10.25387/g3.7464863.v1
Guillaume P. Ramstein
Guillaume P.
Ramstein
Michael D. Casler
Michael
D. Casler
Supplemental Material for Ramstein and Casler, 2019
GSA Journals
2019
genomic prediction
marker-by-population interaction
Panicum virgatum L.
population heterogeneity
kernel functions
Crop and Pasture Improvement (Selection and Breeding)
2019-01-16 14:19:54
Dataset
https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Ramstein_and_Casler_2019/7464863
<p><b>File_S1.csv: Population information</b></p>
<p>File in .csv format
consisting of information about population assignment and geographical origin
of genotypes</p>
<p>Genotype: population
(in BP) or accesion (in AP) + genotype ID within population/accession: maternal
parent of half-sib families in BP (e.g. ‘Liberty-C2_31804’ refers to genotype
31804 in population Liberty-C2), individual plant in AP (e.g., ‘Dacotah_03’
refers to genotype 03 in accession Dacotah)</p>
<p>Latitude: coordinate
of geographical origin in °N</p>
<p>Longitude: coordinate
of geographical origin in °W</p>
<p>Population: WS4U-C2,
Liberty-C2, U4X-N, U8X-W, U8X-E, U8X-S, L4X-NE or L4X-S</p><p><br></p>
<p><b>File_S2.csv: Raw phenotypic data</b></p>
<p>File in .csv format consisting
of trait measurements at plants</p>
<p>Panel: BP (WS4U-C2, Liberty-C2) or AP (U4X-N, U8X-W, U8X-E, U8X-S,
L4X-NE, L4X-S)</p>
<p>Location: WI (for BP) or NY
(for AP)</p>
<p>Year: 2012 to 2014 (for BP),
2009 to 2011 (for AP)</p>
<p>Rep: replicate</p>
<p>Set: set, for AP only (for
which individuals are arranged in a sets-in-reps design)</p>
<p>Genotype: Population (in BP)
or accesion (in AP) + genotype ID within population/accession: maternal parent
of half-sib families in BP, individual plant in AP</p>
<p>PH: plant height,
measured in centimeters as the height from the ground to the top of the tallest
tiller</p>
<p>HD: heading date,
measured in growing degrees days as the cumulated sum of daily average
temperatures (in degrees Celsius; °C) above 10 °C, from January 1<sup>st</sup>
to the day of heading, defined as the emergence of at least half of the
panicles from the boot; daily average temperatures were estimated by the
average of the minimum and maximum daily temperatures</p>
<p>St: standability,
measured on a 0-10 scale to describe plants’ stature and stiffness, with 0
qualifying plants that are prostrate and 10 qualifying upright and rigid plants</p><p><br></p>
<p><b>File_S3.csv: Genotype means</b></p>
<p>File in .csv format
consisting of genotype means for maternal parents in BP and individuals
in AP. In BP, genotype means are the intercept +
two times adjusted half-sib families means. In AP, genotype means are the
intercept + adjusted genotype means. Models used to estimate adjusted half-sib
families means in BP were fitted in WS4U-C2 and Liberty-C2 separately. Models
used to estimate adjusted genotype means in AP were fitted on all AP
individuals.</p>
<p>Genotype: population
(in BP) or accesion (in AP) + genotype ID within population/accession: maternal
parent of half-sib families in BP, individual plant in AP<b></b></p>
<p>PH: plant height,
measured in centimeters as the height from the ground to the top of the tallest
tiller</p>
<p>HD: heading date,
measured in growing degrees days as the cumulated sum of daily average
temperatures (in degrees Celsius; °C) above 10 °C, from January 1<sup>st</sup>
to the day of heading, defined as the emergence of at least half of the
panicles from the boot; daily average temperatures were estimated by the
average of the minimum and maximum daily temperatures</p>
<p>St: standability,
measured on a 0-10 scale to describe plants’ stature and stiffness, with 0
qualifying plants that are prostrate and 10 qualifying upright and rigid plants</p><p><br></p>
<p><b>Marker_data.rds: Genotype calls</b></p>
<p>File in .rds format, readable
from the readRDS function in R, containing expected allelic dosages (expected
number of alternate alleles, as per posterior probabilities from genotype
calling) at selected markers for each genotype. Rows correspond to the <i>n</i> = 760 genotypes (maternal parent in
BP, individual in AP). Columns correspond to the <i>m</i> = 717,814 marker loci selected across individuals.</p>
<p>Row names: Population (in BP)
or accesion (in AP) + genotype ID within population/accession: maternal parent
of half-sib families in BP, individual plant in AP </p>
<p>Column name: Chromosome index
+ SNP position as per v1.1 of the reference genome (e.g. ‘Chr05b_1187770’
refers to the SNP at position 1187770 in chromosome 5, subgenome B)</p>