FBLN1 and FABP4 are drivers of resistance to fleece rot in Australian Merino sheep
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ABSTRACT:
ORGANISM(S): Bos taurus Ovis aries
PROVIDER: GSE21022 | GEO | 2010/03/25
SECONDARY ACCESSION(S): PRJNA125771
REPOSITORIES: GEO
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Project description:Transcriptional profiling of Ovine skin samples comparing resistant (RES) to susceptible (SUS) animals following fleece rot induction. Two condition experiment, RES vs SUS biopsies, over 3 time points. 31 RES 31 SUS T0: Prior to commencment of treatment T1: 2-3 days post commencment T2: 11 days post commencment The first skin biopsies were taken on the first day (T0) prior to commencement of the five day regime of simulated rainfall. Subsequent skin biopsies were taken 2-3 days into the wetting regime (T1) and following a recovery period of 11 days from the time that the wetting regime had begun (T2).
2010-06-05 | E-GEOD-21022 | biostudies-arrayexpress
Project description:BACKGROUND: Fleece rot (FR) and body-strike of Merino sheep by the sheep blowfly Lucilia cuprina are major problems for the Australian wool industry, causing significant losses as a result of increased management costs coupled with reduced wool productivity and quality. In addition to direct effects on fleece quality, fleece rot is a major predisposing factor to blowfly strike on the body of sheep. In order to investigate the genetic drivers of resistance to fleece rot, we constructed a combined ovine-bovine cDNA microarray of almost 12,000 probes including 6,125 skin expressed sequence tags and 5,760 anonymous clones obtained from skin subtracted libraries derived from fleece rot resistant and susceptible animals. This microarray platform was used to profile the gene expression changes between skin samples of six resistant and six susceptible animals taken immediately before, during and after FR induction. Mixed-model equations were employed to normalize the data and 155 genes were found to be differentially expressed (DE). Ten DE genes were selected for validation using real-time PCR on independent skin samples. The genomic regions of a further 5 DE genes were surveyed to identify single nucleotide polymorphisms (SNP) that were genotyped across three populations for their associations with fleece rot resistance. RESULTS: The majority of the DE genes originated from the fleece rot subtracted libraries and over-representing gene ontology terms included defense response to bacterium and epidermis development, indicating a role of these processes in modulating the sheep's response to fleece rot. We focused on genes that contribute to the physical barrier function of skin, including keratins, collagens, fibulin and lipid proteins, to identify SNPs that were associated to fleece rot scores. CONCLUSIONS: We identified FBLN1 (fibulin) and FABP4 (fatty acid binding protein 4) as key factors in sheep's resistance to fleece rot. Validation of these markers in other populations could lead to vital tests for marker assisted selection that will ultimately increase the natural fleece rot resistance of Merino sheep.
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Project description:Transcriptional profiling of Ovine skin samples comparing pigmentation samples from piebald and normal Merino sheep
2010-09-18 | GSE24189 | GEO
Project description:Hormonal assessment tools are important for determining the reproductive success of production animals. This study used non-invasive wool assessment to quantify changes in progesterone and cortisol levels in reproducing female merino sheep. Wool samples were collected from a group of n = 46 maiden merino ewes (22-25 months old), naturally joined under natural light conditions in southern New South Wales (NSW), Australia. Three shearing opportunities were conducted as part of standard on-farm management practices. The wool samples were collected at three different dates during 2017, January (prior to rams being put out with the mob and to provide a baseline level since previous shearing in May 2016), September (during very late stages of gestation-approximately 2 weeks prior to parturition) and December (ewes had given birth and ~2-month-old lambs were at foot). Analysis of cortisol and progesterone was conducted concurrently from the same sample of wool. The hormones in wool samples quantified using commercially available cortisol and progesterone enzyme-immunoassay kits. Wool cortisol concentrations increased significantly (p = 3.04E-14) from pre-joining in January (1.33±0.12 ng/g) to late gestation in September (3.59±0.12 ng/g). Concentration of wool cortisol post-lambing in December (3.27±0.14 ng/g) did not decline significantly (p = 0.124) after gestation however remained significantly higher (p = 3.82E-10) than pre-joining levels. Wool progesterone (PG) concentrations increased significantly (p = 1.83E-33) from pre-joining (0.04±0.005 ng/g) in January to late gestation in September (5.53±0.13 ng/g) with a significant (p = 5.44E-59) decline observed in December (0.05±0.003 ng/g) to post- pregnancy concentrations. No significant difference was shown between pre-joining and post lambing PG concentrations (p = 0.057). Our results showed that non-invasive assessment of hormones in Merino sheep wool reflected significant increase in both cortisol and progesterone guided by pregnancy.
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Project description:Transcriptional profiling of Ovine skin samples comparing pigmentation samples from piebald and normal Merino sheep All pair comparison of 5 pigmentation samples with dye swaps. Dye swaps were performed with different biological replicates (labelled 1 or 2) NOR - White sample from a normal, non-affected wild-type individual sheep PBB - Black sample from a piebald individual sheep PBW - White sample from a piebald individual sheep RSB - Black sample from a recessive black sheep RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area.
2010-09-18 | E-GEOD-24189 | biostudies-arrayexpress
Project description:BackgroundMerino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of a global collection of domestic sheep breeds, we analyzed genotype data that were obtained with the OvineSNP50 BeadChip (Illumina) for 671 individuals from 37 populations, including a subset of breeds from the Sheep HapMap dataset.ResultsBased on a multi-dimensional scaling analysis, we highlighted four main clusters in this dataset, which corresponded to wild sheep, mouflon, primitive North European breeds and modern sheep (including Merino), respectively. The neighbor-network analysis further differentiated North-European and Mediterranean domestic breeds, with subclusters of Merino and Merino-derived breeds, other Spanish breeds and other Italian breeds. Model-based clustering, migration analysis and haplotype sharing indicated that genetic exchange occurred between archaic populations and also that a more recent Merino-mediated gene flow to several Merino-derived populations around the world took place. The close relationship between Spanish Merino and other Spanish breeds was consistent with an Iberian origin for the Merino breed, with possible earlier contributions from other Mediterranean stocks. The Merino populations from Australia, New Zealand and China were clearly separated from their European ancestors. We observed a genetic substructuring in the Spanish Merino population, which reflects recent herd management practices.ConclusionsOur data suggest that intensive gene flow, founder effects and geographic isolation are the main factors that determined the genetic makeup of current Merino and Merino-derived breeds. To explain how the current Merino and Merino-derived breeds were obtained, we propose a scenario that includes several consecutive migrations of sheep populations that may serve as working hypotheses for subsequent studies.
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Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma. The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.
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Project description:Ovine mastitis is defined as the inflammation of the sheep udder, most commonly caused in response to intramammary infections. Based on the occurrence of clinical signs, mastitis is characterized as either clinical or subclinical (SCM). The impact of ovine SCM on the overall sustainability of dairy sheep farms has been documented underpinning the significance of efficient diagnosis. Although SCM can be detected in cows, the performance and the validity of the methods used do not transfer in dairy sheep. This fact challenges the development of evidence-based ovine udder health management protocols and renders the detection and control of ovine mastitis rather problematic. Currently, cell culture-based models are being successfully used in biomedical studies and have also been effectively used in the case of bovine mastitis. The objective of the present study was to culture ovine primary mammary cells for the development of 2D and 3D cell culture-based models for the study of ovine SCM. Cells were infected by mastitis-inducing pathogens mimicking the pathogenesis of SCM as derived by natural intramammary infections. The secreted proteins were subjected to mass-spectrometry resulting in the identification of 79 distinct proteins. Among those, several had already been identified in healthy or mastitic milk, while others were detected for the first time in the ovine mammary secretome. The development of cell-based models for the early detection and the overall study of SCM has the potential to be applicable and beneficial for the udder health management in dairy sheep.
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Project description:Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on the infection process of dicots by sedentary nematodes, far less is known about the interaction between monocot plants and nematodes or plant interactions with migratory nematode species. Therefore, to gain deeper insight into the systemic transcriptional changes in rice after migratory root rot nematode infection we have performed mRNA-Seq on the shoots of root rot nematode infected rice plants. The observations were independently validated using qRT-PCR and biochemical analyses. This research reveals significant modifications in the metabolism of the plant, with a general suppression of chlorophyll biosynthesis, and primary metabolic processes involved in plant growth . Differential expression analysis between controls rice shoots and shoots from root rot nematode (H. oryzae) infected rice at two time points.
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Project description:An individual merino sheep's output of wool production is influenced by synergistic interactions of sheep genetics, climate, farm management, and nutrition available to the whole flock. The price paid to the producer for this wool commodity is determined via numerous tested parameters and /or subjective appraisal of the raw greasy wool. This research investigated the level of variation in wool cortisol (a physiological stress biomarker) and wool micron (MIC) in Merino ewes (Ovis aries), pre-partum and post-lambing (lactation/lambs at foot), using maiden ewe (n = 38) managed in an outdoor paddock in a commercial farm. The key findings of this study are; (1) wool quality indicators showed a significant variation between pre- and post- parturition including significant reduction in MIC and (2) there was a negative correlation between wool cortisol levels and wool micron pre-parturition (rs = - 0.179, p < 0.05). This relationship between wool cortisol and wool micron was positive (rs = + 0.29, p < 0.05) during post-parturition suggesting that ewes with lambs at foot ended up with finer wool (reduction in fibre diameter) but they also maintained high levels of wool cortisol. Furthermore, the comfort factor, curvature, standard deviation and spin fineness of the wool were also significantly reduced post-parturition. The results of this study show that metabolic resources partitioning in ewe associated with pregnancy and lambing can result in a reduction in wool quality indices. The activity of the HPA-axis is attenuated during late gestation and parturition as a maternal adaptation; however, the results of our study show that wool cortisol remained similar between pre- and post- lambing. This result indicates that environmental stressors that may have been operating on farm (e.g., cold winter period) could influence on maternal physiological stress response however the exact level of influence of environment conditions on ewe stress levels and productivity traits (e.g., lambing success and wool quality) warrants further investigation. In conclusion, the use of top-knot wool sampling in combination with wool cortisol analysis provides researchers with a convenient method to quantify wool quality and physiological stress simultaneously under commercial sheep production.
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