Biology subjects

Springer, N. M.

Publications and source records attributed to Springer, N. M..

5 recordsLinked to original sources

bioRxiv2018

Classifying cold stress responses of inbred maize seedlings using RGB imaging

Increasing the tolerance of maize seedlings to low temperature episodes could mitigate the effects of increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting seedlings of 40 maize inbred genotypes to a defined, temporary cold stress while collecting digital profile images over a 9-day time course. Image analysis performed with PlantCV software quantified shoot height, shoot area, 14 other morphological traits, and necrosis identified by color analysis. Hierarchical clustering of changes in growth rates of morphological traits and quantification of leaf necrosis over two time intervals resulted in three clusters of genotypes, which are characterized by unique responses to cold stress. For any given genotype, the set of traits with similar growth rates is unique. However, the patterns among traits are different between genotypes. Cold sensitivity was not correlated with the latitude where the inbred varieties were released suggesting potential further improvement for this trait. This work will serve as the basis for future experiments investigating the genetic basis of recovery to cold stress in maize seedlings.

plant biology↗

bioRxiv2018

Targeted epigenomic changes to the maize methylome resulting from tissue culture

DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. A sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ~15Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines suggesting the existence of a targeted process for altering epigenetic state during tissue culture. The consistent changes induced by tissue culture include both gains and losses of DNA methylation and can affect CG, CHG or both contexts within a region. The majority of changes in DNA methylation exhibit stable inheritance although there is some evidence for stochastic reacquisition of the initial epigenetic state in some individuals. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.

plant biology↗

bioRxiv2017

Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation

DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, providing evidence that context-specific DNA methylation directly regulates expression of a small number of genes. The analysis of a diverse set of inbred lines revealed that many genes regulated by CMTs exhibit natural variation for DNA methylation and gene expression. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm, highlighting the importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.

plant biology↗

bioRxiv2017

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

Maize is a diverse paleotetraploid species with widespread presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization and differential fractionation refers to non-shared gene loss events between individuals. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variable syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable compared to syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.\n\nSIGNIFICANCE STATEMENTThere is a large amount of presence/absence variation for gene content in maize. One mechanism that has been hypothesized to contribute to this variation is differential fractionation between individuals following the maize whole genome duplication event. Using comparative genomics, with sorghum and rice representing the ancestral state, we observed little evidence of differential fractionation among elite inbred lines and the few differentially fractionated genes identified did not appear to confer functional significance.

plant biology↗

bioRxiv2017

Genotype-by-Environment Interactions Affecting Heterosis in Maize

The environment can influence heterosis, the phenomena in which the offspring of two inbred parents exhibits phenotypic performance beyond the inbred parents for specific traits. In this study we measured 25 traits in a set of 47 maize hybrids and their inbred parents grown in 16 different environments, and each had varying levels of average productivity. By quantifying 25 vegetative and reproductive traits across the life cycle we were able to analyze interactions between the environment and multiple distinct instances of heterosis. The magnitude and rank among hybrids of better-parent heterosis (BPH) varied for the different traits and environments. Across the traits, a higher within plot variance was observed for inbred lines compared to hybrids. However, for most traits, variance across environments was not significantly different for inbred lines compared to hybrids. Further, for many traits the correlations of BPH to hybrid performance and BPH to better parent performance were of comparable magnitude. These results indicate that inbreds and hybrids are showing similar trends in environmental response and are both contribute to genotype-by-environment interactions for heterosis. This study highlights that degree of heterosis is not an inherent trait of a specific hybrid, but varies depending on the trait measured and the environment where that trait is measured. Studies that attempt to correlate molecular processes with heterosis are hindered by the fact that heterosis is not a consistent attribute of a specific hybrid.

genetics↗