This codebook.txt file was generated on 2021/06/01 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Phenotypic and genotypic data of barley Gen10 population to study a pericentromeric region on chromosome 6H 2. Author Information Principal Investigator Contact Information Name: Lu Yin Institution: University of Minnesota Email: yinxx134@umn.edu Associate or Co-investigator Contact Information Name: Kevin Smith Institution: University of Minnesota Email: smith376@umn.edu Associate or Co-investigator Contact Information Name: Yadong Huang Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Ahmad Sallam Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Shane Heinen Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Karen Beaubien Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Ruth Dill-Macky Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Yanhong Dong Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Brian Steffenson Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Gary Muehlbauer Institution: University of Minnesota 3. Date of data collection: 2015-04-15 to 2018-12-20 4. Geographic location of data collection (where was data collected?): 5. Information about funding sources that supported the collection of the data: Sponsorship: University of Minnesota Small Grains Initiative; USDA-National Institute of Food and Agriculture Triticeae CAP -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: "Genetic dissection of a pericentromeric region of barley chromosome 6H associated with Fusarium head blight resistance, grain protein content, and agronomic traits" submitted to the Theoretical and Applied Genetics Journal 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s): 6. Recommended citation for the data: Yin, Lu; Huang, Yadong; Sallam, Ahmad; Heinen, Shane; Li, Lin; Beaubien, Karen; Dill-Macky, Ruth; Dong, Yanhong; Steffenson, Brian; Smith, Kevin; Muehlbauer, Gary. (2021). Phenotypic and genotypic data of barley Gen10 population to study a pericentromeric region on chromosome 6H. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/hwkm-ev34. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Gen10_50Kgenotype101linesAll6H.xlsx Short description: Genotypic data (Illumina 50K SNP chip) of 101 Gen10 recombinant near-isogenic barley lines across chromosome 6H B. Filename: Gen10PhenotypeDataByTrial.xlsx Short description: Phenotypic data of 79 Gen10 recombinant near-isogenic barley lines oragnized by trials 2. Relationship between files: -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: This Gen10 population is a population of Chevron-derived (a landrace from Switzerland) backcrossed to the elite malting barley Lacey multiple generations consisting of recombinant near-isogenic lines (selected from a population of 1941 near-isogenic lines). The idea was to break the unfavorable linkage between the resistance locus of Fusarium head blight (FHB) or kernel discoloration (KD) and grain protein content (GPC) among other other agronomic traits on chromosome 6H to breed for a desirable variety. 79 of the Gen10 lines have been phenotyped in the field of St. Paul, MN and Crookston, MN in 2015 and 2016 for different traits in the yield trial, FHB trial, and the greenhouse. Traits phenotyped in yield trial: Heading date (HD), height (HT), lodging (Ldg), days to senescence (SEN), normalized difference vegetation index (NDVI), percent stem breakage (StemBrk), GPC, and yield. Traits phenotyped in FHB trial: FHB, KD, deoxynivalenol (DON) accumulation. Traits phenotyped in the greenhouse: net blotch (NB). For details, please see below and/or the above listed publication which has been submitted to Theoretical and Applied Genetics. 2. Methods for processing the data: The submitted phenotypic data were mostly raw data with some unit conversions. The submitted genotypic data were were generated from 50K SNP chip (Bayer et al. 2017) in fall 2018 from five plants per line grown in the greenhouse with SNPs were called by GenomeStudio where at each SNP, the Lacey genotype was assigned “BB” and the alternative genotype “AA” 3. Instrument- or software-specific information needed to interpret the data: Phenotypic data need to be analyzed using analysis of variance (ANOVA) and the average across trials to be calculated by best linear unbiased prediction (BLUP). Excel to view the graphical genotypes and impute the parental genotypes from that of summer 2018. Alternatively, a quantitative trait locus (QTL) mapping approach can be used to interpret the data: using the MSTmap (http://mstmap.org) (Wu et al. 2008) or equivalent to construct a linkage map and Windows QTL Cartographer V2.5 using the composite interval mapping algorithm (Wang et al. 2012; Zeng 1994) is needed to conduct QTL mapping. 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: Field for yield and FHB trials (St. Paul and Crookston, MN), greenhouse for net blotch trial (at 15-20°C and 18 h photoperiod and inoculumn sprayed onto plants until run-off). 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: RD and BS supervised FHB field trials. YD analyzed mycotoxin data. LL and KB aided with genotyping of populations. SH helped with development of the Gen10/Lacey population. YH, LY, and AS performed greenhouse and field trials, and analyzed genotypic and phenotypic data. YH submitted the data related to Gen10/Lacey populations and LY submitted the data here (related to Gen10). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Gen10PhenotypeDataByTrial.xlsx ----------------------------------------- Excel workbook that contains 10 sheets: - Yld_CR15 | 23 variables | 168 rows - Yld_CR16 | 23 variables | 168 rows - Yld_StP15 | 20 variables | 168 rows - Yld_StP16 | 22 variables | 168 rows - FHB_CR15 | 19 variables | 247 rows - FHB_CR16 | 18 variables | 168 rows - FHB_StP15 | 21 variables | 247 rows - FHB_StP16 | 19 variables | 168 rows - NB_FGH15 | 16 variables | 247 rows - NB_WGH15 | 17 variables | 247 rows 1. Missing data codes: Code/symbol NA Definition: not available Code/symbol Definition 2. Variable List (across all sheets) Example. Name: Gender Description: Gender of respondent 1 = Male 2 = Female 3 = Other A. Name: trial_name Description: Trial name B. Name: location Description: Location of trial C. Name: year Description: Year of trial D. Name: design_type Description: Random complete block design (RCBD) Value labels if appropriate E. Name: plot_width (m) Description: Width of plot F. Name: plot_length (m) Description: Length of plot G. Name: plot_area (m2) Description: Area of plot H. Name: field_size Description: Value labels if appropriate I. Name: planting_date Description: Planting date J. Name: harvest_date Description: Harvest date K. Name: accession_name Description: Value labels if appropriate L. Name: plot_number Description: Plot number M. Name: rep_number Description: Replication number Value labels if appropriate N. Name: row_number Description: Row number O. Name: col_number Description: Column number P. Name: NDVI Description: Normalized difference vegetation index Q. Name: Senescence date Description: the number of days after planting when 90% or more of the peduncles had lost their green color Days after planting Julian Day R. Name: Stem breakage Description: recorded just prior to harvest by visual assessment of the percentage of plants that had broken stems Severity (%) S. Name: Heading date Description: the number of days after planting when 50% or more of the heads were emerged halfway from the boot Days after planting Julian Day T. Name: Yield Description: the weight of harvested, threshed, and cleaned seeds in a two-row-plot and coverted to Kg/Ha grams Bu/A Kg/Ha U. Name: Height Description: after heading as the height from the ground to the tip of the spike (not including awns) on representative plants in the middle of the plot Inches cm V. Name: Lodging Description: the percentage of the plants that severely fallen over at maturity degree (0-9) Severity (%) W. Name: Grain protein content Description: was assessed on a 110 ml-sample of the cleaned grain using near-infrared reflectance spectroscopy (NIRS) (Perten Instrument Inc., Springfield, IL) % X. Name: Fusarium head blight (FHB) Description: the percentage of infected kernels in each of ten arbitrarily selected spikes per plot was estimated and averaged Y. Name: Kernel discoloration (KD) Description: was scored visually on a 1-5 scale by placing a sample of grain from each plot on a white paper plate under fluorescent lights and comparing to control samples in that environment a 1-5 scale (1 for brightest kernels and 5 for darkest kernels) Z. Name: Deoxynivalenol (DON) Description: was measured on a sample of 25 g of cleaned seeds from each plot by gas chromatography/mass spectrometry (Mirocha et al. 1998) parts per million (ppm) (µg g-1) AA. Name: Seedling Net Blotch (NB) Description: assessed visually using a 1-10 scale (Tekauz 1985) a 1-10 scale with 1 being most resistant and 10 being most susceptible BB. Name: Notes Description: Notes ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Gen10_50Kgenotype101linesAll6H.xlsx ----------------------------------------- 1. Number of variables: 4 2. Number of rows: 3,718 3. Missing data codes: Code/symbol -- Definition: error or not available Code/symbol Definition 4. Variable List Example. Name: Gender Description: Gender of respondent 1 = Male 2 = Female 3 = Other A. Name: chr Description: chromosome B. Name: pos Description: physical positions based on 100719_Barley_Morex_V2_pseudomolecules database (IPK barley BLAST server https://webblast.ipk-gatersleben.de/barley_ibsc/) bp C. Name: cM Description: genetic positions centimorgan (cM) D. Name: Name Description: SNP marker name