DNA was extracted using DNeasy Plant Mini Kit (QIAGEN). Libraries were prepared according to TruSeq DNA PCR-Free Library Prep (Illumina). DNA samples isolated from one tetrasomic Dp4 and its diploid sibling were sequenced on a NextSeq High Output Flow Cell - SE75 (Illumina) at the DNA core of University of Missouri. DNA samples extracted from a trisomic 10L18, 6Sa, and their respective diploid sibling were subjected to the same procedure. Adaptor trimming and low-quality read removal were performed the same as in the mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters (Langmead and Salzberg, 2012 (link)). Uniquely mapped read counts were extracted and then subjected to Reads Per Kilobase per Million mapped reads (RPKM) normalization. Subsequently, ratios of normalized counts of tetrasomic Dp4 to diploid were generated on a per gene basis, which was used for determination of Dp4 breakpoints later (Supplemental Figure S14A). Ratios of normalized counts of trisomic 10L or 6S to the diploid were computed to determine the breakpoint of TB-10L18 and TB-6Sa (Supplemental Figure S14). Breakpoints of other distal aneuploids were determined as described in the companion study (Yang et al., 2021 ).