Mapping of multiple quantitative trait loci affecting bovine spongiform encephalopathy

A whole-genome scan was conducted to map quantitative trait loci (QTL) for BSE resistance or susceptibility. Cows from four half-sib families were included and 173 microsatellite markers were used to construct a 2835-cM (Kosambi) linkage map covering 29 autosomes and the pseudoautosomal region of the sex chromosome. Interval mapping by linear regression was applied and extended to a multiple-QTL analysis approach that used identified QTL on other chromosomes as cofactors to increase mapping power. In the multiple-QTL analysis, two genome-wide significant QTL (BTA17 and X/Y ps) and four genome-wide suggestive QTL (BTA1, 6, 13, and 19) were revealed. The QTL identified here using linkage analysis do not overlap with regions previously identified using TDT analysis. One factor that may explain the disparity between the results is that a more extensive data set was used in the present study. Furthermore, methodological differences between TDT and linkage analyses may affect the power of these approaches.

On the prediction of simultaneous inbreeding coefficients at multiple loci

A new deterministic method for predicting simultaneous inbreeding coefficients at three and four loci is presented. The method involves calculating the conditional probability of IBD (identical by descent) at one locus given IBD at other loci, and multiplying this probability by the prior probability of the latter loci being simultaneously IBD. The conditional probability is obtained applying a novel regression model, and the prior probability from the theory of digenic measures of Weir and Cockerham. The model was validated for a finite monoecious population mating at random, with a constant effective population size, and with or without selfing, and also for an infinite population with a constant intermediate proportion of selfing. We assumed discrete generations. Deterministic predictions were very accurate when compared with simulation results, and robust to alternative forms of implementation. These simultaneous inbreeding coefficients were more sensitive to changes in effective population size than in marker spacing. Extensions to predict simultaneous inbreeding coefficients at more than four loci are now possible.

Genome-wide search for markers associated with bovine spongiform encephalopathy

A genome-wide search for markers associated with BSE incidence was performed by using Transmission-Disequilibrium Tests (TDTs). Significant segregation distortion, i.e., unequal transmission probabilities of alleles within a locus, was found for three marker loci on Chromosomes (Chrs) 5, 10, and 20. Although TDTs are robust to false associations owing to hidden population substructures, it cannot distinguish segregation distortion caused by a true association between a marker and bovine spongiform encephalopathy (BSE) from a population-wide distortion. An interaction test and a segregation distortion analysis in half-sib controls were used to disentangle these two alternative hypotheses. None of the markers showed any significant interaction between allele transmission rates and disease status, and only the marker on Chr 10 showed a significant segregation distortion in control individuals. Nevertheless, the control group may have been a mixture of resistant and susceptible but unchallenged individuals. When new genotypes were generated in the vicinity of these three markers, evidence for an association with BSE was confirmed for the locus on Chr 5.

Greenhouse gas emissions in livestock production systems

Agriculture is responsible for a significant proportion of total anthropogenic greenhouse gas emissions (perhaps 18% globally), and therefore has the potential to contribute to efforts to reduce emissions as a means of minimising the risk of dangerous climate change. The largest contributions to emissions are attributed to ruminant methane production and nitrous oxide from animal waste and fertilised soils. Further, livestock, including ruminants, are an important component of global and Australian food production and there is a growing demand for animal protein sources. At the same time as governments and the community strengthen objectives to reduce greenhouse gas emissions, there are growing concerns about global food security. This paper provides an overview of a number of options for reducing methane and nitrous oxide emissions from ruminant production systems in Australia, while maintaining productivity to contribute to both objectives. Options include strategies for feed modification, animal breeding and herd management, rumen manipulation and animal waste and fertiliser management. Using currently available strategies, some reductions in emissions can be achieved, but practical commercially available techniques for significant reductions in methane emissions, particularly from extensive livestock production systems, will require greater time and resource investment. Decreases in the levels of emissions from these ruminant systems (i.e., the amount of emissions per unit of product such as meat) have already been achieved. However, the technology has not yet been developed for eliminating production of methane from the rumen of cattle and sheep digesting the cellulose and lignin-rich grasses that make up a large part of the diet of animals grazing natural pastures, particularly in arid and semi-arid grazing lands. Nevertheless, the abatement that can be achieved will contribute significantly towards reaching greenhouse gas emissions reduction targets and research will achieve further advances.

Genetic Parameters for Production Traits in Queensland Merinos

Genetic and phenotypic parameters are presented for production traits, greasy fleece weight (GFW), yield (YLD), clean fleece weight (CFW), average fibre diameter (DIAM) and liveweight (LWT), in 15 month old medium Peppin Merino sheep at Longreach and Julia Creek, Queensland. Heritabilities for GFW, YLD, CFW, DIAM and LWT were respectively 0.35, 0.62, 0.34, 0.74, and 0.37 for Longreach and 0.23, 0.52, 0.20, 0.67 and 0.56 for Julia Creek. Most estimates were consistent with other reported values. AAABG 13th Conference; Proceedings of the Association for the Advancement of Animal Breeding and Genetics.

Genetic Parameters for Physiological Characters in Merino Rams in Central and North West Queensland

Genetic and phenotypic parameters for respiration rate (RR) and rectal temperature (RT) are presented for weaner and hogget Merino rams, at Longreach and Julia Creek, Queensland. Heritability estimates for RT and RR at both sites and at both ages ranged from moderate to very high. Phenotypic and genetic correlations between these characters are also reported. AAABG 14th Conference; Proceedings of the Association for the Advancement of Animal Breeding and Genetics. AAABG

Optimising between and within family selection for harvest weight in prawns with restricted harvest size.

Manual grading of prawns restricts the number that can be harvested. A restricted harvest size places a limit on the opposing within family and between family sources of selection pressure. A simulation study with inbreeding constrained at 0.5% per generation, a harvest size of 2000, heritability of 0.3, common family environmental effect of 0.1, indicates that maximum response to selection could be achieved with as few as 40 families. Increasing the number of families above 80 may reduce total selection response. It is important to be aware that increasing the number of families may not always yield a greater genetic response.

Genetic diversity of Atlantic salmon (Salmo salar) and European whitefish (Coregonus lavaretus) in the Baltic Sea

We described the patterns and extent of microsatellite DNA variation in historical and present-day Atlantic salmon (Salmo salar L.) stocks in the Baltic Sea and neighbouring areas, and in European whitefish (Coregonus lavaretus) ecotypes, populations and run-timing types in Finland. Moreover, the amount and pattern of genetic diversity in historical salmon populations before human impact were described, and the proportion of diversity maintained in the present hatchery stocks evaluated. Salmon populations in the Baltic Sea were, on average, significantly less variable than eastern Atlantic populations, and the diversity of landlocked populations (Lakes Vänern, Saimaa, Onega and Ladoga) was in turn significantly lower than that of anadromous salmon populations in the Baltic Sea populations. Within the Baltic Sea, the anadromous populations of Atlantic salmon formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin) and southern (western Baltic Main Basin) regions. Based on microsatellite data, three salmon population groups in the Baltic Sea were considered potentially different colonization lineages. In short- and long-term breeding programmes of Atlantic salmon, the average observed rate of loss of alleles was 4.9% and 2.0% per generation and the average rate of loss of heterozygosity was 1.4% and 1% per generation, respectively. When comparing the genetic parameters of stocks before and after hatchery breeding of several successive generations (Rivers Iijoki and Oulujoki), statistically significant changes in allele frequencies were common, while large wild stock in the Teno River has remained temporally very stable over 56 years. Despite the observed losses of genetic diversity in broodstock breeding, a large proportion of the genetic resources of the extirpated stocks are still conserved in the broodstocks. Genetic differentiation among European whitefish ecotypes was generally low, thus giving support to the hypothesis of one native European whitefish species in Fennoscandia. Among the ecotypes, the northern, large sparsely rakered, bottom-dwelling whitefish was the most unique. The known genetic differences in quantitative traits have thus either developed independently of potential phylogenetic lineages, or the lineages have mixed and the quantitative traits of the ecotypes, like gill-raker number, have later changed according to environment and selection pressures. Overall, genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Wild whitefish populations studied had slightly higher allelic diversity than hatchery-reared populations in corresponding rivers.

A dynamic programming model for optimising feeding and slaughter decisions regarding fattening pigs

Costs of purchasing new piglets and of feeding them until slaughter are the main variable expenditures in pig fattening. They both depend on slaughter intensity, the nature of feeding patterns and the technological constraints of pig fattening, such as genotype. Therefore, it is of interest to examine the effect of production technology and changes in input and output prices on feeding and slaughter decisions. This study examines the problem by using a dynamic programming model that links genetic characteristics of a pig to feeding decisions and the timing of slaughter and takes into account how these jointly affect the quality-adjusted value of a carcass. The model simulates the growth mechanism of a pig under optional feeding and slaughter patterns and then solves the optimal feeding and slaughter decisions recursively. The state of nature and the genotype of a pig are known in the analysis. The main contribution of this study is the dynamic approach that explicitly takes into account carcass quality while simultaneously optimising feeding and slaughter decisions. The method maximises the internal rate of return to the capacity unit. Hence, the results can have vital impact on competitiveness of pig production, which is known to be quite capital-intensive. The results suggest that producer can significantly benefit from improvements in the pig's genotype, because they improve efficiency of pig production. The annual benefits from obtaining pigs of improved genotype can be more than €20 per capacity unit. The annual net benefits of animal breeding to pig farms can also be considerable. Animals of improved genotype can reach optimal slaughter maturity quicker and produce leaner meat than animals of poor genotype. In order to fully utilise the benefits of animal breeding, the producer must adjust feeding and slaughter patterns on the basis of genotype. The results suggest that the producer can benefit from flexible feeding technology. The flexible feeding technology segregates pigs into groups according to their weight, carcass leanness, genotype and sex and thereafter optimises feeding and slaughter decisions separately for these groups. Typically, such a technology provides incentives to feed piglets with protein-rich feed such that the genetic potential to produce leaner meat is fully utilised. When the pig approaches slaughter maturity, the share of protein-rich feed in the diet gradually decreases and the amount of energy-rich feed increases. Generally, the optimal slaughter weight is within the weight range that pays the highest price per kilogram of pig meat. The optimal feeding pattern and the optimal timing of slaughter depend on price ratios. Particularly, an increase in the price of pig meat provides incentives to increase the growth rates up to the pig's biological maximum by increasing the amount of energy in the feed. Price changes and changes in slaughter premium can also have large income effects. Key words: barley, carcass composition, dynamic programming, feeding, genotypes, lean, pig fattening, precision agriculture, productivity, slaughter weight, soybeans

Management of broodstock and quality control of fish seed in Hungary

Common carp (Cyprinus carpio) breeding has a long tradition in Hungary. However, recent economic changes in Eastern Europe and new developments in aquaculture necessitated the need for ensuring quality of the brood stock used in hatcheries and the legal and institutional frameworks needed to implement the program. In addition to good research and development programs and gene banking, it became essential to establish an appropriate legal framework, organize, coordinate and control breeding activities, and provide financial support. It was a major breakthrough for carp breeding when C.carpio was recognized as one of the cultivated animals in the Animal Breeding Act in 1993. The Carp Breeding Section of the Hungarian Fish Producers Association plays an important role in carp breeding programs. Thirteen breeding farms of the Carp Breeding Section have 24 certified C.carpio varieties. In Hungary, about 80 % of the seed used as stocking for commercial production are from high quality certified breeders.

Growth and milk performance of yak in southern Qinghai area

The Study carried out in Xueshan Township, Guoluo prefecture, Qinghai Province, P. R. China from 1997 to 1999 on 1) Growth regulation of yak from born to adult and 1/4 wild yak from born to one and half year; 2) The effect of nursing or not on the growth and development of dam; 3) Meat performance of local yak; 4)Milk productivity of female yak. It can be served as the theory basis from which crossbreed improvement of yak and government decision could be drawn.

The effect of the 'Gait keeper' mutation in the DMRT3 gene on gaiting ability in Icelandic horses

A nonsense mutation in DMRT3 ('Gait keeper' mutation) has a predominant effect on gaiting ability in horses, being permissive for the ability to perform lateral gaits and having a favourable effect on speed capacity in trot. The DMRT3 mutant allele (A) has been found in high frequency in gaited breeds and breeds bred for harness racing, while other horse breeds were homozygous for the wild-type allele (C). The aim of this study was to evaluate further the effect of the DMRT3 nonsense mutation on the gait quality and speed capacity in the multigaited Icelandic horse and demonstrate how the frequencies of the A- and C- alleles have changed in the Icelandic horse population in recent decades. It was confirmed that homozygosity for the DMRT3 nonsense mutation relates to the ability to pace. It further had a favourable effect on scores in breeding field tests for the lateral gait tölt, demonstrated by better beat quality, speed capacity and suppleness. Horses with the CA genotype had on the other hand significantly higher scores for walk, trot, canter and gallop, and they performed better beat and suspension in trot and gallop. These results indicate that the AA genotype reinforces the coordination of ipsilateral legs, with the subsequent negative effect on the synchronized movement of diagonal legs compared with the CA genotype. The frequency of the A-allele has increased in recent decades with a corresponding decrease in the frequency of the C-allele. The estimated frequency of the A-allele in the Icelandic horse population in 2012 was 0.94. Selective breeding for lateral gaits in the Icelandic horse population has apparently altered the frequency of DMRT3 genotypes with a predicted loss of the C-allele in relatively few years. The results have practical implications for breeding and training of Icelandic horses and other gaited horse breeds.

Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits

The morphology of a sample of four bulls and 43 cows, presumed to be descendants of the extinct cattle breed ‘Algarvia’ (AG), was used to assign their relationship with animals from other Portuguese autochthonous breeds – Arouquesa (AR), Barrosa˜ (BA), Cachena (CA), Marinhoa (MA), Maronesa (MO), Minhota (MN), Mirandesa (MI), (only bulls), Alentejana (AL), Garvonesa (GA), Mertolenga (ME) and Preta (PR). Standard numerical taxonomic methods were applied to a set of 183 (cows) and 170 (bulls) traits, to derive average pairwise taxonomic distances among the sample of 257 cows and 76 bulls. Distance coefficients (morphological index of distance) ranged from 0.22 to 2.62 (cows) and from 0.49 to 2.13 (bulls). Unweighted pair group method using arithmetic averages (UPGMA)-based phenograms and a principal coordinate analysis showed that bulls were highly clustered and cows showed a tendency to cluster according to their geographical and breed origin. The AG population grouped together with GA, AL, ME and MN breeds in the Red Convex group. The average taxonomic distance among breeds was 1.02, the highest being 1.39 (ME versus BA) and the lowest being 0.64 (MA versus AR). The approach allowed for the identification of a phenotypically differentiated set of animals, comprising 19 cows and four bulls representative of the AG breed, and which can be targeted in further studies aiming at the recovery of this extinct breed.

Neue Ansätze für die ökologische Milchrinderzucht

Die Milchrinderzucht hat im ökologischen Landbau kein deutliches eigenes Profil. Üblicherweise wird auf Biobetrieben mit konventionellen Zuchtlinien gearbeitet, die meistens die Veranlagung zu hohen Milchleistungen haben. Diese Kühe können nicht immer adäquat gefüttert werden, weil das betriebseigene Futter der Biobetriebe nicht immer dem Bedarf der Tiere entspricht, aber möglichst wenig Futter zugekauft wird und nur wenig Kraftfutter eingesetzt werden darf. Energiemangel und gesundheitliche Probleme der Kühe können daraus resultieren. Daher braucht es neue Ansätze für die ökologische Milchrinderzucht, die besser berücksichtigen, dass die Tiere und ihre Umwelt zusammenpassen müssen und die die Tiergesundheit besser fördern. In den vergangenen 100 Jahren wurde der Umweltbezug der Tiere in der konventionellen Milchrinderzucht immer mehr vernachlässigt. Die Zucht wurde auf Produktionsleistungsmerkmale ausgerichtet. Es widerspricht jedoch dem Leitbild des Biolandbaus, nur einzelne Merkmale der Tiere zu fördern, ohne das ganze Tier und den ganzen Betrieb mit zu berücksichtigen. Es gibt bereits einige Ansätze für eine ökologische Milchrinderzucht, die den Bezug der Tiere zu ihrer Umwelt und ein ganzheitliches Tierverständnis einbeziehen (z. B. das Konzept der Lebensleistungszucht und die Linienzucht mit Kuhfamilien). Diese Ansätze sind jedoch nicht weit verbreitet und mit hohem Forschungs- und / oder Beratungsbedarf verbunden. Ein in der konventionellen Milchviehzucht immer wichtiger werdender Ansatz, der auch gut mit den Ideen des Biolandbaus übereinstimmt, ist die stärkere züchterische Gewichtung von Gesundheitsmerkmalen (teilweise anstelle der Produktionsleistung). Da die direkte Erfassung der Tier-gesundheit als Merkmal aufwändig ist, werden häufig Hilfsmerkmale für Gesundheit züchterisch bearbeitet. In der vorliegenden Arbeit wurden neue Hilfsmerkmale für die Zucht auf Gesundheit gesucht. Der Schwerpunkt wurde auf ethologische Merkmale gelegt, welche einen eigenaktiven Bezug der Tiere zu ihrer Umwelt zeigen sowie auf Eigenschaften, die in einem Zusammenhang mit Verdauungs- und Stoff-wechselprozessen stehen. Das Ziel der Untersuchungen war, die individuelle Ausprägung der beobachteten Eigenschaften und deren Zusammenhang zur Tiergesundheit zu ermitteln, um neue Merkmale für die Zucht auf eine gute Tiergesundheit zu identifizieren. Die Beobachtungen wurden über einen Zeitraum von 13 Monaten in einer Milchviehherde mit 60 Kühen auf einem biologisch-dynamischen Betrieb in der Schweiz durchgeführt. In zwei Projekten mit 27 bzw. 34 Tieren wurden das Wiederkäuverhalten, das Liegeverhalten, das Temperament, die Körperkondition (BCS) und die Kotbeschaffenheit untersucht. Die Untersuchungen wurden unter für alle beobachteten Tiere gleichen Praxisbedingungen durchgeführt. Die Gesundheit der Tiere wurde kontinuierlich anhand des Behandlungs-journals, der Tierarztrechnungen, der Milchleistungsprüfungsdaten und der Abkalbedaten erfasst und für jedes Tier in einem Gesundheitsindex zusammengefasst. Zusätzlich wurde ein Euter-gesundheitsindex berechnet, in dem nur die Eutererkrankungen berücksichtigt wurden. Die individuelle Konsistenz der beobachteten Eigenschaften wurde anhand der Reproduzier-barkeit der wiederholten Beobachtungen berechnet. Korrelationen zwischen dem Gesundheitsindex und den beobachteten Parametern und lineare, multivariate Regressionsanalysen mit dem Gesundheitsindex bzw. dem Eutergesundheitsindex als abhängige Variable wurden berechnet. Das Wiederkäuverhalten, das Liegeverhalten, die Kotbeschaffenheit und das Temperament der Tiere waren individuell konsistent. Die Variation der Wiederkäugeschwindigkeit, die Anzahl Abliegevorgänge und die Höhe der BCS-Noten (1. Quartil) waren positiv und die Spannweite der BCS-Noten war negativ mit der Tiergesundheit korreliert. Zwischen einem ruhigen Temperament der Kühe und der Eutergesundheit zeigte sich eine positive Korrelation. Die Regressionsanalysen ergaben, dass die Variation der Tiergesundheit im Projekt 1 durch die Variation der Wiederkäugeschwindigkeit und die Anzahl Abliegevorgänge zu 23% und im Projekt 2 durch die Höhe und die Spannweite der BCS-Noten zu 32% erklärt werden konnte. Die Variation der Eutergesundheit konnte durch das Temperament zu 24% erklärt werden. Die Ergebnisse zum Temperament und zur Körperkondition sind für die Tierzucht im Biolandbau interessant, zumal sie einfach zu erfassen sind und in anderen Studien ihre relativ hohe Erblichkeit festgestellt wurde. Die beiden Merkmalskomplexe zeigen zudem, wie gut das Tier sich an seine Umwelt anpassen kann. Das ist unter nichtstandardisierten Umweltbedingungen, wie sie auf Biobetrieben üblich sind, wichtig. Für die Umsetzung in der Zucht auf Betriebsebene braucht es Beratung. Um diese Eigenschaften in Zuchtprogramme auf Populationsebene zu integrieren, sind weitere Forschungsarbeiten zur Methodik einer routinemässigen Erhebung von BCS- und Temperamentsdaten und zur Implementation nötig.

Equine conceptus development : a mini review

Many aspects of early embryonic development in the horse are unusual or unique; this is of scientific interest and, in some cases, considerable practical significance. During early development the number of different cell types increases rapidly and the organization of these increasingly differentiated cells becomes increasingly intricate as a result of various inter-related processes that occur step-wise or simultaneously in different parts of the conceptus (i.e., the embryo proper and its associated membranes and fluid). Equine conceptus development is of practical interest for many reasons. Most significantly, following a high rate of successful fertilization (71-96%) (Ball, 1988), as many as 30-40% of developing embryos fail to survive beyond the first two weeks of gestation (Ball, 1988), the time at which gastrulation begins. Indeed, despite considerable progress in the development of treatments for common causes of sub-fertility and of assisted reproductive techniques to enhance reproductive efficiency, the need to monitor and rebreed mares that lose a pregnancy or the failure to produce a foal, remain sources of considerable economic loss to the equine breeding industry. Of course, the potential causes of early embryonic death are numerous and varied (e.g. persistent mating induced endometritis, endometrial gland insufficiency, cervical incompetence, corpus luteum (CL) failure, chromosomal, genetic and other unknown factors (LeBlanc, 2004). However, the problem is especially acute in aged mares with a history of poor fertility in which the incidence of embryonic loss between days 2 and 14 after ovulation has been reported to reach 62-73%, and in which embryonic death is due primarily to embryonic defects rather than to uterine pathology (Ball et al., 1989; Carnevale & Ginther, 1995; Ball, 2000).