pvdiv_metadata: Metadata table for the Panicum virgatum diversity panel
In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum

Description Usage Format Details Author(s) References

A dataset containing the collected metadata information for individuals in the Panicum virgatum diversity panel. The variables are as follows:

1	data(pvdiv_metadata)

A data frame with 1347 rows and 37 variables.

PLANT_ID Individual plant name. Unique to each plant. The column we should be using for analyses.
SUBPOP Using clustering from an additive kinship matrix, which genetic subpopulation does the PLANT_ID belong to? 4X and 8X individuals have been assigned a ploidy by flow cytometry, but not a subpopulation by sequencing, as of the end of 2020.
LIBRARY Four letter library code used for sequencing. IF NA, the plant has not been sequenced as of the end of 2020.
GENETIC_SUBPOP_KINSHIP Using clustering from an additive kinship matrix, which genetic subpopulation does the PLANT_ID belong to? NA individuals were not included in the kinship matrix.
KINSHIP_ORDER Order of individuals in an additive kinship matrix. Roughly speaking, closer numbers represent more similar individuals.
GENETIC_SUBPOP_50PER From hierarchical k=3 analysis done early 2020. Which genetic subpopulation does the PLANT_ID belong to, at 50% assignment or more. Admixed individuals are unassigned PLANT_IDs included in the analysis; NA individuals were not included.
GENETIC_SUBPOP_95PER From hierarchical k=3 analysis done early 2020. Which genetic subpopulation does the PLANT_ID belong to, at 95% assignment or more. Admixed individuals are unassigned PLANT_IDs included in the analysis; NA individuals were not included.
GULF_Q From hierarchical k=3 analysis done early 2020. Structure Q value for assignment to the Gulf genetic subpopulation. NA individuals were not included in the Structure analysis.
ATLANTIC_Q From hierarchical k=3 analysis done winter 2020. Structure Q value for assignment to the Atlantic subpopulation. NA individuals were not included in the Structure analysis.
MIDWEST_DA From hierarchical k=3 analysis done winter 2020. DAPC value for assignment to the Midwest subpopulation. NA individuals were not included in the DAPC analysis.
ECOTYPE From John's phenotypic analysis of Ecotypes. Which phenotypic group does the PLANT_ID belong to, at 50% assignment or more. NA individuals did not have phenotypic data for this classification.
ECOTYPE_NNET From John's neural network extending ecotype classification to individuals without phenotypic data.
ECOTYPE_PC1 From John's phenotypic analysis of ecotypes done summer 2019. The first principle component separating individuals into ecotypes.
UPLAND_ASSIGNMENT From John's phenotypic analysis of Ecotypes done summer 2019. Assignment to the Upland ecotype.
LOWLAND_ASSIGNMENT From John's phenotypic analysis of Ecotypes done summer 2019. Assignment to the Texas ecotype.
COASTAL_ASSIGNMENT: From John's phenotypic analysis of Ecotypes done summer 2019. Assignment to the Coastal ecotype.
LIB_GROWN For tetraploid plants with sequencing libraries, was the PLANT_ID grown at one or more of the 10 common garden sites in 2018? "Y" = yes, "N" = no. Does not include plants where LIB_PHENO is "N".
LIB_BIOCLIM Do we have bioclim variables for this PLANT_ID? "Y" = yes, "N" = no. Does not include plants where LIB_CLIMATE is "N".
LIB_CLIMATE John & Jason's decision on whether this PLANT_ID should be used for climate analyses done summer 2019. "Y" = yes, "N" = no.
LIB_PHENO John & Jason's decision on whether this PLANT_ID should be used for phenotypic analyses done summer 2019. "Y" = yes, "N" = no.
LIB_ACC John & Jason's decision on whether this PLANT_ID should be used for analyses of a single plant per location done summer 2019 . "Y" = yes, "N" = no.
LIB_NOTES Notes on John & Jason's decisions for the above 3 columns. This analysis was done summer 2019.
PLOIDY Ploidy as determined by both sequencing & flow cytometry analyses done in 2019. Typically 4X (tetraploid) or 8X (octoploid).
COLLECTION_TYPE Original plant collection metadata. What kind of collection was this? Breeding selection, Natural collection, Cultivar.
COLLECTION_METHOD How was the plant collected?
COLLECTOR Who collected this plant?
STATE State of the United States that the plant was collected from.
COUNTY County that the plant was collected from.
LATITUDE Latitude of origin of the collected plant.
LONGITUDE Longitude of origin of the collected plant.
ELEVATION Elevation of origin of the collected plant.
NOTE_LATLONG Notes on exactness of latitude & longitude of collection
LOCALITY Additional details on plant collection location.
TAXON Genus & species of the collected plant.
HABITAT Details on habitat of plant collection location, if known.
COLL_DATE Information on plant collection date, if known.
PLANTED_2018 All plants clonally replicated and transplanted into one or more common garden in the summer of 2018.