Limited role of differential fractionation in genome content variation and function in maize (<i>Zea mays L.</i>) inbred lines

Brohammer, Alex B.; Kono, Thomas J. Y.; Springer, Nathan M.; McGaugh, Suzanne E.; Hirsch, Candice N.

doi:10.1101/179119

Cited by 8 publications

(18 citation statements)

References 53 publications

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“…Numbers around the outside of the pie chart indicate the module and numbers beneath the boxes indicate the number of genes present in each module. Boxes around the pie chart indicate organ‐specific, stress‐related, and presence−absence variant (Brohammer et al ., ) enrichment within the module. Tissues in parentheses after an organ indicate enrichment of those tissue‐specific genes.…”

Section: Resultsmentioning

confidence: 99%

“…Brohammer et al . () identified 11 971 PAVs from the anchored AGPv4 B73 loci using resequencing data from 62 inbreds and defining a gene as a PAV if the CDS coverage was less than 20% (Brohammer et al ., ). Of the PAVs identified in the Brohammer et al .…”

Section: Resultsmentioning

confidence: 99%

“…In plants, CNVs and PAVs have been shown to function in environmental adaptation responses including flowering time (Díaz et al ., ), secondary metabolism (Winzer et al ., ), and stress tolerance (Hattori et al ., ; Gaines et al ., ; Cook et al ., ). In maize, several pan‐genome studies have been conducted using array comparative genomic hybridization (Springer et al ., ; Swanson‐Wagner et al ., ), RNA‐sequencing (Hirsch et al ., ), whole genome resequencing (Lai et al ., ; Jiang et al ., ; Brohammer et al ., ), genotyping‐by‐sequencing (Lu et al ., ), and whole genome comparison (Hirsch et al ., ; Sun et al ., ). Recently, using resequencing data from 62 inbred lines with a CDS (coding sequence) coverage threshold of 20%, Brohammer et al .…”

Section: Introductionmentioning

confidence: 99%

“…Recently, using resequencing data from 62 inbred lines with a CDS (coding sequence) coverage threshold of 20%, Brohammer et al . () identified 30.7% of the anchored B73 v4 loci as absent in at least one inbred line; and 581 loci were absent in 41 to 61 of the inbreds (Brohammer et al ., ). The pervasiveness of PAVs in the maize genome led Swanson‐Wagner et al .…”

Section: Introductionmentioning

confidence: 99%

“…Using these gene expression analyses, core genes and PAVs identified by Brohammer et al . () were studied to determine the differential and co‐expression characteristics across a diverse set of maize inbreds and provide a foundational dataset to infer function. To facilitate use by the community, the data along with search and analysis tools are available via the Maize Genomics Resource (MGR; maize.plantbiology.msu.edu) and the Bio‐Analytic Resource for Plant Biology (BAR) Maize electronic Fluorescent Pictograph (eFP) Browser (bar.utoronto.ca/efp_maize).…”

Section: Introductionmentioning

confidence: 99%

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An updated gene atlas for maize reveals organ‐specific and stress‐induced genes

et al. 2019

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SummaryMaize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ‐specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence−absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co‐expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data‐mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes

et al. 2019

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Whole-genome variation of transposable element insertions in a maize diversity panel

Qiu

O’Connor

Coletta

et al. 2021

G3 Genes|Genomes|Genetics

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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 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 445,418 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. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 < 0.5) that potentially represent information that has not been well captured in previous SNP based marker-trait association studies. 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.

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

Qiu

O’Connor

Coletta

et al. 2020

Preprint

Self Cite

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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.

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Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

Cited by 8 publications

References 53 publications

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes

Whole-genome variation of transposable element insertions in a maize diversity panel

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

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