Forschungsdaten

Dauerhafte URI für die Sammlung

jlupub.ub.uni-giessen.de/handle/jlupub/2

Stöbern nach

Gerade angezeigt 1 - 14 von 14

Data for "Direct genetic effects, maternal genetic effects and maternal genetic sensitivity on prenatal heat stress for calf diseases and corresponding genomic loci in German Holsteins"
(2022-04-20) Yin, Tong
The aim of this study was to infer the effects of heat stress (HS) during late gestation of dams on direct and maternal genetic parameters for pneumonia (PNEU, 112,563 observations), diarrhea (DIAR, 176,904 observations) and omphalitis (OMPH, 176,872 observations) in Holstein calves kept in large-scale co-operator herds. The genotype dataset included 41,135 SNPs from 19,247 male and female cattle. Temperature-humidity indices (THI) during the last eight weeks of pregnancy were calculated, using the climate data from the nearest public weather station for each herd. Heat load effects were considered for average weekly THI larger than 60, and THI lower than 60 were treated equally. Phenotypically, regression coefficients of calf diseases on prenatal THI during the last eight weeks of gestation were estimated in eight consecutive runs. Strongest detrimental effects on PNEU and DIAR due to prenatal HS were identified for the last week of pregnancy (WK1). Thus, only WK1 was considered in ongoing genetic analyses. In an advanced model considering prenatal HS, random regression coefficients on THI in WK1 nested within maternal genetic effects (maternal slope effects for heat load) were considered to infer maternal sensitivity in response to prenatal THI alterations. Direct heritabilities from the advanced model ranged from 0.10 (THI 60) to 0.08 (THI 74) for PNEU, and were close to 0.16 for DIAR. Maternal heritabilities for PNEU increased from 0.03 to 0.10 along the THI gradient. For DIAR, the maternal heritability was largest (0.07) at the minimum THI (THI = 60), and decreased to 0.05 at THI 74. Genetic correlations smaller than 0.80 for PNEU and DIAR recorded at THI 60 with corresponding diseases at THI 74 indicate genotype by climate interactions for maternal genetic effects. Genome-wide associations studies (GWAS) were performed using de-regressed proofs of genotyped sires for direct genetic, maternal genetic and maternal slope effects. 30 suggestive and 2 significant SNPs were identified from GWAS. 43 genes located close to the suggestive SNPs (±100 kb) were annotated as potential candidate genes. Three biological processes were inferred on the basis of the identified potential candidate genes, addressing the negative regulation of the viral life cycle, innate immune response and protein ubiquitination. Hence, genetics of prenatal heat stress mechanisms are associated with immune physiology and disease resistance mechanisms.
Data for "Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle"
(2021-10-29) Abbasi Moshaii, Bita; Hossein Moradi, Mohammad; Rahimi-Mianji, Ghodratollah; Ardeshir, Nejati-Javaremi; König, Sven
The data include the materials for the research article "Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis". The aim of this study was to identify the genomic regions associated with mastitis, using the genotypes from the national project of Holstein dairy cattle in Germany. The samples were genotyped with Bovine 50K SNP chip. Based on random residual effects of the mastitis diagnoses, 133 healthy and sick samples from 13290 genotyped dairy cows were selected, respectively. Selection signatures between cows in healthy and sick groups were detected using XP-EHH statistic. Detailed analyses and methods can be found in the article. The data used in this study are presented in the following three files: PhenoMast.txt: Mastitis records of the 13276 genotyped cows. First row includes column names, i.e., cow ID, herd, year-season, mastitis diagnoses. GenoHealth.txt: Genotypes of the 133 healthy cows. First column is cow ID and following 45613 columns are genotypes of the 133 cows (one SNP marker per column). GenoSick.txt: Genotypes from the 133 sick cows. First column is cow ID and following 45613 columns are genotypes of the 133 cows (one SNP marker per column).
Data for "Patterns of enzyme activities and nutrient availability within biocrusts under increasing aridity in Negev desert"
(2022-01-31) Drahorad, Sylvie; Heinze, Stefanie
This dataset contains the raw data of the open access article "Patterns of enzyme activities and nutrient availability within biocrusts under increasing aridity in Negev desert". All raw data is listed in two excel sheets. Excel sheet one contains the soil related data provided by the first author at the Justus-Liebig-University Gießen, excel sheet two contains the enzyme data provided by the last author at the Ruhr-Universität Bochum. The soil data presents 5 replicates of biocrust samples at two study sites (S1-S5 and N1-N5). Three samples of each site were choosen for enzyme measurements, each provided as four pseudoreplicates. The methods of data production can be found in the original open access published article "Patterns of enzyme activities and nutrient availability within biocrusts under increasing aridity in Negev desert".
Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle
(2021-09) Yin, Tong
lact_yield_1lact_275.dat: the file contains lactation production traits (first row shows the column names) cowproduction_geno_blupf90.dat: the file contains test-day production traits and somatic cell score (first row shows the column names) KUHL_genotypen1612.txt_clean: genotypes Kuhl_blupf90.map_clean: map file of the SNP
Raw Genotype Data for "Unravelling Admixture, Inbreeding and Recent Selection Signatures in West-African Indigenous Cattle Populations in Benin"
(2021-07-13) Vanvanhossou, Sèyi Fridaïus Ulrich
The data presented here are genotype data generated and exploited for different analyses in our study entitled "Unravelling Admixture, Inbreeding and Recent Selection Signatures in West-African Indigenous Cattle Populations in Benin" The folders are organized from 1. to 4. following the order in which the data were generated (from our own data to the extended datasets). In each folder, a README file provides an extensive description of the dataset, the number of variants and animals, the breeds, the statistical analyses and further references.
Raw Microsatellite Genotyping Data for "Spatial and temporal genetic variation of Drosophila suzukii in Germany"
(2021-03-12) Petermann, Sarah
The data presented here is raw data generated for different analyses in our study titled "Spatial and temporal genetic variation of Drosophila suzukii in Germany", published in the Journal of Pest Science in March 2021 (https://doi.org/10.1007/s10340-021-01356-5). The data is further used in a doctoral thesis, which is still in progress (effective September 2021). The zip file contains three Excel files. The first one is named “001_Fragment_Length_Analysis_raw_data” and it was generated by using the microsatellite external plugin of Geneious Prime 2019.2. Microsatellite genotyping data were exported for further analysis in GenAlex software v.6.41 (Peakall and Smouse, 2012), implemented in Excel. The second file is named “002_Null_allele_detection” and contains the data generated with FreeNA (Chapuis and Estoup, 2007). The third file is named “003_Bottleneck_result” and contains the results obtained with Bottleneck v.1.2.2 (Piry et al., 1999).
RNA uptake in fungi
(2021-02-09) Kogel, Karl-Heinz
Power point file showing the uptake of double-stranded RNA by various fungi from liquid cultures.
Supplemental Data for "Genetic evaluations and genome-wide association studies for specific digital dermatitis diagnoses in dairy cows considering genotype x housing system interactions"
(2023-12-13) Sölzer, Niklas; Yin, Tong
The present study aimed to use detailed phenotyping for the claw disorder digital dermatitis (DD) considering specific DD stages in two housing systems (conventional cubicle barns = CON and compost bedded pack barns = CBPB) to infer possible genotype x housing system interactions. The DD-stages included 2,980 observations for the three traits DD-sick, DD-acute and DD-chronic from 1,311 Holstein-Friesian and 399 Fleckvieh-Simmental cows. Selection of the 5 CBPB and 5 CON herds was based on a specific protocol to achieve a high level of herd similarity with regard to climate, feeding, milking system and location, but with pronounced housing system differences. Five other farms had “a mixed system” with two sub-herds, one representing CBPB and the other one CON. 899 cows (1530 observations) represented the CBPB system, and 811 cows (1450 observations) the CON system. The average disease prevalence was 20.47 % for DD-sick, 13.88 % for DD-acute and 5.34 % for DD-chronic, with a higher prevalence in CON than in CBPB. After quality control of 50K genotypes, 38,495 SNPs from 926 cows remained for the ongoing genomic analyses.
Supplemental Figure for "Genotype by heat stress interactions for production and functional traits in dairy cows from an across-generation perspective"
(2021) Kipp, Cordula
The dataset includes supplementary figure S1 for the manuscript accepted for publication in the Journal of Dairy Science.
Supplemental Figures for "Genome-wide associations for heat stress response infer potential candidate genes underlying milk fatty acid composition in dairy cattle"
(2022-01-14) Bohlouli, Mehdi; Halli, Kathrin; Yin, Tong; König, Sven
The data are supplementary materials for the research article "Genome-wide associations for heat stress response infer potential candidate genes underlying milk fatty acid composition in dairy cattle" The objective of this study was to define FA heat stress indicators, considering FA breeding values in response to temperature-humidity index (THI) alterations. Genome-wide association studies (GWAS) were conducted to annotate potential candidate genes for FA traits under different climate conditions. The phenotypic dataset consisted of 39,600 test-day milk FA records from 5,757 first-lactation Holstein dairy cows. The FA traits were C18:0, poly-unsaturated fatty acids (PUFA), saturated fatty acids (SFA) and unsaturated fatty acids (UFA). Meteorological data from the weather station in closest herd distance were used for the calculation of maximum hourly daily THI. The Supplementary Materials include two Figures: Figure S1. Manhattan plot of -log10 P-values of the tested SNP markers for C18:0 (A), poly-unsaturated fatty acids (B), saturated fatty acids (C) and unsaturated fatty acids (D) in different lactation stages under thermoneutral conditions (TNC), under heat stress conditions (HSC) and for heat stress response (HSR). The red dashed line is the significance threshold for the Bonferroni correction. Genomic estimated breeding values were used as pseudo-phenotypes. Figure S2. Supplemental Figure S2. Venn diagrams for the number of significant SNP markers and genes associated with heat stress response overlapping across FA traits (A), associated with heat stress response for FA traits overlapping across lactation stages (B) and associated with FA traits overlapping across environmental conditions (C). Genomic estimated breeding values were used as pseudo-phenotypes. FA traits are C18:0, poly-unsaturated fatty acids (PUFA), saturated fatty acids (SFA) and unsaturated fatty acids (UFA). Lactation stages are the first (S1), the second (S2) and the third (S3) stages. Environmental conditions are thermoneutral conditions (TNC), heat stress conditions (HSC) and heat stress response (HSR).
Supplemental Material for "Effects of temperature-humidity index on blood metabolites of German dairy cows and their female calves"
(2023) Halli, Kathrin
The data tables are supplemental material for the research article "Effects of temperature-humidity index on blood metabolites of German dairy cows and their female calves". The aims of the present study were (a) to compare differences in blood plasma metabolite concentrations of German Holstein dairy cows either suffering from high mean THI (mTHI) on the day before blood sampling during late gestation or not suffering from high mTHI, and (b) to compare differences between blood plasma metabolite concentrations of their female calves either suffering from high mTHI on the day before blood sampling during the first week of life or not suffering from high mTHI. The supplementary data include 3 tables: Supplemental table S1: List of Metabolites: MxP® Quant 500 Kit (Biocrates Life Sciences AG, Innsbruck, Austria), Version: 2_02/2019 Supplemental table S2: Effects of fixed effects in the models 1a-c on metabolites of cows. The table includes log transformed Least-squares means (LSMeans) with corresponding SE, number of observations (n) and P-value. Supplemental table S3: Effects of fixed effects in models 2a-d on metabolites of calves. The table includes log transformed Least-squares means (LSMeans) with corresponding SE, number of observations (n) and P-value.
Supplemental Material for "First DNA sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants"
(2021-10) Vanvanhossou, Sèyi Fridaïus Ulrich; Giambra, Isabella Jasmin; Yin, Tong; Brügemann, Kerstin; Dossa, Luc Hippolyte; König, Sven
The data are supplementary materials for the research article "First DNA sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants". The aim of the study was to investigate polymorphisms in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB, and casein haplotypes in Beninese indigenous cattle. For this purpose, the exon sequences, flanking intron sequences and parts of the 5’-upstream regions of milk protein genes were sequenced in 67 Beninese indigenous cattle. Further details in the methodology and the main findings are provided in the article. The supplementary data include five tables: Table S1. Primer sequences utilized for the sequencing of the six milk protein genes (CSN1S1, CSN2, CSN1S2, CSN3, LALBA, LGB) in the Beninese indigenous cattle breeds; Table S2. List of the bovine miRNA and their corresponding seed sequences retrieved from the TargetScan website and used in “targetscan_60.pl” tool for the detection of miRNA target sites; Table S3. List of the polymorphisms detected within the exon sequences, flanking intron sequences and parts of the 5’-upstream regions of milk protein genes (CSN1S1, CSN2, CSN1S2, CSN3, LALBA, LGB) in Beninese indigenous cattle breeds; Table S4. Distributions of variant types (according to their positions and consequence) de-tected within each of the six milk protein genes (CSN1S1, CSN2, CSN1S2, CSN3, LALBA, LGB) and total in Beninese indigenous cattle breeds; Table S5. Functional consequence of the frameshift insertion of nucleotide A at BTA11:103257980 on the translational reading frame and on mature protein.
Supplemental Material for "Single-step GBLUP genetic parameter estimations and genome-wide associations for milk fatty acid profiles, interval from calving to first insemination and ketosis in Holstein cattle"
(2021) Klein, Sarah-Luisa
The dataset includes supplementary table S1 and figures S1-S2 for the manuscript "Single-step GBLUP genetic parameter estimations and genome-wide associations for milk fatty acid profiles, interval from calving to first insemination and ketosis in Holstein cattle" accepted for publication in the Journal of Dairy Science.
Supplemental Material for "Wealth for Health? Affordability of a Healthy and Sustainable Diet - A Food Basket Study"
(2024-03) Arendt, Svenja
This dataset contains Supplemental Material 4 for the publication "Wealth for Health? Affordability of a Healthy and Sustainable Diet – A Food Basket Study" The file provides: - Assessed prices for conventional and organic food products in REWE with product name, price and quantity - Assessed prices for conventional and organic food products in ALDI Süd with product name, price and quantity - Amounts in g/day for the heavy meat consumption diet - Quantities per day and month for the girl in the reference family - Quantities per day and month for the boy in the reference family - Quantities per day and month for the mother in the reference family - Quantities per day and month for the father in the reference family - Amounts in g/day for the moderate meat consumption diet - Quantities per day and month for the girl in the reference family - Quantities per day and month for the boy in the reference family - Quantities per day and month for the mother in the reference family - Quantities per day and month for the father in the reference family - Amounts in g/day for the light meat consumption diet - Quantities per day and month for the girl in the reference family - Quantities per day and month for the boy in the reference family - Quantities per day and month for the mother in the reference family - Quantities per day and month for the father in the reference family - Calculation of total cost and affordabiliy - Calculation of cost shares - Calculation of the share of vegetables and fruits according to the BMEL - Creation of graphs - References

Stöbern nach

Auflistung Forschungsdaten nach Auflistung nach Fachbereich/Einrichtung "FB 09 - Agrarwissenschaften, Ökotrophologie und Umweltmanagement"

Treffer pro Seite

Sortieroptionen