Major Livestock Species Research Articles

Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples.

BackgroundWhile much attention has focused on the development of high-density single nucleotide polymorphism (SNP) assays, the costs of developing and running low-density assays have fallen dramatically. This makes it feasible to develop and apply SNP assays for agricultural species beyond the major livestock species. Although low-cost low-density assays may not have the accuracy of the high-density assays widely used in human and livestock species, we show that when combined with statistical analysis approaches that use quantitative instead of discrete genotypes, their utility may be improved. The data used in this study are from a 63-SNP marker Sequenom® iPLEX Platinum panel for the Black Tiger shrimp, for which high-density SNP assays are not currently available.ResultsFor quantitative genotypes that could be estimated, in 5% of cases the most likely genotype for an individual at a SNP had a probability of less than 0.99. Matrix formulations of maximum likelihood equations for parentage assignment were developed for the quantitative genotypes and also for discrete genotypes perturbed by an assumed error term. Assignment rates that were based on maximum likelihood with quantitative genotypes were similar to those based on maximum likelihood with perturbed genotypes but, for more than 50% of cases, the two methods resulted in individuals being assigned to different families. Treating genotypes as quantitative values allows the same analysis framework to be used for pooled samples of DNA from multiple individuals. Resulting correlations between allele frequency estimates from pooled DNA and individual samples were consistently greater than 0.90, and as high as 0.97 for some pools. Estimates of family contributions to the pools based on quantitative genotypes in pooled DNA had a correlation of 0.85 with estimates of contributions from DNA-derived pedigree.ConclusionsEven with low numbers of SNPs of variable quality, parentage testing and family assignment from pooled samples are sufficiently accurate to provide useful information for a breeding program. Treating genotypes as quantitative values is an alternative to perturbing genotypes using an assumed error distribution, but can produce very different results. An understanding of the distribution of the error is required for SNP genotyping platforms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-014-0051-y) contains supplementary material, which is available to authorized users.

Applications of genomics to improve livestock in the developing world

Nearly 25 years have passed since much of the original molecular genetics research began in livestock. Since then activities in the livestock community have been associated with gene identification, gene mapping, QTL identification, genome-wide association studies and more recently the completion of initial sequencing of all the major livestock species. Many individual genes have been identified and incorporated into selection schemes in livestock, and more recently whole genome analysis and genomic selection have begun to be applied. The advent of cheaper, faster sequencing technologies and the realization of good draft sequences and development of SNP chip technologies for livestock species have contributed to our understanding on many ways to further improve our important food species. Such discoveries generally have benefitted three groups: livestock producers, consumers in the developed world and biomedical researchers. However, increased food insecurity and a worldwide food production crisis loom in the future as the most significant scientific challenge facing us in the next 30 years. Expectations are that human population growth will soon go from 7.3 billion to 9.6 billion by 2050, and food production must double despite evidence of climate change and limited land and water resources. There is a significant increased demand for animal source foods especially in the poorer countries of the developing world where most livestock are produced by small holders but also in countries like China and Brazil which are transforming quickly. Many researchers have touted that the genomic revolution offers solutions to increasing food in the developing world. These opportunities certainly exist, from identifying signatures of selection associated with adaptations for these environments to reducing susceptibility to major disease agents. Direction and focus of research, funding issues and human capacity training all will be required for success. Genomic discoveries will need to be embedded within sustainable programs that address implementation from the outset, and benefiting small holder production will be crucial to meeting this challenge.

Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013

Between June and September 2013, sera from 11 dromedary camels, 150 goats, 126 sheep and 91 cows were collected in Jordan, where the first human Middle-East respiratory syndrome (MERS) cluster appeared in 2012. All sera were tested for MERS-coronavirus (MERS-CoV) specific antibodies by protein microarray with confirmation by virus neutralisation. Neutralising antibodies were found in all camel sera while sera from goats and cattle tested negative. Although six sheep sera reacted with MERS-CoV antigen, neutralising antibodies were not detected.

Genetic Selection and Conservation of Genetic Diversity*

For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development.

식육감별을 위한 미토콘드리아 12S rRNA와 16S rRNA 유전자의 종 특이적 multiplex PCR 기법 개발

Species-specific PCR assay was developed for detection of cattle, sheep, goat, horse, dog, pig, chicken, duck, goose, and turkey using mitochondrial 12S rRNA and 16S rRNA as target genes. Also, an internal positive control was used to detect possible false negatives by using 18S rRNA gene. We designed species-specific primers with amplicon length of 190, 219, 350, 467, 241, 119, 171, 229, 111 and 268 bp for cattle, sheep, goat, horse, dog, pig, chicken, duck, goose, and turkey respectively. The specificity of the primers was tested against the other 10 non-target animal species and a cross-reaction was not observed. We developed two multiplex PCR assays for the simultaneous identification of Korea's major livestock species (cattle, pig, chicken and duck) and poultry species (chicken, duck, goose and turkey) from analogous samples, retaining the same specificity. The limit of detection of the multiplex PCR assay (cattle, pig, chicken and duck) ranged between 1 pg and 0.1 pg of template DNA extracts from raw meat. Applying multiplex PCR assays to DNA extracts from experimental pork/beef and pork/chicken tested raw and heat-treated (<TEX>$120^{\circ}C$</TEX> for 30 min) mixtures respectively, detection limit was 0.1% level beef in pork, pork in beef and chicken in pork and 1.0% level pork in chicken. In conclusion, this assay using gel-based capillary electrophoresis would be very useful in highly sensitive and rapid identification of animal species or ingredients in minced meat and other meat products.

Coat colour and sex identification in horses from Iron Age Sweden

Domestication of animals and plants marked a turning point in human prehistory. To date archaeology, archaeozoology and genetics have shed light on when and where all of our major livestock species were domesticated. Phenotypic changes associated with domestication have occurred in all farm animals. Coat colour is one of the traits that have been subjected to the strongest human selection throughout history. Here we use genotyping of coat colour SNPs in horses to investigate whether there were any regional differences or preferences for specific colours associated with specific cultural traditions in Iron Age Sweden. We do this by identifying the sex and coat colour of horses sacrificed at Skedemosse, Öland (Sweden) during the Iron Age, as well as in horses from two sites in Uppland, Ultuna and Valsgärde (dated to late Iron Age). We show that bay, black and chestnut colours were all common and two horses with tobiano spotting were found. We also show how the combination of sex identification with genotyping of just a few SNPs underlying the basic coat colours can be used to identify the minimum number of individuals at a site on a higher level than morphological methods alone. Although separated by 500 km and from significantly different archaeological contexts the horses at Skedemosse and Ultuna are quite homogenous when it comes to coat colour phenotypes, indicating that there were no clear geographical variation in coat colouration in Sweden during the late Iron Age and early Viking Age.

Managing Livestock Species under Climate Change in Australia.

Simple SummaryWorld communities are concerned about the impacts of a hotter and drier climate on future agriculture. By examining Australian regional livestock data on sheep, beef cattle, dairy cattle, and pigs, the authors find that livestock production will expand under such conditions. Livestock revenue per farm is expected to increase by more than 47% by 2060 under the UKMO, the GISS, and a high degree of warming CSIRO scenario. The existence of a threshold temperature for these species is not evident.This paper examines the vulnerabilities of major livestock species raised in Australia to climate change using the regional livestock profile of Australia of around 1,400 regions. The number of each species owned, the number of each species sold, and the aggregate livestock revenue across all species are examined. The four major species analyzed are sheep, beef cattle, dairy cattle, and pigs. The analysis also includes livestock products such as wool and milk. These livestock production statistics are regressed against climate, geophysical, market and household characteristics. In contrast to crop studies, the analysis finds that livestock species are resilient to a hotter and more arid climate. Under the CSIRO climate scenario in which temperature increases by 3.4 °C, livestock revenue per farm increases significantly while the number of each species owned increases by large percentages except for dairy cattle. The precipitation reduction by about 8% in 2060 also increases the numbers of livestock species per farm household. Under both UKMO and GISS scenarios, livestock revenue is expected to increase by around 47% while the livestock population increases by large percentage. Livestock management may play a key role in adapting to a hot and arid climate in Australia. However, critical values of the climatic variables for the species analyzed in this paper are not obvious from the regional data.

The future of animal production: improving productivity and sustainability

SUMMARYThe challenge for the next 50 years is to increase the productivity of major livestock species to address the food needs of the world, while at the same time minimizing the environmental impact. The present review presents an optimistic view of this challenge. The completion of genome sequences, and high-density analytical tools to map genetic markers, allows for whole-genome selection programmes based on linkage disequilibrium for a wide spectrum of traits, simultaneously. In turn, it will be possible to redefine genetic prediction based on allele sharing, rather than pedigree relationships and to make breeding value predictions early in the life of the peak sire. Selection will be applied to a much wider range of traits, including those that are directed towards environmental or adaptive outcomes. In parallel, reproductive technologies will continue to advance to allow acceleration of genetic selection, probably including recombinationin vitro.Transgenesis and/or mutagenesis will be applied to introduce new genetic variation or desired phenotypes. Traditional livestock systems will continue to evolve towards more intensive integrated farming modes that control inputs and outputs to minimize the impact and improve efficiency. The challenges of the next 50 years can certainly be met, but only if governments reverse the long-term disinvestment in agricultural research.

Conservation status of wild relatives of animals used for food

The Global Plan of Action for Animal Genetic Resources calls for action to conserve the wild species that are related to livestock. The global conservation status of wild species is monitored through the IUCN Red List. This shows that at present 21 percent of the world's 5 488 mammal species and 12 percent of its 9 990 bird species are threatened with extinction. In contrast, a greater proportion of wild relatives of the major mammal livestock species are at risk of extinction: 44 percent of sheep and goats, 50 percent of pigs and 83 percent of cattle. More wild relatives of the chicken are also at risk (25 percent) than bird species overall. These figures indicate the need to pay much more attention to the relationship between the conservation of biological diversity and human well-being. Therefore, there is an urgent need to coordinate responses to the loss of biodiversity and the reduction in variation that may prove vital for animal genetic resources in the future. Intergovernmental meetings being held this autumn offer the prospect of beginning this process.

Human and livestock genetics: parallel evolution and horizontal exchange

Human and livestock genetics: parallel evolution and horizontal exchange

The comparative role of cattle, goats and pigs in the epidemiology of livestock trypanosomiasis on the plateau of eastern Zambia

To determine and compare the prevalence of trypanosome infections in different livestock species (cattle, pigs and goats) in areas where game animals are scarce and livestock constitute the main food source of tsetse, a survey was conducted on the plateau of the Eastern Province of Zambia in Katete and Petauke districts where Glossina morsitans morsitans is the only tsetse species present. Blood was collected from a total of 734 cattle, 333 goats and 324 pigs originating from 59 villages in both districts and was examined using the buffy coat method and the PCR-RFLP as diagnostic tools.The prevalence of trypanosome infections differed substantially between livestock species. Using microscopic diagnostic methods, trypanosome infections were detected in 13.5% of the cattle and 0.9% of the pigs. All goats were parasitologically negative. The PCR-RFLP analyses increased the trypanosomiasis prevalence to 33.5, 6.5 and 3.3% in cattle, pigs and goats respectively. The majority of the infections (91.2%) were due to Trypanosoma congolense. The presence of a trypanosome infection in cattle and pigs resulted in a significant decline in the packed cell volume. The outcome of the study clearly shows that despite the availability of goats and pigs, cattle seem to be the major livestock species affected by the disease in trypanosomiasis endemic areas. The high proportion of infections in cattle could be partly attributed to their higher availability and attractiveness to tsetse.

Reproductive endocrinology and biotechnology applications among buffaloes

Buffalo, as the major livestock species for milk and meat production, contribute significantly to the economy of many countries in south & south-east Asia, South America, Africa and the Mediterranean. Improved buffalo production could significantly enhance the economy and the living standards of farmers in countries where buffaloes predominate; particularly, in countries with a tropical climate. The major factors limiting the efficient utilization of buffaloes in countries with a tropical climate are: late maturity; poor estrus expressivities, particularly in summer months; long postpartum calving intervals; low reproductive efficiencies and fertility rates which are closely linked with environmental stress; as well as managerial problems. As good reproductive performance is essential for efficient livestock production, the female buffalo calves must grow rapidly to attain sexual maturity, initiate estrous cycles, ovulate and be mated by fertile males or inseminated with quality semen to optimize conception and production. In the last two decades, considerable attention has been focused on understanding some of the causes for the inherent limitations in reproduction among buffaloes by studying their reproductive endocrinology as well as developing biotechniques for augmenting their reproductive efficiency. This review provides an overview of buffalo reproductive endocrinology and also of the research done to date towards the enhancement of buffalo reproductive efficiency through endocrine and embryo biotechniques.

Current and Future Developments in Patents for Quantitative Trait Loci in Dairy Cattle

Many studies have proposed that rates of genetic gain in dairy cattle can be increased by direct selection on the individual quantitative loci responsible for the genetic variation in these traits, or selection on linked genetic markers. The development of DNA-level genetic markers has made detection of QTL nearly routine in all major livestock species. The studies that attempted to detect genes affecting quantitative traits can be divided into two categories: analysis of candidate genes, and genome scans based on within-family genetic linkage. To date, 12 patent cooperative treaty (PCT) and US patents have been registered for DNA sequences claimed to be associated with effects on economic traits in dairy cattle. All claim effects on milk production, but other traits are also included in some of the claims. Most of the sequences found by the candidate gene approach are of dubious validity, and have been repeated in only very few independent studies. The two missense mutations on chromosomes 6 and 14 affecting milk concentration derived from genome scans are more solidly based, but the claims are also disputed. A few PCT in dairy cattle are commercialized as genetic tests where commercial dairy farmers are the target market.

Proteomics of lipid oxidation‐induced oxidation of porcine and bovine oxymyoglobins

Myoglobin (Mb) redox state affects meat color and is destabilized by lipid oxidation products such as 4-hydroxy-2-nonenal (HNE). Our objective was to investigate lipid oxidation-induced oxymyoglobin (OxyMb) oxidation in Mb from two major meat-producing livestock species utilizing MS and proteomics tools. Porcine OxyMb was incubated with HNE and analyzed for metmyoglobin (MetMb) formation. MetMb formation was greater in the presence of HNE than controls at pH 7.4 and 37 degrees C (p <0.05). MALDI-TOF MS was used to identify adduct formation; only mono-adducts of HNE (via Michael addition) with porcine Mb were detected. LC-ESI-MS/MS identified three histidine (HIS) residues in porcine Mb that were readily adducted by HNE (HIS 24, 36 and 119), whereas in bovine Mb seven histidine residues (HIS 24, 36, 81, 88, 93, 119 and 152) were adducted. Quantitation of HNE-adducted peptides using isotope-labeled phenyl isocyanate indicated that, initially, HIS 36 was preferentially adducted in porcine Mb whereas HIS 81, 88 and 93 were the predominant sites of early HNE adduction in bovine Mb. Preferential HNE adduction at the proximal histidine (HIS 93) was observed exclusively in bovine OxyMb and may explain why lipid oxidation-induced OxyMb oxidation appears more extensive in beef, than in pork.

Situación, fuerzas motrices y tendencias de los sistemas de producción agropecuaria en los países en desarrollo

This paper describes and assesses the current status of livestock production systems, the drivers of global livestock production, and the major trends in such production. The analysis covers the six major livestock species: cattle and buffaloes, goats and sheep, pigs and chickens. Global drivers of the livestock sector include economic growth and income, demographic and land use changes, dietary adjustments and technological change. The rate of change and direction of livestock development vary greatly among world regions, with Asia showing the most rapid growth and structural change. The paper also examines system dynamics, by analysing the ways livestock production has adjusted to external forces. A brief discussion of how these trends link to food safety concludes the paper.

Present situation of cystic echinococcosis in Central Asia

Cystic echinococcosis (CE) caused by Echinococcus granulosus has always been an endemic disease in central Asia. During the period of Soviet Administration up to 1991, human surgical incidence rates tended to be relatively low with perhaps at most 1–5 cases per 100,000 per year. Following the collapse of the Soviet Union and the emergence of the New Independent States there has been profound economic and social changes. Associated with this has been a serious epidemic of CE throughout the region. In many areas figures suggest the surgical incidence is now greater than 10 cases per 100,000. Furthermore, official government figures are believed to substantially under report the extent of the problem. For example, official figures in Uzbekistan reported 819 cases of CE surgically treated in 2001. However, a detailed analysis of hospital records suggests that the true figure was 4089, more than 4 fold higher. The latter figure represents an annual surgical incidence rate of nearly 25 cases/100,000 per year. Similarly high endemic areas are seen in southern Kazakhstan, Kyrgystan and Tadjikistan with incidence rates of up to 13 cases/100,000, 20 cases/100,000 and 27 cases/100,000 respectively. A disproportionate number of cases are in children and the unemployed. The rates of infection have also increased in major livestock species such as sheep with a doubling of reported prevalence in some areas. In the dog population, independent studies in Uzbekistan and Kazakhstan have demonstrated that the rural dog population, closely associated with the sheep industry, is highly infected, with prevalences approaching 25%. Village and urban dogs have a considerably lower prevalence.

Current Status of Comparative Mapping in Livestock

Comparative maps, representing chromosomal locations of homologous genes in different species, are useful sources of information for identifying candidate disease genes and genes determining complex traits. They facilitate gene mapping and linkage prediction in other species, and provide information on genome organization and evolution. Here, the current gene mapping and comparative mapping status of the major livestock species are presented. Two techniques were widely used in comparative mapping: FISH (Fluorescence In Situ Hybridization) and PCR-based mapping using somatic cell hybrid (SCH) or radiation hybrid (RH) panels. New techniques, using, for example, ESTs (Expressed Sequence Tags) or CASTS (Comparatively Anchored Sequence Tagged Sites), also have been developed as useful tools for analyzing comparative genome organization in livestock species, further enabling accurate transfer of valuable information from one species to another.

It took many mares to form the domestic horse

Most zebras are rather alike, but members of another species from the genus Equus are quite diverse creatures – an Exmoor Pony and an Arabian could easily be taken for different species. The phenotypic diversity displayed by many domestic animals is indeed extraordinary compared with what we usually see among natural populations. However, phenotypic diversity does not necessarily translate into a corresponding degree of genetic diversity and in the case of domesticates, it is clear that very strong artificial selection, rather than unusual genetic diversity, caused the contrasting appearance of the various breeds we recognize today. In fact, recent analyses of major livestock species indicate that most of them have a rather narrow genetic basis, consistent with domestication from a limited number of wild populations and geographical regions.

Meat Tenderisation – The Role of Calpains

In recent years there has been a shift in emphasis in livestock production away from increased muscle growth towards improved meat quality. The final eating quality of meat depends on a number of organoleptic properties including appearance, colour, fat content, taste, texture and tenderness. Whilst colour and fat content are important in influencing meat purchase, consumer studies indicate that it is the degree to which muscle tenderises after slaughter that is the most important factor contributing to overall meat quality (Warkupet al, 1995). Despite efforts to standardise breeding, husbandry, nutrition, transport, lairage and slaughter regimes, ensuring a consistently tender product still remains difficult to control or predict. The problem is international, with beefsteak toughness a major concern in the USA and pork toughness difficult to eradicate in the UK. The tenderisation process involves complex changes in muscle metabolism in the immediate post slaughter period and is dependent on genetic makeup, protein complement, metabolic status and environmental factors such as physiological stress. In the early postmortem period, glycogen depletion, lactic acid accumulation, pH decline and rate of entry and exit into rigor can all influence the ultimate tenderness of the meat some 8 - 20 days later following a period of conditioning (Gollet al, 1995). However, the main determinant of ultimate tenderness appears to be the extent of proteolysis of key target proteins within muscle fibres (Tayloret al, 1995). Research in all major livestock species has pointed to the calpain proteolytic enzyme family being a major factor responsible for key peptide bond cleavage (Koohmaraie, 1996). Whilst opinion is divided as to which isoform of calpain is the most important under specified conditions, most workers agree that the major factor is the level at slaughter of the specific calpain inhibitor calpastatin. The evidence for this is reviewed here, highlighting potential means of regulating the system in order to assure a consistently high quality tender product.

Mapping genes for growth rate and fatness in a Large White x Meishan F2 pig population

DNA-based markers and genetic maps of major livestock species have been developed in the last few years. These, together with experimental populations and appropriate statistical methods, provide the tools to dissect causes of economically important genetic variation in livestock. A cross between genetically diverse lines is a powerful experimental design for such a study. In an F2 or backcross population from such a cross, markers are likely to be highly informative and the genes that control the differences between the lines will be segregating. We have been developing such a resource population based on a cross between the British Large White and Chinese Meishan pigs. These breeds differ for many traits, with the Meishan being inferior for growth rate and fatness, but superior for reproduction traits. Here we report the mapping of major genetic effects on growth rate and fatness in our cross.