bred pasture (6AE3% compared with 7AE3%). Neutral detergent fibre content was similar (72AE8% vs. 69AE8%) for both pasture types. Farmers' perceptions of indicator plant species were important for allocation of pasture. Hyparrhenia rufa, Brachiaria spp., Themeda triandra and Chloris gayana were identified as the preferred pasture species. Sporobolus pyramidalis and Cymbopogon afronardus were the most undesirable pasture species. Brachiaria spp. offers an opportunity for utilization as hay for dry season supplementation.

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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.

BackgroundCopy number variations (CNV) are a significant source of variation in the genome, as such they are essential to the genetic characterization of animal breeds. 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. ResultsA total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 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 6,231 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. ConclusionsThis 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.