DOI: 10.5061/dryad.pk0p2nh3g
title: Genetic maps and marker effects of four maize biparental crosses

description: This dataset includes genetic maps from four maize biparental crosses
 (A/B, C/B, C/D, and E/F) and marker effects for five traits: grain yield
 (t ha⁻¹ at 150 g H₂O kg⁻¹), grain moisture (g kg⁻¹), test weight (g L⁻¹),
 plant height (cm), and ear height (cm). Marker effects were estimated
 separately for two testers per population. Testers are designated as T1,
 T2, T3, and T4.
description: Four maize biparental crosses (A/B, C/B, C/D, E/F) with 130 to
 242 doubled haploid (DH) lines were crossed to two inbred testers, which
 were designated as T1, T2, T3, and T4. The eight testcross populations
 were evaluated in up to 18 year-location combinations in the U.S. Corn
 Belt. The measured traits included grain yield (t
 ha<sup>-1</sup> at 150 g H<sub>2</sub>O
 kg<sup>-1</sup>), grain moisture (g
 kg<sup>-1</sup>), test weight (g L<sup>-1</sup>),
 plant height (cm), and ear height (cm). Testcross phenotypic data were
 adjusted according to the incomplete block design used at each location to
 obtain best linear unbiased estimates (BLUEs) per location.
 Across-environment BLUEs were subsequently calculated. Variance components
 were estimated with testcross and environment effects treated as
 random. The DNA marker data consisted of 3072 single
 nucleotide polymorphisms (SNPs) generated using the Illumina iScan
 platform (Illumina Inc., San Diego, CA). Within each population, SNPs with
 &gt; 10 % missing values, &gt; 5 % of heterozygosity, or minor
 allele frequency &lt; 0.1 were excluded. Missing marker data were
 imputed via the most correlated SNP. Linkage maps for each population were
 constructed using QTL IciMapping version 4.2 (Meng et al., 2015). When
 multiple markers mapped to the same position, only one was retained.
 Between 354 and 754 SNPs were retained per population, with chromosome map
 lengths ranging from 93.9 to 432.7 cM.
description: # Dryad dataset Dataset DOI:
 [10.5061/dryad.pk0p2nh3g](https://doi.org/10.5061/dryad.pk0p2nh3g) ##
 Description of the data and file structure This dataset contains genetic
 maps and tester-specific marker effect estimates for four maize biparental
 populations: A×B, C×B, C×D, and E×F. A full description of the populations
 and field data processing methods can be found in Krchov et al. (2015):
 [https://doi.org/10.2135/cropsci2014.09.0608](https://doi.org/10.2135/cropsci2014.09.0608). ### Files and variables ##### **1. Genetic Maps** Each population has an associated genetic map file. Each genetic map includes the following columns: * SNP – Marker name * CHR – Chromosome number * POS – Marker position in centimorgans (cM) **2. Marker Effects** Marker effects were estimated separately for two testers within each biparental population. Tester were designated as T1, T2, T3, and T4. Each marker-effect file contains the following columns: * SNP – Marker name * YLD – Grain yield (t ha⁻¹ at 150 g H₂O kg⁻¹) * MST – Grain moisture (g kg⁻¹) * TWT – Test weight (g L⁻¹) * PLHT – Plant height (cm) * EHT – Ear height (cm) Files are organized so that each population × tester combination has its own marker effect dataset.