The cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blight (BB) disease of rice and is widely used as a resistance donor. The present study was carried out to decipher the genetics of BB resistance in Ajaya and map the gene(s) conferring resistance. Genetic analysis in the F2 indicated a quantitative/additive nature of resistance governed by two loci with equal effects. Linked marker analysis and allelic tests revealed that one of the resistance genes is xa5. Sequence analysis of a 244 bp region of the second exon of the gene-encoding Transcription factor IIAγ (the candidate gene for xa5) confirmed the presence of xa5. Bulked-segregant analysis (BSA) revealed the putative location of the two quantitative trait loci (QTLs)/genes associated with resistance on chromosomes 5 and 8. Composite interval mapping located the first locus on Chr. 5S exactly in the genomic region spanned by xa5 and the second locus (qtl BBR 8.1) on Chr. 8L. Owing to its differential disease reaction with a set of seven hyper-virulent isolates of Xanthomonas oryzae, a map location on Chr. 8L, which was distinct from xa13 and data from allelism tests, the second resistance locus in Ajaya was determined to be novel and was designated as xaAj. A contig map spanning xaAj was constructed in silico and the genomic region was delimited to a 13·5 kb physical interval. In silico analysis of the genomic region spanning xaAj identified four putatively expressed candidate genes, one of which could be involved in imparting BB resistance in Ajaya along with xa5.

For genomic selection methods, the statistical challenge is to estimate the effect of each of the available single-nucleotide polymorphism (SNP). In a context where the number of SNPs (p) is much higher than the number of bulls (n), this task may lead to a poor estimation of these SNP effects if, as for genomic BLUP (gBLUP), all SNPs have a non-null effect. An alternative is to use approaches that have been developed specifically to solve the ‘p>>n’ problem. This is the case of variable selection methods and among them, we focus on the Elastic-Net (EN) algorithm that is a penalized regression approach. Performances of EN, gBLUP and pedigree-based BLUP were compared with data from three French dairy cattle breeds, giving very encouraging results for EN. We tried to push further the idea of improving SNP effect estimates by considering fewer of them. This variable selection strategy was considered both in the case of gBLUP and EN by adding an SNP pre-selection step based on quantitative trait locus (QTL) detection. Similar results were observed with or without a pre-selection step, in terms of correlations between direct genomic value (DGV) and observed daughter yield deviation in a validation data set. However, when applied to the EN algorithm, this strategy led to a substantial reduction of the number of SNPs included in the prediction equation. In a context where the number of genotyped animals and the number of SNPs gets larger and larger, SNP pre-selection strongly alleviates computing requirements and ensures that national evaluations can be completed within a reasonable time frame.

The fat mass and obesity associated (FTO) gene has been implicated with obesity and dietary intake predominantly in European populations. We assessed the association between the FTO rs9939609 variant with body fat distribution and dietary intake in a multi-ethnic population. Aboriginal, Chinese, European and South Asian participants living in Canada (n=706) were assessed for body fat and inner-abdominal fat using imaging techniques, dietary intake and genotyped for the FTO rs9939609 variant. Linear regression was used to study the associations between the minor allele of the variant and measures of adiposity and dietary intake. Minor allele frequencies were: Aboriginals (17%), Chinese (17%), Europeans (39%) and South Asians (31%). The rs9939609 variant was associated with intake of dietary macronutrients in Aboriginals and Europeans only. In the total population, there were positive associations between the rs9939609 minor allele and greater fat mass (0·94±0·56 kg, P=0·045), per cent body fat (0·7±0·4%, P=0·031), relative greater subcutaneous abdominal adipose tissue (4·9±2·8%, P=0·039) and percent daily calories from fat (0·4±0·2%, P=0·064). Our findings suggest that the FTO rs9939609 minor allele may be associated with dietary intake in adults and is positively associated with regional fat deposition.

A few occurrences of miniature inverted-repeat transposable elements (MITEs) have been reported in species of the genus Drosophila. Here, we describe msechBari, a MITE-like element in Drosophila sechellia. The element is short, approximately 90 bp in length, AT-rich and occurs in association with, or close to, genes, characteristics that are typical for MITEs. The identification was performed in silico using the sequenced genome of D. sechellia and confirmed in a laboratory strain. This short element is related to the Bari_DM transposon of Drosophila melanogaster, having terminal inverted repeats (TIRs) of a similar length and a high identity with the full-length Bari_DM element. The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests that msechBari could be active in D. sechellia.

Predicting functional gene annotations remains a significant challenge, even in well-annotated genomes such as yeast and Drosophila. One promising, high-throughput method for gene annotation is to use correlated gene expression patterns to annotate target genes based on the known function of focal genes. The Drosophila melanogaster transcriptome varies genetically among wild-derived inbred lines, with strong genetic correlations among the transcripts. Here, we leveraged the genetic correlations in gene expression among known seminal fluid protein (SFP) genes and the rest of the genetically varying transcriptome to identify 176 novel candidate SFPs (cSFPs). We independently validated the correlation in gene expression between seven of the cSFPs and a known SFP gene, as well as expression in male reproductive tissues. We argue that this method can be extended to other systems for which information on genetic variation in gene expression is available.

Grasslands being used in sheep farming systems are managed under a variety of agricultural production, recreational and conservational objectives. Although sheep grazing is rarely considered the best method for delivering conservation objectives in seminatural temperate grasslands, the literature does not provide unequivocal evidence on the impact of sheep grazing on pasture biodiversity. Our aim was therefore to review evidence of the impacts of stocking rate, grazing period and soil fertility on plant communities and arthropod populations in both mesotrophic grasslands typical of agriculturally improved areas and in native plant communities. We therefore conducted a literature search of articles published up to the end of the year 2010 using ‘sheep’ and ‘grazing’ as keywords, together with variables describing grassland management, plant community structure or arthropod taxa. The filtering process led to the selection of 48 articles, with 42 included in the stocking rate dataset, 9 in the grazing period dataset and 10 in the soil fertility dataset. The meta-analysis did not reveal any significant trends for plant species richness or plant community evenness along a wide stocking rate gradient. However, we found frequent shifts in functional groups or plant species abundance that could be explained by the functional properties of the plants in the community. The meta-analysis confirmed that increasing soil fertility decreased plant species richness. Despite the very limited dataset, plant species richness was significantly greater in autumn-grazed pastures than in ungrazed areas, which suggests that choosing an appropriate grazing period would be a promising option for preserving biodiversity in sheep farming systems. Qualitative review indicated that low grazing intensity had positive effects on Orthoptera, Hemiptera (especially phytophagous Auchenorrhyncha) and, despite a diverse range of feeding strategies, for the species richness of Coleoptera. Lepidoptera, which were favoured by more abundant flowering plants, also benefited from low grazing intensities. Spider abundance and species richness were higher in ungrazed than in grazed pastures. In contrast, there are insufficient published studies to draw any firm conclusions on the benefits of late grazing or stopping fertilization on insect diversity, and no grounds for including any of this information in decision support tools at this stage.

A potential role for epigenetic mechanisms in the regulation of mammary function in the dairy cow is emerging. Epigenetics is the study of heritable changes in genome function that occur because of chemical changes rather than DNA sequence changes. DNA methylation is an epigenetic event that results in the silencing of gene expression and may be passed on to the next generation. However, recent studies investigating different physiological states and changes in milk protein gene expression suggest that DNA methylation may also play an acute, regulatory, role in gene transcription. This overview will highlight the role of DNA methylation in the silencing of milk protein gene expression during mastitis and mammary involution. Moreover, environmental factors such as nutrition may induce epigenetic modifications of gene expression. The current research investigating the possibility of in utero, hence cross-generational, epigenetic modifications in dairy cows will also be discussed. Understanding how the mammary gland responds to environmental cues provides a potential to enhance milk production not only of the dairy cow but also of her daughter.

The recently sequenced cattle (Bos taurus) genome unraveled the unique genomic features of the species and provided the molecular basis for applying a systemic approach to systematically link genomic information to metabolic traits. Comparative analysis has identified a variety of evolutionary adaptive features in the cattle genome, such as an expansion of the gene families related to the rumen function, large number of chromosomal rearrangements affecting regulation of genes for lactation, and chromosomal rearrangements that are associated with segmental duplications and copy number variations. Metabolic reconstruction of the cattle genome has revealed that core metabolic pathways are highly conserved among mammals although five metabolic genes are deleted or highly diverged and seven metabolic genes are present in duplicate in the cattle genome compared to their human counter parts. The evolutionary loss and gain of metabolic genes in the cattle genome may reflect metabolic adaptations of cattle. Metabolic reconstruction also provides a platform for better understanding of metabolic regulation in cattle and ruminants. A substantial body of transcriptomics data from dairy and beef cattle under different nutritional management and across different stages of growth and lactation are already available and will aid in linking the genome with metabolism and nutritional physiology of cattle. Application of cattle genomics has great potential for future development of nutritional strategies to improve efficiency and sustainability of beef and milk production. One of the biggest challenges is to integrate genomic and phenotypic data and interpret them in a biological and practical platform. Systems biology, a holistic and systemic approach, will be very useful in overcoming this challenge.

To access the fermentative response of equine caecal microbial population to nitrogen availability, an in vitro study was conducted using caecal contents provided with adequate energy sources and nitrogen as limiting nutrient. Two nitrogen (N) sources were provided, protein (casein) and non-protein (urea). Caecal fluid, taken from three cannulated horses receiving a hay–concentrate diet, was mixed with a N-free buffer–mineral solution. The influence of four N levels (3.7, 6.3, 12.5 or 25 mg of N in casein or urea) was studied using the gas production technique. Total volatile fatty acids (VFA), NH3-N and gas production were measured after a 24-h incubation period. Microbial biomass was estimated using adenine and guanine bases as internal markers, and ATP production was estimated stoichiometrically. Microbial growth efficiency (YATP) and gas efficiency (Egas) were estimated. Fermentation with casein as the sole N source was generally characterized by lower total VFA, NH3-N, total gas production and higher acetate : propionate (A : P) ratio and YATP than with urea. Results herein presented indicate that, under these in vitro conditions, caecal microbial population does in fact use urea N, but less efficiently than casein in terms of microbial growth.

The effect of two feeding systems (indoors and at pasture) on intake and digestion of fresh grass was studied at two stages of regrowth (21 and 35 days of regrowth) in two parallel experiments. In Experiment 1, 10 adult Martinik rams weighing, on average, 50.5 (±0.9) kg, including four fitted with rumen cannula, were randomly allocated to two groups according to a 2 × 2 Latin Square design. These rams consumed a 21-day regrowth of Digitaria decumbens grass diet during two successive 28-day periods, indoors (five rams) or at pasture (five tethered rams). In Experiment 2, 10 other Martinik rams weighing, on average, 45.5 (±0.9) kg, including four fitted with rumen cannula, were randomly allocated to two groups according to a 2 × 2 Latin Square design. These rams consumed a 35-day regrowth of D. decumbens grass diet during two successive 28-day periods, either indoors (five rams) or at pasture (five tethered rams). For the indoors groups, in vivo organic matter digestibility (OMD) was measured by total collection of feces. In addition, OMD was estimated indoors and at pasture using the fecal CP (CPf) method (OMDCPf). Organic matter intake (OMI) was then estimated using OMDCPf and fecal organic matter output (OMICPf). Correlations of 0.49 and 0.77 were found between in vivo OMD and OMDCPf (P < 0.05) and between OMI and OMICPf (P < 0.001), respectively. OMDCPf was 1.8% (P < 0.05) and 2.7% (P < 0.01) lower indoors than at pasture at 21 and 35 days of regrowth, respectively, whereas OMICPf indoors was 1.1 and 1.16 times that registered at pasture at 21 and 35 days of regrowth, respectively. The higher OMDCPf at pasture was linked to the higher selective behavior of rams at pasture, whereas the differences in OMICPf between the two feeding systems were linked to differences in the total bulk density of the grass. These studies show that differences in OMDCPf and OMICPf exist between animals fed indoors and at pasture with the same forage and that these differences may vary according to the stage of regrowth of the grass offered.

This study was conducted to investigate the pattern of plasma carotenoid concentration (PCC) in lambs switching from a low to a high dietary carotenoid level. A total of 12 Romane lambs were individually penned indoors and fed a low dietary carotenoid level for 23 days (period 1) and then a high dietary carotenoid level for 15 days (period 2). At the beginning of period 2, the lambs were 15 weeks old and weighed 29.9 kg (s.d. 2.7) on average. Lambs were fed daily (dry matter) 0.558 kg alfalfa pellets, 0.181 kg straw and 0.181 kg barley. Plasma content of total carotenoids was measured daily in period 2 by spectrophotometry. PCC (μg/l) varied with the animal (P < 0.001) and with time elapsed since the beginning of alfalfa distribution (P < 0.001). Mean PCC was 8 μg/l (s.d. 3.3) at the beginning of period 2, then increased curvilinearly with the time elapsed since the beginning of alfalfa distribution. As early as 24 h on the alfalfa diet, PCC was already higher than before the switch (P < 0.001). Mean PCC continued to increase until day 6 on average and reached a plateau thereafter. We propose a monomolecular function to model this pattern, the equation obtained on the mean data being: PCC = 97 (s.e. 2.2) × (1−exp(−0.3378 (s.e. 0.0282)×d)), where r2 = 0.997, r.s.d. = 4.47, n = 15 and d = day. The percentage of variance explained by the model ranged between 95.9% and 99.2%, depending on the animal. The parameters of the monomolecular function varied among animals, confirming the interindividual variability in animal response. Plateau for PCC was reached slightly earlier for the six lambs with the lowest values of the asymptote than for the six lambs with the highest values of the asymptote.

More robust cattle have the potential to increase farm profitability, improve animal welfare, reduce the contribution of ruminant livestock to greenhouse gas emissions and decrease the risk of food shortages in the face of increased variability in the farm environment. Breeding is a powerful tool for changing the robustness of cattle; however, insufficient recording of breeding goal traits and selection of animals at younger ages tend to favour genetic change in productivity traits relative to robustness traits. This paper has extended a previously proposed theory of artificial evolution to demonstrate, using deterministic simulation, how choice of breeding scheme design can be used as a tool to manipulate the direction of genetic progress, whereas the breeding goal remains focussed on the factors motivating individual farm decision makers. Particular focus was placed on the transition from progeny testing or mass selection to genomic selection breeding strategies. Transition to genomic selection from a breeding strategy where candidates are selected before records from progeny being available was shown to be highly likely to favour genetic progress in robustness traits relative to productivity traits. This was shown even with modest numbers of animals available for training and when heritability for robustness traits was only slightly lower than that for productivity traits. When transitioning from progeny testing to a genomic selection strategy without progeny testing, it was shown that there is a significant risk that robustness traits could become less influential in selection relative to productivity traits. Augmentations of training populations using genotyped cows and support for industry-wide improvements in phenotypic recording of robustness traits were put forward as investment opportunities for stakeholders wishing to facilitate the application of science on robust cattle into improved genetic selection schemes.

Foot disorders are the main cause of dairy cow lameness and are considered to have a major impact on the welfare of dairy cattle. This study adopts a modeling approach, using a dynamic stochastic model, to provide more insight into the welfare impact of different types of foot disorders, both clinical and subclinical. The impact of specific foot disorders on welfare was assessed by simulating the incidence and duration of foot disorders and the pain associated with them. Pain assessment was based on locomotion scores, with underlying knowledge obtained from scientific literature and experts. The results demonstrated the seriousness of the welfare impact of foot disorders. The negative welfare impact was measured on a scale from 0 to 60, where the maximum outcome represents a cow having very severe pain during the whole year. On average, each cow achieves a welfare impact score of 12, which is 20% of the maximum welfare impact score. This welfare score equals having severe pain for a period of 3 months, indicating a serious impact on welfare. On average, digital dermatitis impacts most on welfare, which is caused by a high incidence of the painful clinical stage, followed by sole hemorrhages (SoH) and interdigital dermatitis and heel horn erosion (IDHE). The combination of a high incidence and long duration of SoH and IDHE causes this relatively high welfare impact of foot disorders that occur mostly subclinically. On average, over 1 year, 46% of the welfare impact due to foot disorders is caused by clinical foot disorders. The fact that subclinical foot disorders contribute more or less equally to the effects on welfare as clinical ones, indicates that farmers may readily underestimate the welfare impact by a factor two. Modeling welfare impact at cow level, individual cases of foot disorders, stresses the importance of pain intensity, indicating the importance of clinical foot disorders. This study demonstrated the serious welfare impact of foot disorders in dairy cattle and pointed out the considerable impact of subclinical foot disorders. Furthermore, the approach of welfare assessment, for example herd v. cow level, influenced the ranking of foot disorders for their impact on animal welfare. Potentially, this leads to different prioritization of specific solution strategies for dairy farmers, for example, focusing on cow comfort, hygiene or preventive medical treatments, foot trimming and/or health monitoring. The findings in this study support in raising awareness about this welfare issue.

The life science industries have a strong interest in screening for novel bioactives in complex mixtures like milk and dairy products. Food bioactives are not only important for public health in general, but also have potential therapeutic applications for the treatment of a number of diseases. To identify these novel bioactives, establishment of robust screening assays is essential. The use of in vitro cell-based models for screening and testing have the advantage that several concentrations of mixtures or specific compounds can be assayed at the same time in cells from specific tissues. Primary cell cultures from target organs or established cell lines can be used to identify the most sensitive cells. In addition, a large number of transfected cell lines with very specific sensitivities have been developed. Different endpoints inherent to basal or more sophisticated cellular functions can be investigated, such as cell viability, apoptosis, migration, intracellular signalling, regulation of gene expression, morphology and metabolic alterations. The gastrointestinal tract is an obvious target for bioactive molecules delivered through milk and dairy products, because it lies at the interface between dietary components in the lumen and the internal processes of the host. Identification of bioactive factors that affects proliferation or migration of epithelial cells may have potential applications in promoting gastrointestinal health in both humans and animals. The mammary gland is another target organ of considerable interest since it has been estimated that up to 50% of all newly diagnosed breast cancers may be related to dietary factors. A large number of gastrointestinal and mammary epithelial cell lines are commercially available, but in order to study some cellular functions, primary cultures of freshly isolated cells are often preferred, as established cell lines do not always express specialised properties in culture.

A study was conducted to evaluate the excretion pattern of melamine from feed into eggs, plasma, kidney, liver and muscle of laying hens. In particular, 90 laying hens were randomly allocated to three dietary treatments and fed diets contaminated with melamine at a level of 2.5, 25 and 250 mg of melamine/kg of diet for T1, T2 and T3 groups, respectively. The diets were offered in six replicate boxes (five hens each) for 13 days. Eggs were collected from each group for melamine quantification on days 0, 1, 3, 6, 9 and 13. At the end of the experimental period, one hen per box was randomly selected and slaughtered to collect plasma, liver, kidney and muscle samples. During the experiment, feeding diets with increasing levels of melamine had no effect (P > 0.05) on weight gain, feed intake, egg production, egg weight and mortality of laying hens. The melamine in eggs increased from day 1 after melamine ingestion and reached a plateau between days 6 and 13 of melamine ingestion. At steady-state condition, the melamine egg concentrations increased (P < 0.01) with treatments, being 0.026, 0.352 and 4.631 mg/kg for T1, T2 and T3, respectively. Similarly, the carryover of melamine from feed to egg increased (P < 0.05) with the levels of melamine in the diets, varying from 0.50 to 0.70 and 0.84 for T1, T2 and T3, respectively. The melamine was detected in plasma of all tested groups, increasing (P < 0.01) with levels of melamine in the diets (0.030, 0.266 and 4.102 mg/l in T1, T2 and T3, respectively). Melamine was not detected in kidney, liver and muscle of hens fed T1. Except for kidney sampled in the T3, no melamine concentration higher than 2.5 mg/kg, representing the maximum allowable limit set by the US Food and Drug Administration and European Union for food and feeds, was measured. The melamine resulted higher in plasma and kidneys than in the liver and muscle both in T2 and T3. The results confirmed the presence of an excretion pattern of melamine from feed to eggs and tissues in laying hens.

The dry period is required to facilitate cell turnover in the bovine mammary gland in order to optimize milk yield in the next lactation. Traditionally, an 8-week dry period has been a standard management practice for dairy cows based on retrospective analyses of milk yields following various dry period lengths. However, as milk production per cow has increased, transitioning cows from the nonlactating state to peak milk yield has grown more problematic. This has prompted new studies on dry period requirements for dairy cows. These studies indicate a clear parity effect on dry period requirement. First parity animals require a 60-day dry period, whereas lactations following later parities demonstrate no negative impact with 30-day dry period or even eliminating the dry period when somatotropin (ST) is also used to maintain milk yields. Shortened dry periods in first parity animals were associated with reduced mammary cell turnover during the dry period and early lactation and increased numbers of senescent cells and reduced functionality of lactating alveolar mammary cells postpartum. Use of ST and increased milking frequency postpartum reduced the impact of shortened dry periods. The majority of new intramammary infections occur during the dry period and persist into the following lactation. There is therefore the possibility of altering mastitis incidence by modifying or eliminating the dry period in older parity animals. As the composition of mammary secretions including immunoglobulins may be reduced when the dry period is reduced or eliminated, there is the possibility that the immune status of cows during the peripartum period is influenced by the length of the dry period.

Effects of partial substitution of barley grain and soybean meal with fleabane (FB) Conyza bonariensis on growth performances and body compositions of 24 male local Awassi lambs were studied. All lambs were male with an average BW of 20.3 kg (s.d. = 2.0 kg) at the beginning of the experiment. Animals were randomly divided into four groups of six lambs each. Lambs in each group received individually their cereal–soybean-based total mixed rations with levels of FB: 0, 50, 100 and 150 g/kg dry matter (DM) diet, which replaced similar values of barley and soybean meal. All rations were isonitrogenous and isocaloric. The fattening experiment lasted 9 weeks, after which all lambs were slaughtered. The composition of nutrients in the C. bonariensis were 89.6%, 15.0%, 28.0%, 30.0% and 10% for organic matter, CP, NDF, ADF and lignin, respectively. At the end of the experiment, lambs fed 100 and 150 g FB/kg DM diets gained more weight (P < 0.05) than those fed the control and 50 g FB/kg DM diets. The DM intake was lower in lambs fed the highest level of FB compared with intakes of lambs in other treatments. Diet content of FB had significant effect (P < 0.05) on weights of empty body, carcass, gut and external (hide, head and feet) among all animals. However, FB had no effects on lambs’ thoracic organs (lungs and heart) and liver. Muscle, bone, omental and mesenteric fat, subcutaneous, intermuscular, pelvic and kidney fat weights (g/kg empty BW) were not affected by FB feeding. Carcass fat was decreased (P < 0.05) by the increase of FB. Total body fat was the same in all animals of the experiment.

Because not all animal factors influencing profitability can be included in total merit breeding indices for profitability, the association between animal total merit index and true profitability, taking cognisance of all factors associated with costs and revenues, is generally not known. One method to estimate such associations is at the herd level, associating herd average genetic merit with herd profitability. The objective of this study was to primarily relate herd average genetic merit for a range of traits, including the Irish total merit index, with indicators of performance, including profitability, using correlation and multiple regression analyses. Physical, genetic and financial performance data from 1131 Irish seasonal calving pasture-based dairy farms were available following edits; data on some herds were available for more than 1 year of the 3-year study period (2007 to 2009). Herd average economic breeding index (EBI) was associated with reduced herd average phenotypic milk yield but with greater milk composition, resulting in higher milk prices. Moderate positive correlations (0.26 to 0.61) existed between genetic merit for an individual trait and average herd performance for that trait (e.g. genetic merit for milk yield and average per cow milk yield). Following adjustment for year, stocking rate, herd size and quantity of purchased feed in the multiple regression analysis, average herd EBI was positively and linearly associated with net margin per cow and per litre as well as gross revenue output per cow and per litre. The change in net margin per cow per unit change in the total merit index was €1.94 (s.e. = 0.42), which was not different from the expectation of €2. This study, based on a large data set of commercial herds with accurate information on profitability and genetic merit, confirms that, after accounting for confounding factors, the change in herd profitability per unit change in herd genetic merit for the total merit index is within expectations.