Whole Genome Variation of Transposable Element Insertions in a Maize Diversity Panel

Abstract

Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due in part to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short read sequencing data from 509 diverse inbred lines to classify the presence/absence of 494,564 non-redundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e. LTRs, Helitrons, TIRs) had different frequency distributions within the population. Across the different orders, TE family size was negatively correlated with average population frequency of TEs in the family and nested TEs are at lower frequency than non-nested TEs. Age of LTR elements was positively correlated with population frequency. Comparison with SNP data revealed that while a majority of TEs are tagged by nearby SNPs (r2 > 0.9) there are also many TEs in low to moderate linkage disequilibrium with nearby SNPs. This study provides a population scale genome-wide assessment of TE variation in maize, and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.

Single‐parent expression drives dynamic gene expression complementation in maize hybrids

“…To determine TE PAV, every TE was characterized as present, absent or ambiguous, as previously reported (O’Connor et al ., 2020). Briefly, two points of reference, the left and right inner edges of a TE, were used to determine the TE status in a particular genotype.…”

Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel

“…These genotypes were primarily drawn from temperate germplasm 21 and hence previously reported large effect qualitative resistance loci such as RPP9 which are near exclusively drawn from tropical germplasm pools are unlikely to be segregating in this population 1 . Employing a genotype dataset consisted of 2.7 million SNP markers with a minor allele frequency >0.1 generated from a combination of the published maize hapmap3 22 , deep resequencing data for 509 Wisconsin Diversity Panel 23 and RNAseq data 21,24 multiple loci associated with quantitative resistance to southern rust were identified through a combination of genome wide association and transcriptome wide association. The latter utilized published expression data collected from seedlings 21,24 .…”

Genetic Architecture of Kernel Compositional Variation in a Maize Diversity Panel

“…To determine the genetic architecture of our compositional traits we utilized a GWAS approach, as this population was originally developed for this purpose (Hansey et al, 2011). For this analysis we utilized a set of 2,386,666 SNPs that had been previously called from whole genome resequencing data (O’Connor et al, 2020). Principal component analysis (PCA) using these SNPs showed clear separation of the three major maize dent heterotic groups: Stiff Stalk, Iodent, and Non-Stiff Stalk (Figure 4a).…”

“…A subset of 501 lines from the full WiDiv population was used for this study (Supplemental Table 1). These lines all have available whole genome resequencing data with approximately 20x sequence depth, and SNPs from these data were previously identified (O’Connor et al, 2020). Briefly, reads were aligned to the B73 v4 reference genome assembly (Jiao et al, 2017) and joint SNP calling was performed using freebayes v1.3.1-17 (Garrison & Marth, 2012).…”

“…Genetic distance comparison between shared inbreds for RNA-seq (Mazaheri et al, 2019) and WGS (O’Connor et al, 2020) data. a) All inbreds included in GD comparison.…”