DCARv2 L8708 x Z020 Linkage Map Variants JBrowse VCF

L8708 × Z020 Linkage Map Variants

The F₂ population, L8708 × Z020, was identified from prior field screening as segregating for plant height, shoot biomass, and root storage shape and color. This population was derived from a cross between L8708, an orange inbred line with a medium-long storage root and compact shoots, and Z020, a yellow, cultivated landrace from Uzbekistan with a short, blunt-tipped storage root and broad, prostrate leaves. A single F₁ plant was selected from this cross and selfed to produce the F₂ population used for mapping in this study.

Variants were obtained using genotyping-by-sequencing (GBS). Genomic DNA was digested with ApeK1, barcoded, and pooled for sequencing with 85–95 pooled samples per Illumina HiSeq 2000 lane. Samples were sequenced using single end, 100 nt reads and v3 SBS reagents (Illumina, San Diego, CA, United States).

SNPs were called using the TASSEL-GBS pipeline version 5.2.31. Filtering was conducted in VCFtools version 0.1.14 with the following parameters: a minimum minor allele frequency of 0.1 and maximum missing data of 10% for both genotype and marker.

The filtered vcf file contains 116,030 variants. Only the 640 mapped markers have PASS status in the vcf file. This file can be downloaded from the link below.

The linkage map from this publication can be viewed at L8708×Z020

Data from this analysis can be viewed in JBrowse here.