Molecular typing can help to manage and contain food-borne pathogen contamination in poultry and poultry products by providing a means to accurately evaluate sources and transmission routes of specific strains. Moreover, it provides an opportunity to identify the virulence determinant genes characterising the poultry strains that may cause human diseases.

This paper summarises the main applications of genotyping methods in the epidemiological investigations of Campylobacter and Salmonella, in order to identify clonally related and sporadic strains as well as to keep track of the geographical spread and prevalence shifts of epidemic and endemic clones.

Moreover, examples of applications of comparative genomics, by whole genome sequencing and microarray, are given in order to demonstrate how to investigate the difference in virulence determinant genes among Salmonella poultry strains and to distinguish different genotypes among Campylobacter strains. Although virulence determinants have been defined for Escherichia coli and Salmonella enterica, despite use of molecular typing and virulence assays for many years, virulence determinant genes have not been identified for Campylobacter. Putative virulence genes, such as cdt, have been discovered, but for the majority a clear role in disease causation has not been established. It is unlikely that comparative molecular typing using the methods available to a single laboratory will elucidate the virulence mechanisms and associated determinants. It is also, therefore, not yet possible to investigate differences in virulence gene complement for Campylobacter by genome sequencing and microarray in the same way as has been described for E. coli and S. enterica.

It appears possible for free-flying native or feral wild birds to be responsible for direct or indirect spread of infectious agents from contaminated poultry product wastes to susceptible commercial poultry. Direct spread involves infected wild birds gaining access to commercial poultry. Indirect spread involves secondary spread to other free-flying birds that may subsequently gain access to commercial poultry.

In analysing the level of risk of such spread consideration is given to three elements. These are the susceptibility of wild birds to infection by the agents concerned, the opportunity for susceptible species coming into direct or indirect contact with both poultry product wastes and commercial poultry, and the occurrence of actual cases of such spread.

The scenario being considered is one in which poultry product wastes contain an infective dose of one of the agents of concern, namely avian influenza, Newcastle disease or infectious bursal disease. A review of the literature was undertaken to assist in assessing the likelihood of spread of these agents by wild birds.

Exposure of wild birds, to any of the three viruses of concern at product waste disposal sites, is a potential threat but the likelihood of spread to commercial poultry appears to be low. More obvious means of spread occur in the poultry industry, as biosecurity is often rudimentary. Spread of infectious agent by fomites, live poultry and infected wild birds could well be involved in transmission of disease agents between farms. Where live bird poultry markets or semi-feral village poultry exist they provide an obvious means of spread of these agents and involvement of access of wild birds to poultry product wastes is probably of little importance.

The likelihood of wild bird involvement in virus spread from poultry products could increase if a susceptible species with gregarious habits (flocking behaviour) leading to high population densities, were to frequent both poultry product waste disposal sites and commercial poultry premises. Some passerines are likely to frequent waste disposal facilities and poultry premises, but it appears that different species congregate at poultry premises than at waste disposal sites.

There is little evidence of spread of disease from waste poultry products to commercial poultry premises having occurred.

A review of QTL for production, behaviour and disease resistance traits published to the end of 2004 is presented. QTL were located randomly over the genome and there was little commonality between different studies for similar traits. However, there were several reports of QTL from different experiments in similar regions of chromosomes 1 (at 250 and 450 cM), 4 and 8 and for disease resistance on chromosome 5. Generally there were 6 to 8 QTL affecting the major production traits in experimental breed crosses and collectively they accounted for a substantial proportion of the line difference where this information was provided. The size of typical genome-wide significant effects for production traits was 0.3 to 1.0 phenotypic standard deviations. Genetic effects for growth traits were generally additive whereas about one-third of QTL for other production traits showed significant dominance effects. Variable reporting standards were noted and proposals for minimum published information are presented. Currently there are scientific opportunities for meta-analyses of results from experiments on body weight gain and considerable potential for combining data and results from different studies for other traits in the future.

The modern poultry industry has a remarkable record in reducing mortality, applying a combination of effective disease control, adequate nutrition, good husbandry and genetic selection. Primary breeders, specialized in the adaptation of layers, broilers and turkeys to changing demands of a global food market, have made three major contributions in the past: (1) eradication of vertically transmitted disease agents such as lymphoid leucosis viruses, mycoplasmas and salmonellae; (2) selection between and within lines for general liveability and specific disease resistance; and (3) dissemination of management recommendations which may help customers to minimize losses at the commercial level. Current focus is on components of liveability which are directly or indirectly linked to poultry welfare: selection against feather pecking and cannibalism in egg-type chickens and selection against leg disorders and heart/lung dysfunction in rapidly growing meat poultry.

This paper describes, under laboratory and/or field conditions, an approach that could be used to predict nitrogen (N) mineralization of poultry litter. Proper composting of poultry litter results in N mineralization, reducing or eliminating the environmentally harmful effects of ammonia (NH3) odours and nitrate leaching. Addition of straw to poultry manure provides sufficient available carbon and increases NH3 binding capacity, overruling any greater influence of diet composition on methane (CH3) formation. C:N ratio ranges (6–25) vary in the amount of low N loss depending on substrates. Aerobic decomposition of manure results in formation of humified organic compounds and decreased nutrient availability, while anaerobic decomposition forms low molecular weight compounds (volatile fatty acids and NH3+- N). The differences in the size of the composted particles results in physical separation and decomposability of high and low C:N ratio substrates. Temperatures ranging from 14 to 35°C did not affect the rate of N mineralization, but affected N loss from poultry manure pellets by decay nitrification at 14 and 35°C compared with 25°C. Uric acid and undigested proteins in poultry litter have optimal degradation rates at pH of 5.5 or higher, with the optimum pH for uricase being about 9. Variations in manure composition are seen between different species such as cattle, swine and poultry. The chemical composition of the manure and not the substrate N status influences the rate of decomposition or microbial availability. The N mineralization potential of some vegetable residues correlated better with the total and water soluble N contents than with their C:N ratios. Poultry manures are applied to agricultural soils at rates determined by the amount of available N that they are assumed to contribute to the crops. Many equations have been developed to calculate these application rates.

FPD is a common condition amongst commercially grown turkey poults. It causes the skin of the footpad to become hard and scaly, often developing horn-like pegs of abnormal keratin. The footpad can become swollen, frequently splitting. In the centre of the lesion the epidermis separates, and is often totally necrotic. Heterophils filter into the stratum germinativum.

The cause of FPD is complex, but many contributing factors have been suggested, such as dietary intake, skin structure, bird weight and sex, litter moisture and litter type. Litter quality is affected by many other factors such as stocking density, air temperature and moisture, season, consistency and amount of faeces (affected by diet), and drinker design.

Wet litter is the most likely factor affecting FPD, followed by biotin deficiency. Experimental evidence suggests that biotin deficiency causes FPD, and that commercial rations do not contain enough biotin to prevent these lesions. Supplementations of biotin have been shown to reduce the severity and incidence of lesions. Wet litter has also been identified as a possible causative agent. Broilers and poults reared on wet litter have an increased incidence and severity of FPD lesions, but the problem is alleviated by replacing the wet litter with dry. Biotin supplementations are able to reduce FPD to a certain extent if birds are reared on dry litter, but if on wet litter, lesions may still occur. Biotin intake and wet litter appear to be the factors most likely to influence the development of FPD.

Experimental results are difficult to compare because rearing conditions differ. Further experimentation is needed to determine the optimum amount of biotin required for healthy growth and lesion free foot pads, and to ascertain the real effects of other suggested causes.

Any approach which aims to improve the quality and safety of eggs, is of limited value unless it can relate to the incidence of breakages in the field, and can be applied either directly to breeding programmes or used as online tools for quality assurance. Online systems require the method of assessment to be non-destructive. This is probably not so important for breeding companies who tend to gauge the usefulness of an eggshell quality measurement by its ease of measurement, its heritability and, its genetic correlation with other phenotypic traits. Historically, qualitative measures such as shell breaking or puncture strength, non-destructive deformation and specific gravity have been widely adopted as tools in selection programmes. The dynamic stiffness is a novel eggshell quality measurement, which could be utilised by poultry breeders as it has a moderate heritability and high genetic and phenotypic correlation with other shell quality traits including eggshell breaking strength. This non-destructive measurement could also be applied on-line to monitor shell quality. An alternative approach is to use genetic markers as tools to aid conventional breeding programmes where an important eggshell quality trait is practically too difficult or expensive to fully exploit. Marker-assisted selection for the genes coding for organic matrix proteins may provide a way of incorporating other beneficial egg quality traits into selection programmes in the future.

An increased knowledge of endocrine systems during incubation not only results in a better understanding of fundamental aspects of embryonic development, but also may lead to new practical applications. A first and immediate aspect is the possibility of early sex diagnosis based on current knowledge of sex determination. The current practice of killing day-old male chicks of layers results essentially from the improved efficiency of modern egg and meat lines, which were selected in opposite directions. The disposal of unwanted male chicks from layer lines causes increased welfare and ethical concern. Therefore, attempts have been made to interfere with sex determination or to identify the unwanted gender of the embryo at a certain stage of development (e.g. based on endocrine differences) where public concern is no longer a point of resistance against elimination. Thyroid hormones as well as glucocorticoids are known to be involved in several events leading to hatch and in the quality of the hatchling. Both seem to be strongly influenced by a common hypothalamic factor in the late chick embryo: corticotrophin-releasing hormone (CRH), CRH-related urocortines or analogues for CRH-receptor activity may be combined with in ovo vaccination for stimulating or synchronizing hatching activity. A next question to be asked is whether incubation conditions that produce the best hatchability also automatically result in chicks of the highest quality with the best desired postnatal performance. During prenatal development, most of the functional systems develop from an open loop system without feedback into a closed control system with feedback. This is already documented for endocrine systems such as the thyroid, the corticotroph and the gonadal axis. For functional systems, critical periods seem to exist and it is presumed that these coincide with the transition from an open into a closed feedback control system. In consequence, variation in incubation conditions such as temperature may induce a lifelong determination of physiological control systems, most probably via long-term changes in the expression of related effector genes and this may be defined as epigenetic adaptation. This opens possibilities to improve incubation conditions, not only in view of hatchability/chick quality but also taking long-term effects into account. Also it may redirect, at least to some extent, development as a function of the aims set forward, e.g. metabolic conditioning.

Tibial Dyschondroplasia (TD) is one of the most prevalent skeletal abnormalities observed in avian species; it causes enormous economic losses and is a major animal welfare problem. It is characterized by lesions composed of uncalcified, unvascularized cartilage that can extend from the epiphyseal growth plate into the metaphysis. The disease development and progress have been attributed to dietary, environmental and genetic factors. Irregular cell differentiation of the chondrocytes that populate the growth plate, with consequently aberrant cartilage vascularization and mineralization, has been hypothesized to be involved in the etiology of the disease.

Various tools available for the study of TD are described in the present review, and their advantages and limitations are discussed. We describe the morphology of the growth plate, with especial emphasis on the differences between the mammalian and the avian ones. We highlight vascularization as a possible cause of TD, and suggest that matrix metalloproteinases (MMPs) play an important role in cartilage vascularization and TD development. The disparity between broilers and turkeys MMPs suggests that they differ in their regulation of vascularization, so that different strategies may be required in dealing with TD in broilers and in turkeys. The high body mass of the modern meat-type birds has been implicated in the development of TD. A model was established to evaluate the effect of mechanical loading on the bones of young chickens, without any dietary manipulations: increased loading caused enhanced vascularization of the growth plate together with increased MMP-9 expression, without any changes in the incidence of TD, which suggests that the increased loading is not in itself the cause of TD.

At present, the cause of TD is not known, but multidisciplinary research at various levels such as a genomic approach based on microarray technology and the chicken genome project, together with cell and organ culture methodology, genetic selection, nutritional manipulation and environmental approaches will provide us with better understanding of the molecular mechanisms underlying TD, and should pave the way for future reduction in its incidence.

Corn and soyabeans may not be available in many countries particularly those which do not have sufficient foreign currency or the capacity to grow them. This paper outlines strategies that may be important under these circumstances. Alternative feedstuffs and various feeding systems may be used to support poultry production. Alternative ingredients such as rice bran, pearl millet, cottonseed meal and grain legumes are discussed. Evidence is presented showing that amino acid requirements of layers and broilers may be too generous particularly in countries where climate, management and disease can impose production constraints. The ability of finishing broilers to perform well on very low-energy diets allows the inclusion of alternative feeds and by-products into formulations. Very low protein diets based on cereals and free amino acids can be used for layers without loss of performance. Self-selection of feedstuffs may be an important strategy in reducing feed costs of broilers and layers. The concept of matching production with available feed resources may compromise broiler growth and egg production, but in many countries this may be the most economical choice. Countries in the humid tropics usually have reduced poultry performance. The effects of high temperature and humidity are difficult to overcome. The vexed questions of the escalation in the price of fossil fuel and the outbreak of avian influenza, both seemingly without a solution, are clouds hanging over an otherwise buoyant industry.

This paperprovides a short history of poultry production development in Lithuania and the results of breeding work achieved overa thirty-year period.

The year 1965 can be considered as the beginning of breeding work, when the development of specialised strains of laying hens began. On the basis of these strains, after testing them for combining ability, the first two-way cross of laying hens “Neringa” was developed in 1975. The egg production of the commercial layers of this cross on poultry farms in Lithuania was 239 eggs in 10 laying months. After nearly ten years' purposeful work with initial lines, “Hisex White” from the Euribrid company, a more productive three-way hybrid combination was developed (1984), which was denominated as the cross “Kelmò–1”. As a result of further breeding work, the laying rate of commercial hens increased to 276 eggs peryear.

In 1968, breeding work with the initial lines of meat poultry was started. Using lines developed by “Shaver”, “Euribrid”, and “Arbor Acres” companies, Lithuanian breeders developed 5 lines of Plymouth Rock and 3 lines of Cornish breeds.

On the basis of the results from the analysis of the combining ability, a four-way broiler cross “Baltika–4” was developed in 1971 with a daily weight gain of 26.8 grams, and a four-way cross “Baltika–10” with a daily weight gain of 37.5 grams was developed in 1983. During the period of 1989–1990, the experimental four-way cross with a daily weight gain of 41.8 grams was developed.

The activities of Lithuanian researchers in the fields of poultry breeding, nutrition and housing technologies together with the results of breeding and those of commercial farms, exerted a positive effect on the development of Lithuanian poultry production1.

One of the keys to success was the development of a closed vertically intergrated farming system, i.e. primary breeding farm, grandparent reproduction farm, parent stock reproduction farm, the multiplication results of which are used by production farms and large poultry farms.

As a results of complex work, Lithuanian state poultry production farms produced 13.5 kg of poultry meat and 273 eggs per capita in 1990.