Supplemental Material for Ramstein and Casler, 2019

2019-01-16T14:19:54Z (GMT) by Guillaume P. Ramstein Michael D. Casler

File_S1.csv: Population information

File in .csv format consisting of information about population assignment and geographical origin of genotypes

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)

Latitude: coordinate of geographical origin in °N

Longitude: coordinate of geographical origin in °W

Population: WS4U-C2, Liberty-C2, U4X-N, U8X-W, U8X-E, U8X-S, L4X-NE or L4X-S


File_S2.csv: Raw phenotypic data

File in .csv format consisting of trait measurements at plants

Panel: BP (WS4U-C2, Liberty-C2) or AP (U4X-N, U8X-W, U8X-E, U8X-S, L4X-NE, L4X-S)

Location: WI (for BP) or NY (for AP)

Year: 2012 to 2014 (for BP), 2009 to 2011 (for AP)

Rep: replicate

Set: set, for AP only (for which individuals are arranged in a sets-in-reps design)

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

PH: plant height, measured in centimeters as the height from the ground to the top of the tallest tiller

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 1st 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

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


File_S3.csv: Genotype means

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.

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

PH: plant height, measured in centimeters as the height from the ground to the top of the tallest tiller

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 1st 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

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


Marker_data.rds: Genotype calls

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 n = 760 genotypes (maternal parent in BP, individual in AP). Columns correspond to the m = 717,814 marker loci selected across individuals.

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

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)