Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. Ruminal wall samples from two randomly chosen animals per group were obtained, totaling four samples. The animals were born, raised and maintained at the Wye Angus farm. This herd, which has been closed for almost 75 years and yielded genetically similar progenies, constitutes an excellent resource to perform transcriptomic analysis. The genetic resemblance among individuals permits us to better control the cause of variation between experimental clusters and individuals. The randomly chosen pairs of animals were part of larger sets of steers that received a particular treatment. All animals received the same diet until weaning. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain. Then, the calves were randomly assigned to one diet and exclusively received that regimen until termination. Grain–fed animals reached the market weight around the age of 14 month-old, however, grass-fed steers required approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD) a small piece of ruminal wall was excised, cleaned and preserved at -80°C for posterior processing.

Project description:Sporobolus stapfianus is a desiccation tolerant (DT) grass and a member of the Poaceae family alongside prominent crop and forage species. Despite the worldwide distribution of this family, most of its species are vulnerable to water loss within their vegetative tissues. As a DT species, S. stapfianus, could, therefore, serve as a model species for identifying the molecular changes that enabled such a rare occurrence of the DT phenotype in resurrection grasses and the implications of such a unique adaptation for agriculture. A comprehensive gene expression profiling was performed in plants subjected to a dehydration/rehydration cycle using NimbleGen microarrays hybridization method. Our results showed that most transcripts were high in the hydrated state of S. stapfianus leaf tissues and that minor dehydration (> 60% relative water content; RWC) did not induce most transcripts, but did repress photosynthetic activity, which show the importance of curtailing the production of toxic elements to the DT phenotype. It took a loss of 40% RWC for induction of most transcripts. This shows that this species is pre-equipped to deal with mild dehydration, but requires stress-induced activation mechanisms to prepare for desiccation. In agreement with our transcriptomic data, a global metabolic analysis conducted in this species has shown that most metabolites accumulate to their highest levels below 45% RWC, which suggests the importance of those late stages of dehydration in preparing resurrection grasses for desiccation and for early stages of rehydration. In most cases, a 12-h rehydration was sufficient to reinstate pre-stress expression levels, which shows that only partial damage occurred during drying. Unlike during dehydration, our metabolomic data profiled after rehydration showed that there is no clear correlation between gene expression and metabolic abundance, which suggests that most of the compounds that are produced during rehydration are quickly utilized in active metabolism of restoration. The findings of the paper show that S. stapfianus is primed to respond to mild dehydration, although severe dehydration require inducible response, with 40-30% RWC being the peak of gene expression. As for photosynthesis, this species cease its photosynthetic activity even at high water levels (85% RWC) alleviating the need to activate antioxidants activity during mild dehydration.

Dataset Information

Transcriptomic study of couch grass rhizomes exposed to dehydration

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