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The main objective was to contribute to a better understanding of molecular characteristics of the local goat in order to improve its productivity and specifically to: analyse genetic polymorphism of three prolificacy genes (BMP15, BMPR1B, and GDF9) and test the association of genetic polymorphism and prolificacy of local goats. Tissue samples were collected from 446 animals, and 24 representative female goats were selected to analyse the genetic polymorphism of the prolificacy genes. The selected goats were divided into two groups of 12 females for high prolificacy (more than three kids consecutively in four parity) and 12 females for low prolificacy (less than two kids consecutively in four parity). Chi-square was used to test the association between genetic polymorphism and prolificacy of local goat. The main results showed that BMP15 gene is monomorphic, whereas the two other genes (BMPR1B and GDF9) display polymorphism. For BMPR1B gene, the ten mutations found did not change the corresponding amino acid. Allelic and genotypes frequencies of mutations of this gene varied from one mutation to another and between the two groups of females (high and low prolificacy). Chi-square test of the polymorphism of this gene shows that C34T and A120G mutations of exon 3 are significantly associated (p < 0.05) with prolificacy and can be considered as potential genetic markers for improving prolificacy in the native goat. For the GDF9 gene, three mutations were detected in exon 1 with alleles A and G1 of frequency 0.261 and 0.130 for A35G; G2 and C1 of frequency 0.696 and 0.304 for G81C; then G3 and C2 of frequency 0.696 and 0.304 for G255C. The mutations G81C and G255C appeared under BLAST and were missense mutations P27A and A85G respectively while A35G is located in the non-translated 5’ region of the gene. Chi-square test between each genotype for any site and the prolificacy was not significant (P > 0.01) suggesting that these two characters are not associated. Two mutations were detected in exon 2 at C881T and A1160G sites with C and T and A and G alleles respectively. The two mutations changed the corresponding amino acid from Alanine to Valine at the position 273 in the protein and from Valine to Isoleucine at the position 397 in the protein respectively. Allelic and genotypes frequencies of mutations varied from one mutation to another and between the two groups of females (high and low prolificacy). Chi-square test of the polymorphism shows that, although C881T and A1160G mutations were not significantly associated (P > 0.05) with prolificacy, the alleles responsible for the variation of amino acid increased the litter size. Therefore, further studies with increased sample size will help to verify the results.

Simple Summary The Nubian ibex is a wild relative of the domestic goat found in hot deserts of Northern Africa and Arabia. The domestic goat is an important livestock species that is mainly found in arid and semi-arid regions of Africa and Asia. The Nubian ibex is well adapted to challenging environments in hot deserts characterized by high diurnal temperatures, intense solar radiation, and scarce water resources. It is therefore important to understand the genetic basis of its adaptation for scientific and economic importance. To identify genes with adaptive traits, the Nubian ibex genome was sequenced and compared with that of related mammals. We identified twenty-five genes under selection in the Nubian ibex that play diverse biological roles such as immune response, visual development, signal transduction, and reproduction. Three other genes under adaptive evolution involved in protective functions of the skin against damaging solar radiation in the desert were identified in Nubian ibex genome. Our finding provides valuable genomic insights into the adaptation of Nubian ibex to desert environments. The genomic information generated in this study can be used in developing appropriate breeding programs aimed at enhancing adaptation of local goats to less favorable habitats in response to changing climates. Abstract The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging environments in hot deserts characterized by intense solar radiation, thermal extremes, and scarce water resources. The economic importance of C. hircus breeds, as well as the current trends of global warming, highlights the need to understand the genetic basis of adaptation of C. nubiana to the desert environments. In this study, the genome of a C. nubiana individual was sequenced at an average of 37x coverage. Positively selected genes were identified by comparing protein-coding DNA sequences of C. nubiana and related species using dN/dS statistics. A total of twenty-two positively selected genes involved in diverse biological functions such as immune response, protein ubiquitination, olfactory transduction, and visual development were identified. In total, three of the twenty-two positively selected genes are involved in skin barrier development and function (ATP binding cassette subfamily A member 12, Achaete-scute family bHLH transcription factor 4, and UV stimulated scaffold protein A), suggesting that C. nubiana has evolved skin protection strategies against the damaging solar radiations that prevail in deserts. The positive selection signatures identified here provide new insights into the potential adaptive mechanisms to hot deserts in C. nubiana.

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall HO and HE were 0.57 and 0.75, respectively. Differentiation statistics revealed that a high proportion (97%) of the total genetic variation was explained by differences between individuals within populations. Genotype assignment independent of the population of origin showed K = 2 to be the optimum number of genetic backgrounds present in the dataset. This result was further confirmed by mtDNA D-loop sequences comparison in which the matrilineal genetic origin of eastern Ethiopia sheep is from two haplotype groups (types A and B) among the five haplotypes globally observed. Taken together, our findings suggest that the sheep populations from three breeds originated from two ancestral genetic backgrounds that may have diverged prior to their introduction to Ethiopia. However, to obtain a complete picture of the evolutionary dynamics of Ethiopian indigenous sheep, more samples and populations from within and outside of the country will need to be analyzed.

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall H

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

In order to improve the conservation and sustainable utilization of the African catfish Clarias gariepinus of the Yala Swamp in Kenya, genetic diversity and population structure of Lakes Kanyaboli and Namboyo populations of the species were studied using DNA sequences of the mitochondrial D-loop control region. Genetic diversity inferred as haplotype and nucleotide diversities and number of singletons and shared haplotypes was higher in the Lake Kanyaboli population (LKG) than the Lake Namboyo population (LNG) of C. gariepinus. Thirty-one haplotypes were inferred, of which 25 (80·6%) were private or singletons, while only six (19·4%) haplotypes were shared between LKG and LNG. Both populations were differentiated, with FST value that was significantly different from zero (P 0·05). Individual raggedness indices were 0·015 and 0·154 for LKG and LNG respectively. Fu's Fs was negative for both populations, with LKG recording −14·871, while LNG had −2·565, significantly different from zero for LKG (P 0·05). Tajima's D was negative for both populations, with LKG recording −1·734, while LNG had −1·136. Standardized square differences (SSD) were 0·001 for LKG and 0·048 for LNG and non-significant between them (P > 0·05). Values between all populations were also not significantly different (P > 0·05), mean ± s.d. SSD 0·025 ± 0·033.

Unfortunately, the original article was online published with error in the results section. The error is correction by this erratum.

This project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichment protocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and using RSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of viruses denoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus. Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumen microbial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reported in other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain data that are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknown reads (93.86%) for the sheep obtained may represent novel genomes that need further study.

Sustainable food strategies for meeting nutrient needs in developing countries are not well established. The available evidence shows that more than one-third of the world's population is facing under-nutrition, of which the most affected individuals are children and mothers from poor countries. In most developing countries, losses resulting from malnutrition are between 3 and 16% of the gross domestic product. This burden is far larger than the donor-driven and government programmes can tackle alone. As such, an innovative approach, which is independent and not donor-based, is needed to reduce the burden of malnutrition in low-income countries. In this review, we describe a context specific food-based approach for addressing malnutrition in developing countries. The approach deploys the hybrid public-private delivery model that enables cost sharing and efficiency gains in resource-poor countries. The model influences players to consider consumers' perspectives, which often are neglected and truly engage them as key stakeholders.

Uniquely selected breeds bred over thousands of years of domestication in a wide range of environments have been declared extinct over the last century. Still more breeds are at risk of becoming extinct and the rate continues to accelerate. Assessing the current status and possible future dynamics of livestock breeds is therefore a critical step in the management of Animal Genetic Resources (AnGR). This study applies a qualitative approach to comprehensively analyze cattle genetic resources in selected countries in order to better understand the risk status of cattle breeds and those that need to be considered extinct and/or quasi-extant. The status of each breed, i.e., not at risk, critical, endangered and extinct, was verified using information available at the Domestic Animal Diversity Information System (DAD-IS) web site, as well as cattle statistics (where available) and a breed survey. In most examples, breeds listed as extinct have played important roles in the development of new breeds, and should not be classified as extinct, unless proven otherwise, given that even breeds existing in vivo are developing. Therefore, a new risk status quasi-extant for this category of cattle breeds is suggested. In addition, based on the findings of this study, the concept of breed needs to be questioned as relates to it being a good measure of genetic diversity. Further investigations of the situation of cattle breeds (and other livestock species) in more countries/continents using similar categories are deemed necessary.

Background The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. Results We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds. Conclusions Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1153-y) contains supplementary material, which is available to authorized users.

Background Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results Sequence analysis shows that giraffe has 94–99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0901-7) contains supplementary material, which is available to authorized users.

Background: Achieving nutritional goals of infants and young children while maintaining the intake of local and culture-specific foods can be a daunting task. Diet optimisation using linear goal programming (LP) can effectively generate optimal formulations incorporating local and culturally acceptable foods. Objective: The primary objective of this study was to determine whether a realistic and affordable diet that achieves dietary recommended intakes (DRIs) for 22 selected nutrients can be formulated for rural 6–23-month-old children in Tanzania. Design: Dietary intakes of 400 children aged 6–23 months were assessed using a weighed dietary record (WDR), 24-hour dietary recalls and a 7-days food record. A market survey was also carried out to estimate the cost per 100 g of edible portion of foods that are commonly consumed in the study area. Dietary and market survey data were then used to define LP model parameters for diet optimisation. All LP analyses were done using linear program solver (LiPS) version 1.9.4 to generate optimal food formulations. Results: Optimal formulations that achieved DRIs for 20 nutrients for children aged 6–11 months and all selected nutrients for children aged 12–23 months were successfully developed at a twofold cost of the observed food purchase across age groups. Optimal formulations contained a mixture of ingredients such as wholegrain cereals, Irish potatoes, pulses and seeds, fish and poultry meat as well as fruits and vegetables that can be sourced locally. Conclusions: Our findings revealed that given the available food choices, it is possible to develop optimal formulations that can improve dietary adequacy for rural 6–23-month-old children if food budget for the child’s diets is doubled. These findings suggest the need for setting alternative interventions which can help households increase access to nutrient-dense foods that can fill the identified nutrient gaps.

BackgroundThe capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe’s unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood.MethodsThe recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals.ResultsSignatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence inCRYAAandOPN1LW. Significant selection divergence was identified inSAGwhile positive selection was detected inLUMwhen okapi is compared with ruminants and other mammals. Sequence analysis ofOPN1LWshowed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.DiscussionBy taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.

The origins of giraffe's imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe's closest relative and provides a useful comparison, to identify genetic variation underlying giraffe's long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe's unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe's stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions., Giraffe's unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novo genome assemblies of giraffe and its closest relative okapi and provide comparative analyses to infer insights into evolution and adaptation.

African bovine trypanosomiasis caused by Trypanosoma sp., is a major constraint on cattle productivity in sub-Saharan Africa. Some African Bos taurus breeds are highly tolerant of infection, but the potentially more productive Bos indicus zebu breeds are much more susceptible. Zebu cattle are well adapted for plowing and haulage, and increasing their tolerance of trypanosomiasis could have a major impact on crop cultivation as well as dairy and beef production. We used three strategies to obtain short lists of candidate genes within QTL that were previously shown to regulate response to infection. We analyzed the transcriptomes of trypanotolerant N'Dama and susceptible Boran cattle after infection with Trypanosoma congolense. We sequenced EST libraries from these two breeds to identify polymorphisms that might underlie previously identified quantitative trait loci (QTL), and we assessed QTL regions and candidate loci for evidence of selective sweeps. The scan of the EST sequences identified a previously undescribed polymorphism in ARHGAP15 in the Bta2 trypanotolerance QTL. The polymorphism affects gene function in vitro and could contribute to the observed differences in expression of the MAPK pathway in vivo. The expression data showed that TLR and MAPK pathways responded to infection, and the former contained TICAM1, which is within a QTL on Bta7. Genetic analyses showed that selective sweeps had occurred at TICAM1 and ARHGAP15 loci in African taurine cattle, making them strong candidates for the genes underlying the QTL. Candidate QTL genes were identified in other QTL by their expression profile and the pathways in which they participate.

Interspecies hybridization of bovids occurs between domestic cattle and at least three other species; American bison ( Bison bison ), yak ( Bos grunniens ) and banteng ( Bos banteng ). Birth of a cattle × buffalo ( Bubalus bubalis ) hybrid has reportedly occurred in Russia and in China, but these reports were not authenticated. Such hybrids could be important in improving livestock production and management of diseases that impede production in tropical Africa. This study investigated hybridization between cattle and its closest African wild bovid relative, the African buffalo ( Syncerus caffer caffer ). In an attempt to produce cattle × buffalo hybrid embryos in vitro, matured cattle oocytes were subjected to a standard in vitro fertilization (IVF) procedure with either homologous cattle ( n = 1166 oocytes) or heterologous African buffalo ( n = 1202 oocytes) frozen-thawed epididymal sperm. After IVF, 67.2% of the oocytes inseminated with the homologous cattle sperm cleaved. In contrast, fertilization with buffalo sperm resulted in only a 4.6% cleavage rate. The cleavage intervals were also slower in hybrid embryos than in the IVF-derived cattle embryos. Of the cleaved homologous cattle embryos 52.2% progressed to the morula stage compared with 12.7% for the buffalo hybrid embryos. No hybrid embryos developed beyond the early morula stage, while 40.1% of the cleaved cattle × cattle embryos developed to the blastocyst stage. Transfer of buffalo hybrid IVF embryos to domestic cattle surrogates resulted in no pregnancies at 60 days post-transfer. This study indicates that interspecies fertilization of cattle oocytes with African buffalo epididymal sperm can occur in vitro, and that a barrier to hybridization occurs in the early stages of embryonic development. Chromosomal disparity is likely the cause of the fertilization abnormalities, abnormal development and subsequent arrest impairing the formation of hybrid embryos beyond the early morula stage. Transfer of the buffalo hybrid embryos did not rescue the embryos from development arrest.

To examine differences in cytokine profiles that may confer tolerance/susceptibility to bovine African trypanosomiasis, N'Dama (trypanotolerant, n = 8) and Boran (trypanosusceptible, n = 8) cattle were experimentally challenged with Trypanosoma congolense. Blood samples were collected over a 34-day period, and RNA was extracted from peripheral blood mononuclear cells. The expression levels of a panel of 14 cytokines were profiled over the time course of infection and between breeds. Messenger RNA (mRNA) transcript levels for the IL2, IL8, and IL1RN genes were significantly downregulated across the time course of infection in both breeds. There was an early increase in transcripts for genes encoding proinflammatory mediators ( IFNG, IL1A, TNF, and IL12) in N'Dama by 14 days postinfection (dpi) compared with preinfection levels that was not detected in the susceptible Boran breed. By the time of peak parasitemia, a type 2 helper T cells (TH2)-like cytokine environment was prevalent that was particularly evident in the Boran. Increases in transcripts for the IL6 (29 and 34 dpi) and IL10 (21, 25, and 29 dpi) genes were detected that were higher in the Boran compared with N'Dama. These findings highlight the implications for using murine models to study the bovine immune response to trypanosomiasis, where in some cases cytokine expression patterns differ. Overall, these data suggest that the trypanotolerant N'Dama are more capable of responding very early in infection with proinflammatory and TH1 type cytokines than the trypanosusceptible Boran and may explain why N'Dama control parasitemia more efficiently than Boran during the early stages of infection.

Fish are the only major dietary source for humans of omega-3 highly unsaturated fatty acids (HUFAs) and with declining fisheries farmed fish such as Atlantic salmon (Salmo salar) constitute an increasing proportion of the fish in the human diet. However, the current high use of fish oils, derived from wild capture marine fisheries, in aquaculture feeds is not sustainable in the longer term and will constrain continuing growth of aquaculture activities. Greater understanding of how fish metabolize and biosynthesize HUFA may lead to more sustainable aquaculture diets. The study described here contributes to an effort to determine the molecular genetics of the HUFA biosynthetic pathway in salmon, with the overall aim being to determine mechanisms for optimizing the use of vegetable oils in Atlantic salmon culture. In this paper we describe the cloning and functional characterization of 2 genes from salmon involved in the biosynthesis of HUFA. A salmon desaturase complementary DNA, SalDes, was isolated that include an open reading frame of 1362 bp specifying a protein of 454 amino acids. The protein sequence includes all the characteristics of microsomal fatty acid desaturases, including 3 histidine boxes, 2 transmembrane regions, and an N-terminal cytochrome b(5) domain containing a heme-binding motif similar to that of other fatty acid desaturases. Functional expression in the yeast Saccharomyces cerevisiae showed SalDes is predominantly an omega-3 delta5 desaturase, a key enzyme in the synthesis of eicosapentaenoic acid (20:5n-3) from alpha-linolenic acid (18:3n-3). The desaturase showed only low levels of delta6 activity toward C(18) polyunsaturated fatty acids. In addition, a fatty acid elongase cDNA, SalElo, was isolated that included an open reading frame of 888 bp, specifying a protein of 295 amino acids. The protein sequence of SalElo included characteristics of microsomal fatty acid elongases, including a histidine box and a transmembrane region. Upon expression in yeast SalElo showed broad substrate specificity for polyunsaturated fatty acids with a range of chain lengths, with the rank order being C(18)C(20)C(22). Thus this one polypeptide product displays all fatty acid elongase activities required for the biosynthesis of docosahexaenoic acid (22:6n-3) from 18:3n-3.

Trypanosomosis, or sleeping sickness, is a major disease constraint on livestock productivity in sub-Saharan Africa. To identify quantitative trait loci (QTL) controlling resistance to trypanosomosis in cattle, an experimental cross was made between trypanotolerant African N'Dama ( Bos taurus ) and trypanosusceptible improved Kenya Boran ( Bos indicus ) cattle. Sixteen phenotypic traits were defined describing anemia, body weight, and parasitemia. One hundred seventy-seven F 2 animals and their parents and grandparents were genotyped at 477 molecular marker loci covering all 29 cattle autosomes. Total genome coverage was 82%. Putative QTL were mapped to 18 autosomes at a genomewise false discovery rate of 2 cross between N'Dama and Boran cattle could produce a synthetic breed with higher trypanotolerance levels than currently exist in the parental breeds.

Biomedical engineers have the tools to address some of the world’s most challenging nondisease–focused problems.

Δ5 and Δ6 fatty acid desaturases are critical enzymes in the pathways for the biosynthesis of the polyunsaturated fatty acids arachidonic, eicosapentaenoic, and docosahexaenoic acids. They are encoded by distinct genes in mammals and Caenorhabditis elegans . This paper describes a cDNA isolated from zebrafish ( Danio rerio ) with high similarity to mammalian Δ6 desaturase genes. The 1,590-bp sequence specifies a protein that, in common with other fatty acid desaturases, contains an N-terminal cytochrome b 5 domain and three histidine boxes, believed to be involved in catalysis. When the zebrafish cDNA was expressed in Saccharomyces cerevisiae it conferred the ability to convert linoleic acid (18:2 n -6) and α-linolenic acid (18:3 n -3) to their corresponding Δ6 desaturated products, 18:3 n -6 and 18:4 n -3. However, in addition it conferred on the yeast the ability to convert di-homo-γ-linoleic acid (20:3 n -6) and eicosatetraenoic acid (20:4 n -3) to arachidonic acid (20:4 n -6) and eicosapentaenoic acid (20:5 n -3), respectively, indicating that the zebrafish gene encodes an enzyme having both Δ5 and Δ6 desaturase activity. The zebrafish Δ5/Δ6 desaturase may represent a component of a prototypic vertebrate polyunsaturated fatty acids biosynthesis pathway.

The desaturation and elongation of [1-14C]18:3n-3 was investigated in hepatocytes of the tropical warm freshwater species, zebrafish (Danio rerio) and Nile tilapia (Oreochromis niloticus). The hepatocyte fatty acid desaturation/elongation pathway was assayed before and after the fish were fed two experimental diets, a control diet containing fish oil (FO) and a diet containing vegetable oil (VO; a blend of olive, linseed and high oleic acid sunflower oils) for 10 weeks. The VO diet was formulated to provide 1% each of 18:2n-6 and 18:3n-3, and so satisfy the possible EFA requirements of zebrafish and tilapia. At the end of the dietary trial, the lipid and fatty acid composition was determined in whole zebrafish, and liver, white muscle and brain of tilapia. Both zebrafish and tilapia expressed a hepatocyte fatty acid desaturation/elongation pattern consistent with them being freshwater and planktonivorous fish. The data also showed that hepatic fatty acid desaturation/elongation was nutritionally regulated with the activities being higher in fish fed the VO diet compared to fish fed the FO diet. In zebrafish, the main effect of the VO diet was increased fatty acid Δ6 desaturase activity resulting in the production of significantly more 18:4n-3 compared to fish fed the FO diet. In tilapia, all activities in the pathway were greater in fish fed the VO diet resulting in increased amounts of all fatty acids in the pathway, but primarily eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3). However, the fatty acid compositional data indicated that despite increased activity, desaturation of 18:3n-3 was insufficient to maintain tissue proportions of EPA and DHA in fish fed the VO diet at the same level as in fish fed the FO diet. Practically, these results indicate that manipulation of tilapia diets in commercial culture in response to the declining global fish oil market would have important consequences for fish fatty acid composition and the health of consumers. Scientifically, zebrafish and tilapia, both the subject of active genome mapping projects, could be useful models for studies of lipid and fatty acid metabolism at a molecular biological and genetic level.

Chediak-Higashi Syndrome (CHS) is an autosomal recessive disorder that affects several species including mice, humans, and cattle. Evidence based on clinical characteristics and somatic cell genetics suggests that mutations in a common gene cause CHS in the three species. The CHS locus on human chromosome 1 and mouse chromosome 13 encodes a lysosomal trafficking regulator formerly known as LYST, now known as CHS1, and is defective in CHS patients and beige mice, respectively. We have mapped the CHS locus to the proximal region of bovine chromosome 28 by linkage analysis using microsatellite markers previously mapped to this chromosome. Furthermore, we have identified a missense A:T-->G:C mutation that results in replacement of a histidine with an arginine residue at codon 2015 of the CHS1 gene. This mutation is the most likely cause of CHS in Wagyu cattle. In addition, we describe quick, inexpensive, PCR based tests that will permit elimination of the CHS mutation from Wagyu breeding herds.

We have identified substitutions in the 3' untranslated region of the bovine myoglobin gene, one of which affects an MboII restriction enzyme site resulting in a bi-allelic restriction fragment length polymorphism. Co-dominant inheritance of the alleles in three reference families was observed using a polymerase chain reaction--restriction fragment length polymorphism assay. The distribution of the alleles seems characteristic of cattle type--one of the alleles was not detected in purely taurine breeds. Furthermore, we mapped, using the polymerase chain reaction on a bovine-rodent somatic cell hybrid panel, the myoglobin gene to bovine chromosome five. It is therefore syntenic with gamma-interferon and insulin-like growth factor in which we have not found polymorphism. The myoglobin locus therefore serves as a type one marker on bovine chromosome five.

While the physiological basis of cassava drought tolerance has been characterized, evaluation of the molecular responses to drought stress remains largely unexplored. This study provides an initial characterization of the molecular response of cassava to drought stress resembling field conditions. The candidate drought tolerance genes in cassava identified in this study can be used as expression-based markers of drought tolerance in cassava or be tested in the context of breeding and engineering drought tolerance in transgenics., Cassava is an important root crop to resource-poor farmers in marginal areas, where its production faces drought stress constraints. Given the difficulties associated with cassava breeding, a molecular understanding of drought tolerance in cassava will help in the identification of markers for use in marker-assisted selection and genes for transgenic improvement of drought tolerance. This study was carried out to identify candidate drought-tolerance genes and expression-based markers of drought stress in cassava. One drought-tolerant (improved variety) and one drought-susceptible (farmer-preferred) cassava landrace were grown in the glasshouse under well-watered and water-stressed conditions. Their morphological, physiological and molecular responses to drought were characterized. Morphological and physiological measurements indicate that the tolerance of the improved variety is based on drought avoidance, through reduction of water loss via partial stomatal closure. Ten genes that have previously been biologically validated as conferring or being associated with drought tolerance in other plant species were confirmed as being drought responsive in cassava. Four genes (MeALDH, MeZFP, MeMSD and MeRD28) were identified as candidate cassava drought-tolerance genes, as they were exclusively up-regulated in the drought-tolerant genotype to comparable levels known to confer drought tolerance in other species. Based on these genes, we hypothesize that the basis of the tolerance at the cellular level is probably through mitigation of the oxidative burst and osmotic adjustment. This study provides an initial characterization of the molecular response of cassava to drought stress resembling field conditions. The drought-responsive genes can now be used as expression-based markers of drought stress tolerance in cassava, and the candidate tolerance genes tested in the context of breeding (as possible quantitative trait loci) and engineering drought tolerance in transgenics.

Trypanosoma congolense is a protozoan parasite that causes severe diseases in livestock. Three major quantative trait loci (QTL), Tir1 , Tir2 , and Tir3 , control the survival time of mice after infection with T. congolense . Congenic mice carrying the C57BL/6 resistance alleles on the A/J background were developed for each of these loci. The congenic mice were used to physically map the regions containing the QTL gene(s) and to investigate the physiological effect of each locus. Clinical chemistry data for infected A/J, C57BL/6, and BALB/c mice were obtained for 15 analytes at five time points. Congenic mice were assessed for survival, parasitemia, and anemia as well as seven clinical-chemical analytes. The survival times were significantly increased in the Tir1 and Tir2 mice but not Tir3 congenic mice. The survival time of the parental inbred mice correlated negatively with parasitemia but positively with alanine aminotransferase activities in serum, suggesting that inflammatory reactions in the liver had a beneficial effect possibly associated with reduced parasitemia. However, there was no difference in parasitemia or liver enzyme activities of Tir1 and Tir2 congenic mice relative to their controls, showing that survival, parasitemia, and degree of liver damage are not associated with each other, despite the correlation in the parental lines. These data suggest that the congenic loci affect survival but do not affect control of parasite number. They may therefore act by limiting the pathological consequences of T. congolense infection.

BACKGROUND: Trypanosoma congolense are extracellular protozoan parasites of the blood stream of artiodactyls and are one of the main constraints on cattle production in Africa. In cattle, anaemia is the key feature of disease and persists after parasitaemia has declined to low or undetectable levels, but treatment to clear the parasites usually resolves the anaemia. METHODOLOGY/PRINCIPAL FINDINGS: The progress of anaemia after Trypanosoma congolense infection was followed in three mouse strains. Anaemia developed rapidly in all three strains until the peak of the first wave of parasitaemia. This was followed by a second phase, characterized by slower progress to severe anaemia in C57BL/6, by slow recovery in surviving A/J and a rapid recovery in BALB/c. There was no association between parasitaemia and severity of anaemia. Furthermore, functional T lymphocytes are not required for the induction of anaemia, since suppression of T cell activity with Cyclosporin A had neither an effect on the course of infection nor on anaemia. Expression of genes involved in erythropoiesis and iron metabolism was followed in spleen, liver and kidney tissues in the three strains of mice using microarrays. There was no evidence for a response to erythropoietin, consistent with anaemia of chronic disease, which is erythropoietin insensitive. However, the expression of transcription factors and genes involved in erythropoiesis and haemolysis did correlate with the expression of the inflammatory cytokines Il6 and Ifng. CONCLUSIONS/SIGNIFICANCE: The innate immune response appears to be the major contributor to the inflammation associated with anaemia since suppression of T cells with CsA had no observable effect. Several transcription factors regulating haematopoiesis, Tal1, Gata1, Zfpm1 and Klf1 were expressed at consistently lower levels in C57BL/6 mice suggesting that these mice have a lower haematopoietic capacity and therefore less ability to recover from haemolysis induced anaemia after infection.

Background African animal trypanosomiasis (AAT) caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC) gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR) validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with Trypanosoma congolense across a 34-day infection time course. Results Trypanotolerant N'Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post-infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in response to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO) analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle. Conclusion This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N'Dama cattle respond more rapidly and with a greater magnitude to infection compared to the trypanosusceptible Boran cattle. Specifically, a subset of the genes analyzed by real time qRT-PCR, which display significant breed differences, could collectively contribute to the trypanotolerance trait in N'Dama.

An international multidisciplinary consortium is conducting a programme of research on the host response to trypanosome infection. This builds upon quantitative trait loci (QTL) mapping which identified genome regions influencing susceptibility to pathology following T. congolense infection in both cattle and mice. The approach uses expression analysis to examine the response of both susceptible and resistant strains and a series of novel informatics tools to identify pathways which are activated as a result of challenge, and those which are differentially used by resistant and susceptible strains. Of particular interest are those pathways which simultaneously satisfy both criteria, i.e. are significantly differentially activated and contain genes within QTL regions. However, it is important to stress that it is not required that the genes within the QTL region are differentially expressed themselves.

High-throughputtechnologies inevitably produce vast quantities of data. This presents challenges in terms of developing effective analysis methods, particularly where the analysis involves combining data derived from different experimental technologies. In this investigation, a systematic approach was applied to combine microarray gene expression data, quantitative trait loci (QTL) data and pathway analysis resources in order to identify functional candidate genes underlying tolerance to Trypanosoma congolense infection in cattle. We automated much of the analysis using Taverna workflows previously developed for the study of trypanotolerance in the mouse model. Pathways represented by genes within the QTL regions were identified, and this list was subsequently ranked according to which pathways were over-represented in the set of genes that were differentially expressed (over time or between tolerant N'dama and susceptible Boran breeds) at various timepoints after T. congolense infection. The genes within the QTLthat played a role in the highest ranked pathways were flagged as good targets for further investigation and experimental confirmation.

Thymic-derived lymphocytes (T cells) recognize and respond to antigens through the mediation of the T-cell receptor complex. Here we report polymorphism at each of the five loci that encode the different components of the T-cell receptor complex in cattle. These genes were mapped on the bovine genome by genetic linkage analysis in the International Bovine Reference Panel (IBRP). These mapping data provide additional type I markers for linking the bovine genetic map with the human and mouse maps and also permit investigation of the effect of T-cell receptor polymorphism on immune responsiveness and disease susceptibility.

Enzymes that lengthen the carbon chain of polyunsaturated fatty acids are key to the biosynthesis of the highly unsaturated fatty acids, arachidonic, eicosapentaenoic and docosahexaenoic acids from linoleic and alpha-linolenic acids. A Mortierella alpina cDNA polyunsaturated fatty acid elongase sequence identified mammalian, amphibian, zebrafish and insect expressed sequence tags (ESTs) in GenBank. Consensus primers were designed in conserved motifs and used to isolate full length cDNA from livers of several fish species by Rapid Amplification of cDNA Ends (RACE). The amplified cDNAs encoded putative open reading frames (ORFs) of 288-294 amino acids that were highly conserved among the fish species. Heterologous expression in yeast, Saccharomyces cerevisiae, demonstrated that all of the ORFs encoded elongases with the ability to lengthen polyunsaturated fatty acid substrates with chain lengths from C18 to C22 and also monounsaturated fatty acids, but not saturated fatty acids. There were differences in the functional competence of the elongases from different fish species. Most of the fish elongases showed a pattern of activity towards different fatty acid substrates in the rank order C18>C20>C22, although the tilapia and turbot elongases had similar activity towards 18:4n-3 and 20:5n-3. The fish elongases generally showed greater activity or similar activities with n-3 than with n-6 homologues, with the exception of the cod enzyme which was more active towards n-6 fatty acids.

Enzymes that increase the chain length of fatty acids are essential for biosynthesis of highly unsaturated fatty acids. The gLELO gene encodes a protein involved in the elongation of polyunsaturated fatty acids in the fungus Mortierella alpina. A search of the GenBank database identified several expressed sequence tag sequences, including one obtained from zebrafish (Danio rerio), with high similarity to gLELO. The full-length transcript ZfELO, encoding a polypeptide of 291 amino acid residues, was isolated from zebrafish liver cDNA. The predicted amino acid sequence of the open reading frame shared high similarity with the elongases of Caenorhabditis elegans and human. When expressed in Saccharomyces cerevisiae, the zebrafish open reading frame conferred the ability to lengthen the chain of a range of C18, C20, and C22 polyunsaturated fatty acids, indicating not only that biosynthesis of 22:6n-3 from 18:3n-3 via a 24-carbon intermediate is feasible, but also that one elongase enzyme can perform all three elongation steps required. The zebrafish enzyme was also able to elongate monounsaturated and saturated fatty acids, and thus demonstrates a greater level of promiscuity in terms of substrate use than any elongase enzyme described previously.

We describe a polymorphism in the bovine gene PTHG which can be readily typed by PCR assay. The polymorphism is codominantly inherited and the allele frequencies appear characteristic of Bo indicus and B. taurus cattle.

Human Chromosome (Chr) 18 (HSA18) contains approximately85 million base pairs of DNA (Morton 1991). Thirty genes andpseudogenes have been mapped to HSA18 by somatic cell geneticsor in situ hybridization (Le Beau et al. 1993; Overhauser et al.1993; van Kessel et al. 1994). They include pituitary adenylcyclaseactivating peptide (ADCYAP1), laminin a chain (LAMA1), andmitochondrial NADH-ubiquinone reductase, 24 kDa subunit(NDUFV2) on the short arm, and transthyretin (TTR), B-cell lym-phoma 2 (BCL2), plasminogen activator inhibitor type 2 (PAI2),n-cadherin (CDH2), desmocollin type 2 (DSC2), ferrochelatase(FECH), cytochrome b5 (CYB5) and myelin basic protein (MBP)on the long arm (Fig. 1a). The murine homologs of HSA18 geneshave been mapped to at least four chromosomes as follows: Bcl-2and Planh2 genes are on MMU1, thymidylate synthase (Ts1) geneis on MMU5, Lama1 is on MMU17, and the rest are on MMU18(Mouse Genome Database 3.1, 1996).Two bovine genes—Yamaguchi sarcoma viral oncogene ho-molog 1 (YES1) and desmocollin type 1 (DSC1)—homologous toHSA18 loci have been mapped by in situ hybridization to Chr 24(Chowdhary et al. 1996), and ZOO-FISH analyses show thatHSA18 loci are located entirely on BTA24 (Hayes 1995; Toldo etal. 1995; Chowdhary et al. 1996). We report here the genomiclocalization of eight bovine genes homologous to HSA18 genesADCYAP1, CDH2, CYB5, DSC2, FECH, NDUFV2, PAI2, andTTR, using somatic cell genetics and linkage analysis in the In-ternational Bovine Reference Panel (IBRP).Oligonucleotide primers for PCR were designed on the basisof the published nucleotide sequences of sheep or cattle genesADCYAP1, CDH2, CYB5, DSC2, FECH, NDUFV2 and TTR, andwere used to amplify the corresponding DNA fragments frombovine total genomic DNA. Primers for PAI2 gene fragments weredesigned on the basis of a consensus sequence of the human andmurine genes. PCR amplification and single-strand conformationpolymorphism (SSCP) analysis were performed as described pre-viously (Agaba et al. 1996) except that the annealing and geltemperatures were optimized for each DNA fragment as shown inTable 1. The primers for PAI2 were allelic; that is, under optimumPCR conditions amplification of one allele from some individualswas favored over the alternative (null) allele, and, as expected,dominant inheritance was observed in informative IBRP families.Somatic cell hybrid mapping was achieved by PCR amplifica-tion of bovine sequences in a panel of 27 bovine × rodent somaticcell hybrids kindly provided by J. Womack of TexasA&MUniversity. In the case of the PAI2 gene, bovine fragments weredifferentiated from rodent fragments by SSCP analysis. Sevengenes, ADCYAP1, CDH2, CYB5, DSC2, FECH, PAI2 and TTR,segregated 100% concordantly with each other and with Chr 24,while the NDUFV2 gene segregated 100% concordantly with

Interspecies hybridization of bovids occurs between domestic cattle and at least 3 other species: the American bison (Bison bison), yak (Bos grunniens), and banteng (Bos banteng). Birth of a cattle � buffalo hybrid was reported in Russia, but the report was never authenticated. Such hybrids could be important in improving livestock production and managing diseases that impede production in tropical Africa. We investigated hybridization between cattle and their closest African wild relative, the African buffalo (Syncerus caffer caffer). In an attempt to produce pre-implantation cattle � buffalo hybrid embryos in vitro, matured bovine oocytes were subjected to a standard IVF procedure with either homologous (n = 1166 oocytes) or heterologous (n = 1202 oocytes) buffalo epididymal sperm. After IVF, 67.2% of the oocytes inseminated with homologous sperm cleaved. In contrast, insemination with buffalo sperm resulted in a 4.6% cleavage rate. Cleavage was also slower in hybrids than in cattle embryos. Up to 52.2% of cleaved homologous embryos progressed to the morula stage compared with 12.7% for hybrids. No hybrid embryos developed beyond the 16-cell stage, whereas 40.1% of the cleaved bovine embryos developed to the blastocyst stage. Developmental anomalies such as polyspermy, uneven cleavage, vacuolization, and absence of nuclei in some blastomeres were common in the hybrid embryos. We conclude that interspecies fertilization of cattle oocytes with African buffalo sperm occurs in vitro and that the barrier to hybridization is in the early stages of embryonic development. Also, chromosomal disparity is the likely cause of fertilization abnormalities, abnormal development, and subsequent arrest, impairing the formation of pre-implantation hybrid embryos. Investigation into developmental abnormalities, including reciprocal hybridization and genetic studies of the hybrid embryos, are recommended.