A set of 180 forages (47 alfalfa hays, 26 grass hays, 52 corn silages, 35 small grain silages and 20 sorghum silages) were randomly collected from different locations of the Po Valley (Northern Italy) from 2009 to 2010. The forages were characterised for chemical composition (11 parameters), NDF digestibility (five parameters) and net energy for lactation (NEL). The latter was calculated according to the two approaches adopted by the 2001 Nutrient Research Council and based on chemical parameters either alone (NEL3x-Lig) or in combination with 48 h NDF degradability in the rumen (NEL3x-48h). Thereafter, a principal component analysis (PCA) was used to define forage populations and limit the number of variables to those useful for obtaining a rapid forage quality evaluation on the basis of the calculated NEL content of forages. The PCA identified three forage populations: corn silage, alfalfa hay and a generic population of so-called ‘grasses’, consisting of grass hays, small grain and sorghum silages. This differentiation was also confirmed by a cluster analysis. The first three principal components (PC) together explained 79.9% of the total variation. PC1 was mainly associated with protein fractions, ether extract and lignin, PC2 with ash, starch, NDF and indigestible NDF (iNDF) and PC3 with NDF digestibility. Moreover, PC2 was highly correlated to both NEL3x-Lig (r = −0.84) and NEL3x-48h (r = −0.94). Subsequently, forage-based scores (FS) were calculated by multiplying the original standardised variables of ash, starch, NDF and iNDF with the scoring factors obtained from PCA (0.112, −0.141, 0.227 and 0.170, respectively). The FS showed a high determination coefficient for both NEL3x-Lig (R2 = 0.86) and NEL3x-48h (R2 = 0.73). These results indicate that PCA enables the distinction of different forage classes and appropriate prediction of the energy value on the basis of a reduced number of parameters. With respect to the rumen in situ parameters, iNDF was found to be more powerful at discriminating forage quality compared with NDF digestibility at different rumen incubation times or rates of NDF digestion.

Oxalic acid (OA) is a secondary compound occurring in a wide range of plants consumed by ruminants, especially in saline lands or in arid and semi-arid regions. However, its impact on the rumen microbial community and its changes over time, as well as the potential consequences on ruminal function, remain unknown. To examine this impact, five ewes fitted with a ruminal cannula and fed low-quality grass hay were dosed daily with 0.6 mmol of OA/kg body weight through the cannula for 14 days. On days 0 (before the start), 4, 7 and 14 of the administration period, samples of ruminal digesta were collected throughout the day (0, 3, 6 and 9 h after the morning feeding) for analysis of the bacterial community and fermentation parameters (pH, ammonia and volatile fatty acid (VFA) concentrations). In addition, two feedstuffs were incubated in situ using the nylon bag technique to estimate ruminal degradation. Terminal restriction fragment length polymorphism was employed to monitor the dynamics of total bacteria, and quantitative real-time PCR was used to investigate the abundance of the oxalate-degrading Oxalobacter formigenes. Neither pH nor total VFA concentrations were affected. Nevertheless, OA dosing altered molar proportions of most individual VFA and ammonia concentrations (P < 0.001). The dry matter disappearance of alfalfa hay was reduced on days 7 and 14 and that of barley straw only on day 7 (P < 0.01). These slight changes were related to others observed in the relative frequency of a number of terminal restriction fragments. Variations in the ruminal microbiota occurred rapidly with OA administration, which did not modify the bacterial diversity significantly but altered the structure of the community. However, many of these changes were reversed by the end of the experiment, with no significant differences between days 0 and 14 of dosing. These results suggest a rapid adaptation of the rumen bacterial community linked to the estimated increase in the abundance of O. formigenes (from 0.002% to 0.007% of oxc gene in relation to the total bacteria 16S rDNA; P < 0.01), which is assumed to be responsible for oxalate breakdown.

Dwarfing in rice has dramatically improved and stabilized rice yields worldwide, often controlled by a single dwarf gene, sd1. A novel semidwarf gene d60 complements the gametic lethal gene gal, such that the F1 between ‘Hokuriku 100’ (genotype d60d60GalGal, Gal: mutant non-lethal allele) and ‘Koshihikari’ (D60D60galgal, D60: tall allele) would show 25% sterility due to deterioration of gametes bearing both gal and d60. The F2 would segregate as one semidwarf (1 d60d60GalGal) : two tall and 25% sterile (2 D60d60Galgal) : six tall (2 D60d60GalGal : 1 D60D60GalGal : 2 D60D60Galgal : 1 D60D60galgal), skewed from a Mendelian segregation ratio of one semidwarf : three tall for a single recessive gene. To pyramid d60 and sd1, into the Japanese super-variety ‘Koshihikari’, the F1 (D60d60Galgal) of ‘Koshihikari’ × ‘Hokuriku 100’ was first backcrossed with ‘Koshihikari’, and the BCF1 segregated into a ratio of one tall and 25% sterile (D60d60Galgal) : two tall (1 D60D60Galgal : 1 D60D60galgal). Tall, 25% sterile BC1F1 plants (D60d60Galgal) were then selected for pollen sterility and backcrossed with ‘Koshihikari’ as the recurrent parent. It is unnecessary to grow out and select a semidwarf from the BCnF2 if a pollen parent with ∼70% pollen fertility is chosen from the BCnF1 to backcross with the recurrent parent. Semidwarfing genes d60 and sd1 were successfully pyramided into the ‘Koshihikari’ genome by crossing isogenic lines ‘Koshihikari d60’ and ‘Koshihikari sd1’, to produce ‘Minihikari’, a new parental source of both d60 and sd1. ‘Minihikari’ displayed super-short stature due to the combination of sd1 and d60, which are genetically and functionally independent.

FST, a measurement of the genetic differentiation among subpopulations, is a fundamental parameter in population genetics, with many valuable applications in molecular biology, evolutionary biology, conservation and forensics. One of its close relatives, GST, has been widely used to measure differentiation from highly polymorphic markers such as microsatellites. However, because of the high mutation rate of such markers, GST may underestimate the genomic differentiation due to demographic causes such as migration rate and subpopulation size. A new statistic proposed recently, Jost's D, was claimed to have better properties than GST and was advocated to replace GST as a measure of differentiation. This paper shows that D is not a proper measure of differentiation because it fails to meet some fundamental requirements as a differentiation statistic, and is hardly estimable without bias in practice. D is highly dependent on the gene diversity of a marker and on the unknown parameter of the number of subpopulations, is highly sensitive to how alleles and loci are defined and how data are analysed, does not increase monotonically with either divergence time or drift, and does not always have a maximal value of 1. The maximal D value can be zero or close to zero, depending on the number of alleles at a locus relative to the number of subpopulations. I suggest continuing the use of GST, with caution in its interpretation when highly polymorphic markers are used, before a better estimator of FST that explicitly accounts for mutations is developed.

In previous analyses, the variation in actual, or realized, relationship has been derived as a function of map length of chromosomes and type of relationship, the variation being greater the shorter the total chromosome length and the coefficient of variation being greater the more distant the relationship. Here, the results are extended to allow for the relatives’ ancestor being inbred. Inbreeding of a parent reduces variation in actual relationship among its offspring, by an amount that depends on the inbreeding level and the type of mating that led to that level. For descendants of full-sibs, the variation is reduced in later generations, but for descendants of half-sibs, it is increased.

Gene expression profiling using microarrays and xenograft transplants of human cancer cell lines are both popular tools to investigate human cancer. However, the undefined degree of cross hybridization between the mouse and human genomes hinders the use of microarrays to characterize gene expression of both the host and the cancer cell within the xenograft. Since an increasingly recognized aspect of cancer is the host response (or cancer–stroma interaction), we describe here a bioinformatic manipulation of the Affymetrix profiling that allows interrogation of the gene expression of both the mouse host and the human tumour. Evidence of microenvironmental regulation of epithelial mesenchymal transition of the tumour component in vivo is resolved against a background of mesenchymal gene expression. This tool could allow deeper insight to the mechanism of action of anti-cancer drugs, as typically novel drug efficacy is being tested in xenograft systems.

Two sets of reciprocal introgression lines (ILs) and a population of recombinant inbred lines (RILs) derived from the cross between japonica cultivar Xiushui09 and indica breeding line IR2061-520-6-9 (abbreviated as IR2061) were used to identify QTL for heading date (HD). Phenotyping was conducted in Hainan Island for two winter seasons (2007 and 2009). Nine QTLs were detected in the ILs with Xiushui09 background (XS-ILs), and four of which were repeatedly mapped across 2 years. Five QTLs were identified in the ILs with IR2061 background (IR-ILs), and three of which were commonly detected in 2 years. All commonly detected QTL had the same direction of gene effect. Seven QTL for HD were identified in the RILs in 2009. Only three (25%) QTLs were commonly detected using all the three populations (XS-ILs, IR-ILs and RILs). The number of commonly identified QTLs among populations was related to degree of similarity of their genetic backgrounds, suggesting that the genetic background effect is important for detecting HD QTL. QHd7 and QHd10b stably expressed in different populations and across years thus would be exploited in rice breeding programme. Moreover, lines with both of QHd7 and QHd10b resulted in at least 3 days earlier than lines with only one of them QTL, showing evident pyramiding effect.

A major challenge in complex trait genetics is to unravel how multiple loci and environmental factors together cause phenotypic diversity. Both first (F1) and second (F2) generation hybrids often display phenotypes that deviate from what is expected under intermediate inheritance. We have here studied two chicken F2 populations generated by crossing divergent chicken lines to assess how epistatic loci, identified in earlier quantitative trait locus (QTL) studies, contribute to hybrid deviations from the mid-parent phenotype. Empirical evidence suggests that the average phenotypes of the intercross birds tend to be lower than the midpoint between the parental means in both crosses. Our results confirm that epistatic interactions, despite a relatively small contribution to the phenotypic variance, play an important role in the deviation of hybrid phenotypes from the mid-parent values (i.e. multi-locus hybrid genotypes lead to lower rather than higher body weights). To a lesser extent, dominance also appears to contribute to the mid-parent deviation, at least in one of the crosses. This observation coincides with the hypothesis that hybridization tends to break up co-adapted gene complexes, i.e. generate Bateson–Dobzhansky–Muller incompatibilities.

Water-soluble components of feedstuffs are mainly utilized during the early phase of microbial fermentation, which could be deemed an important determinant of gas production behavior in vitro. Many studies proposed that the fractional rate of degradation (FRD) estimated by fitting gas production curves to mathematical models might be used to characterize the early incubation for in vitro systems. In this study, the mathematical concept of FRD was developed on the basis of the Logistic-Exponential (LE) model, with initial gas volume being zero (LE0). The FRD of the LE0 model exhibits a continuous increase from initial (FRD0) toward final asymptotic value (FRDF) with longer incubation time. The relationships between the FRD and gas production at incubation times 2, 4, 6, 8, 12 and 24 h were compared for four models, in addition to LE0, Generalization of the Mitscherlich (GM), cth order Michaelis–Menten (MM) and Exponential with a discrete LAG (EXPLAG). A total of 94 in vitro gas curves from four subsets with a wide range of feedstuffs from different laboratories and incubation periods were used for model testing. Results indicated that compared with the GM, MM and EXPLAG models, the FRD of LE0 model consistently had stronger correlations with gas production across the four subsets, especially at incubation times 2, 4, 6, 8 and 12 h. Thus, the LE0 model was deemed to provide a better representation of the early fermentation rates. Furthermore, the FRD0 also exhibited strong correlations (P < 0.05) with gas production at early incubation times 2, 4, 6 and 8 h across all four subsets. In summary, the FRD of LE0 model provides an alternative to quantify the rate of early stage incubation, and its initial value could be an important starting parameter of rate.

A study was undertaken to investigate the performance of breeding ewes fed a range of forage and concentrate-based diets in late pregnancy, balanced for supply of metabolizable protein (MP). For the final 6 weeks before lambing, 104 twin-bearing multiparous ewes were offered one of four diets: adlibitum precision-chop grass silage + 0.55 kg/day concentrates (GS); ad libitum maize silage + 0.55 kg/day concentrates (MS); a 1 : 1 mixture (on a dry matter (DM) basis) of grass silage and maize silage fed ad libitum + 0.55 kg/day (GSMS); or 1.55 kg/day concentrates + 50 g/day chopped barley straw (C). The CP content of the concentrates was varied between treatments (157 to 296 g/kg DM) with the aim of achieving a daily intake of 130 g/day MP across all treatments. Compared with ewes fed GS, forage DM intake was higher (P < 0.05) in ewes fed MS (+0.21 kg/day) and GSMS (+0.16 kg/day), resulting in higher (P < 0.001) total DM intakes with these treatments. C ewes had the lowest total DM intake of all the treatments examined (P < 0.001). C ewes lost more live weight (LW; P < 0.001) and body condition score (BCS; P < 0.05) during the first 3 weeks of the study but there were no dietary effects on ewe LW or BCS thereafter. The incidence of dystocia was lower (P < 0.01) in C ewes compared with those offered silage-based diets (7.5% v. 37.4% ewes), and was higher (P < 0.01) in ewes fed MS compared with GS or GSMS (50.7%, 34.7% and 26.9%, respectively). There were no significant dietary effects on the plasma metabolite concentrations of ewes in late pregnancy, pre-weaning lamb mortality, weaned lamb output per ewe or on lamb growth rate. The results of this study demonstrate that both maize silage and all-concentrate diets can replace grass silage in pregnant ewe rations without impacting on performance, provided the supply of MP is non-limiting. The higher incidence of dystocia in ewes fed maize silage as the sole forage is a concern.

The study examined the effects of harvest time of red and white clover silage on eating and ruminating activity and particle size distribution in feed boli, rumen content and faeces in cows. The clover crops were harvested at two stages of growth and ensiled in bales. Red clover crops had 36% and 45% NDF in dry matter (DM) at early (ER) and late (LR) harvest, respectively, and the white clover crops had 19% and 29% NDF in DM at the early (EW) and late (LW) harvest, respectively. The silages were fed restrictively (80% of ad libitum intake) twice daily to four rumen cannulated non-lactating Jersey cows (588 ± 52 kg) in a 4 × 4 Latin square design. Jaw movements (JM) were recorded for 96 h continuously. Swallowed boli, rumen mat, rumen fluid and faeces samples were collected, washed in nylon bags (0.01 mm pore size) and freeze-dried before dry sieving through 4.750, 2.360, 1.000, 0.500, 0.212 and 0.106 mm into seven fractions. The length (PL) and width (PW) values of rumen and faeces particles within each fraction were measured by use of image analysis. The eating activity (min/kg DM intake; P < 0.05) was higher in LR compared with the other treatments. The eating activity (min/kg NDF intake; P < 0.05) was affected by clover type with highest values for white clover silage. The mean ruminating time (min/kg DM), daily ruminating cycles (P < 0.001) and JM during ruminating (P < 0.05) were affected by treatment with increasing values at later harvest time. The proportion of washed particle DM of total DM in boli (P < 0.001), rumen mat (P < 0.001), rumen fluid (P < 0.01) and faeces was (P < 0.001) highest by feeding LR. There were identified two peaks (modes 1 and 2) on the probability density distribution (PDF) of PW values of rumen mat and faeces, but only one peak (mode 1) for PL values. There was no difference in the mean and mode 1 PW and PL value in rumen mat between the four treatments. The mean PL, mode PL, mode 2 PW and mean PW in faeces were highest for LR (P < 0.05). The mean particle size in boli measured by sieving was higher at white clover compared with red clover treatments (P < 0.001) and the highest value in faeces was found in LR (P < 0.01). The two peaks on PDF for width values of rumen mat and faeces particles are most likely related to the leaves and the stems/petioles. In conclusion, the mean total chewing activity per kg DM was lowest for the white clover silage and increased for both silages due to later harvest time. The mean particle size in boli was smallest for LR, whereas the mean PL and PW in faeces were highest for the LR.

Agroecology and industrial ecology can be viewed as complementary means for reducing the environmental footprint of animal farming systems: agroecology mainly by stimulating natural processes to reduce inputs, and industrial ecology by closing system loops, thereby reducing demand for raw materials, lowering pollution and saving on waste treatment. Surprisingly, animal farming systems have so far been ignored in most agroecological thinking. On the basis of a study by Altieri, who identified the key ecological processes to be optimized, we propose five principles for the design of sustainable animal production systems: (i) adopting management practices aiming to improve animal health, (ii) decreasing the inputs needed for production, (iii) decreasing pollution by optimizing the metabolic functioning of farming systems, (iv) enhancing diversity within animal production systems to strengthen their resilience and (v) preserving biological diversity in agroecosystems by adapting management practices. We then discuss how these different principles combine to generate environmental, social and economic performance in six animal production systems (ruminants, pigs, rabbits and aquaculture) covering a long gradient of intensification. The two principles concerning economy of inputs and reduction of pollution emerged in nearly all the case studies, a finding that can be explained by the economic and regulatory constraints affecting animal production. Integrated management of animal health was seldom mobilized, as alternatives to chemical drugs have only recently been investigated, and the results are not yet transferable to farming practices. A number of ecological functions and ecosystem services (recycling of nutrients, forage yield, pollination, resistance to weed invasion, etc.) are closely linked to biodiversity, and their persistence depends largely on maintaining biological diversity in agroecosystems. We conclude that the development of such ecology-based alternatives for animal production implies changes in the positions adopted by technicians and extension services, researchers and policymakers. Animal production systems should not only be considered holistically, but also in the diversity of their local and regional conditions. The ability of farmers to make their own decisions on the basis of the close monitoring of system performance is most important to ensure system sustainability.

One important objective for animal welfare is to maintain animals free from pain, injury or disease. Therefore, detecting and evaluating the intensity of animal pain is crucial. As animals cannot directly communicate their feelings, it is necessary to identify sensitive and specific indicators that can be easily used. The aim of the present paper is to review relevant indicators to assess pain in several farm species. The term pain is used for mammals, birds and fish, even though the abilities of the various species to experience the emotional component of pain may be different. Numerous behavioural changes are associated with pain and many of them could be used on farms to assess the degree of pain being experienced by an animal. Pain, as a stressor, is associated with variations in the hypothalamic–pituitary–adrenal axis as well as in the sympathetic and immune systems that can be used to identify the presence of pain rapidly after it started. However, most of these measures need sophisticated equipment for their assessment. Therefore, they are mainly adapted to experimental situations. Injuries and other lesional indicators give information on the sources of pain and are convenient to use in all types of situations. Histopathological analyses can identify sources of pain in experimental studies. When pronounced and/or long lasting, the pain-induced behavioural and physiological changes can decrease production performance. Some indicators are very specific and sensitive to pain, whereas others are more generally related to stressful situations. The latter can be used to indicate that animals are suffering from something, which may be pain. Overall, this literature review shows that several indicators exist to assess pain in mammals, a few in birds and very few in fish. Even if in some cases, a single indicator, usually a behavioural indicator, may be sufficient to detect pain, combining various types of indicators increases sensitivity and specificity of pain assessment. Research is needed to build and validate new indicators and to develop systems of pain assessment adapted to each type of situation and each species.

It is well documented that global warming is unequivocal. Dairy production systems are considered as important sources of greenhouse gas emissions; however, little is known about the sensitivity and vulnerability of these production systems themselves to climate warming. This review brings different aspects of dairy cow production in Central Europe into focus, with a holistic approach to emphasize potential future consequences and challenges arising from climate change. With the current understanding of the effects of climate change, it is expected that yield of forage per hectare will be influenced positively, whereas quality will mainly depend on water availability and soil characteristics. Thus, the botanical composition of future grassland should include species that are able to withstand the changing conditions (e.g. lucerne and bird's foot trefoil). Changes in nutrient concentration of forage plants, elevated heat loads and altered feeding patterns of animals may influence rumen physiology. Several promising nutritional strategies are available to lower potential negative impacts of climate change on dairy cow nutrition and performance. Adjustment of feeding and drinking regimes, diet composition and additive supplementation can contribute to the maintenance of adequate dairy cow nutrition and performance. Provision of adequate shade and cooling will reduce the direct effects of heat stress. As estimated genetic parameters are promising, heat stress tolerance as a functional trait may be included into breeding programmes. Indirect effects of global warming on the health and welfare of animals seem to be more complicated and thus are less predictable. As the epidemiology of certain gastrointestinal nematodes and liver fluke is favourably influenced by increased temperature and humidity, relations between climate change and disease dynamics should be followed closely. Under current conditions, climate change associated economic impacts are estimated to be neutral if some form of adaptation is integrated. Therefore, it is essential to establish and adopt mitigation strategies covering available tools from management, nutrition, health and plant and animal breeding to cope with the future consequences of climate change on dairy farming.

SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis is a tool widely used to help in decision making in complex systems. It suits to exploring the issues and measures related to the conservation and development of local breeds, as it allows the integration of many driving factors influencing breed dynamics. We developed a quantified SWOT method as a decision-making tool for identification and ranking of conservation and development strategies of local breeds, and applied it to a set of 13 cattle breeds of six European countries. The method has four steps: definition of the system, identification and grouping of the driving factors, quantification of the importance of driving factors and identification and prioritization of the strategies. The factors were determined following a multi-stakeholder approach and grouped with a three-level structure. Animal genetic resources expert groups ranked the factors, and a quantification process was implemented to identify and prioritize strategies. The proposed SWOT methodology allows analyzing the dynamics of local cattle breeds in a structured and systematic way. It is a flexible tool developed to assist different stakeholders in defining the strategies and actions. The quantification process allows the comparison of the driving factors and the prioritization of the strategies for the conservation and development of local cattle breeds. We identified 99 factors across the breeds. Although the situation is very heterogeneous, the future of these breeds may be promising. The most important strengths and weaknesses were related to production systems and farmers. The most important opportunities were found in marketing new products, whereas the most relevant threats were found in selling the current products. The across-breed strategies utility decreased as they gained specificity. Therefore, the strategies at European level should focus on general aspects and be flexible enough to be adapted to the country and breed specificities.