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Comprehensive transcriptome profiling and identification of potential genes responsible for salt tolerance in tall fescue leaves under salinity stress

ABSTRACT: Comprehensive transcriptome profiling and identification of potential genes responsible for salt tolerance in tall fescue leaves under salinity stress

PROVIDER: PRJNA490825 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7829260.fastq.gz	Fastqsanger.gz
	SRR7829261.fastq.gz	Fastqsanger.gz
	SRR7829259.fastq.gz	Fastqsanger.gz

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Comprehensive transcriptome profiling and identification of potential genes responsible for salt tolerance in tall fescue leaves under salinity stress

Project description:illumina RNA sequencing of tall fescue leaves generated a total of raw 144,339 reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to functional databases. Further analysis revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. Totally, 1,862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs 24 h salt treatment. Protein interaction analysis revealed the high interaction of chaperonins and Rubisco proteins in 48h vs 24h salt treatment

2018-09-15 | GSE119957 | GEO

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Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress.

Project description:Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

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Hepatic Gene Expression Profiles of Growing Beef Steers Grazing High vs. Low Endophyte-Infected Tall Fescue Grass

Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on the clinical symptoms and laboratory analyses of blood, it was hypothesized that such affected cattle display liver-specific changes in the expression of gene transcripts that are associated with the metabolic enzymes and transporters critical for beef health and performance. Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects the liver gene expression profiles of growing beef steers. Nineteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 9) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 10) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water and an industry standard mineral-vitamin supplement. 88 days grazing on pasture. Approximately 2 g of tissue from the right lobe of the liver of each steer were collected for RNA extraction and microarray analysis.

2010-11-30 | E-GEOD-23894 | biostudies-arrayexpress

Pituitary Gene Expression Profiles of Growing Beef Steers Grazing High versus Low Endophyte-Infected Tall Fescue Grass

Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on clinical and biochemical blood analyte profiles, hepatic targeted gene and protein analyses, and hepatic transcriptomic profiling, microarray analysis using the WT Btau 4.0 Array (version 1.0, Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects pituitary gene expression profiles of growing beef steers. The specific overall hypothesis tested was that grazing high endophyte-infected pasture would alter the pituitary genomic expression profiles of the same growing steers, especially genes involved in production and secretion of prolactin, growth hormone, thyroid stimulating hormone, and adrenocorticotropic hormone. Sixteen steers were assigned to graze either a low toxic endophyte tall fescue-mixed grass (LE treatment, 5.7 ha, n = 8) or a high toxic endophyte infected tall fescue (HE treatment, 5.7 ha, n = 8) pasture located in the University of Kentucky Agricultural Research Center. All steers had ad libitum access to fresh water, an industry standard mineral-vitamin supplement, and grazed respective pastures for 89 to 105 days. Whole pituitaries were collected for RNA extraction and microarray analysis.

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Hepatic Gene Expression Profiles of Growing Beef Steers Grazing High vs. Low Endophyte-Infected Tall Fescue Grass

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Pituitary Gene Expression Profiles of Growing Beef Steers Grazing High versus Low Endophyte-Infected Tall Fescue Grass

2014-10-23 | GSE62570 | GEO

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Influence of form of Se supplementation and tall fescue endophyte toxicity on the kidney transcriptome of grazing beef steers

Project description:To test the hypothesis that average daily gain (ADG) and clinical parameters of steers grazing novel non-toxic (NTE) or toxic KY-31 (TE) endophyte-infected tall fescue would be improved by ad libitum intake of vitamin-mineral mixes (V-M) that contain 27 ppm Se as a 1:1 blend of SELPLEX:sodium selenite (MIX) vs. sodium selenite (ISe), 32 fescue-naïve beef steers depleted of Se were randomly assigned to ad libitum consumption ISe vs MIX for 35 d and fed enough of a NTE/alfalfa/grain diet to achieve 0.57 kg BW gain/d. Within Se-form treatments, 2 steers were randomly assigned to each of 4 NTE (ISe = 316 ± 31 kg, MIX = 315 ± 22 kg) or TE (ISe = 316 ± 37 kg, MIX = 314 ± 39 kg) paddocks for 84 d and had ad libitum access to their respective V-M. Steers were slaughtered over a 23-d period from day 90 to day 113 (August 27, 2019 to September 19, 2019) of the study and the left kidney removed.

2022-03-17 | GSE198584 | GEO

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