Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Implementation of Epigenetic Variation in Sorghum Selection and Implications for Crop Resilience Breeding

Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de novo epigenetic variation, and have used these materials to evaluate changes in plant growth vigor. Plant crossing and selection in two distinct environments revealed features of phenotypic plasticity derived from MSH1 manipulation. Introduction of an epigenetic variation to an isogenic sorghum population, in the absence of selection, resulted in 10% yield increase under ideal field conditions and 20% increase under extreme low nitrogen conditions. However, incorporation of early-stage selection amplified these outcomes to 36% yield increase under ideal conditions and 64% increase under marginal field conditions. Interestingly, the best outcomes were derived by selecting mid-range performance early-generation lines rather than highest performing. Data also suggested that phenotypic plasticity derived from the epigenetic variation was nonuniform in its response to environmental variability but served to reduce genotype x environment interaction. The MSH1-derived growth vigor appeared to be associated with enhanced seedling root growth and altered expression of auxin response pathways, and plants showed evidence of cold tolerance, features consistent with observations made previously in Arabidopsis. These data imply that the MSH1 system is conserved across plant species, pointing to the value of parallel model plant studies to help devise effective plant selection strategies for epigenetic breeding in multiple crops

Muts Homolog 1-Induced Heritable Stress Memory and Enhanced Growth Vigor Through Grafting Are Associated with the RdDM Pathway

Rapid response to stress in plants is thought to involve epigenomic effects, but the extent to which these changes are inherited is not well characterized. RNAi suppression of MSH1, a plant-specific gene, produces a range of developmental changes. Following segregation of the RNAi transgene, transgene-null progenies with restored MSH1 display a non-genetic phenotype termed msh1 “memory”. Methylation and gene expression analyses of a six-generation inheritance study of memory identified key pathways including circadian rhythm, phytohormone signaling, and stress response. The msh1 memory induction is dependent on HDA6, MET1, and DRM1/2, genes known to participate in targeted DNA methylation. Grafting of wild-type floral stems to the msh1 rootstock produces progeny with heritable enhanced growth vigor in Arabidopsis and tomato, suggesting the involvement of a mobile signal. Disruption of small interfering RNA (siRNA) production in the msh1 rootstock by introducing RdDM mutations obviates the enhanced vigor in graft progeny. Comparison between enhanced and non-enhanced progenies identified differentially methylated loci enriched for auxin-related pathways, and an association to robust root growth in msh1 progeny was confirmed through chemical inhibitor assays. Field studies of msh1 graft progenies in tomato showed significant increase in yield. Together, these results suggest that msh1-induced epigenetic variation could provide environmental resilience and enhanced yield in plants

Ws-2 Introgression in a Proportion of \u3ci\u3eArabidopsis thaliana\u3c/i\u3e Col-0 Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification

Arabidopsis thaliana is an important model organism with a robust network of resources that has been of enormous value to the plant science research community. The use of isogenic material as a reference point or control is critical for many types of experiments in plant molecular biology and genetics. Recently, we noticed that some seed from a common source of the widely used Columbia-0 (Col-0) strain gave rise to plants showing features atypical for this strain. Whole-genome DNA-sequencing and allelespecific PCR assays confirmed that the abnormal individuals contain multiple introgressions from the ecotype Wassilewskija-2 (Ws-2), as described below. This emphasizes the importance of practices necessary to maintain the integrity of seed stocks and other biological collections. We urge research groups to evaluate whether they may have been affected and to revisit their materials if needed

LETTER TO THE EDITOR \u3ci\u3eWs-2\u3c/i\u3e Introgression in a Proportion of \u3ci\u3eArabidopsis thaliana Col-0\u3c/i\u3e Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification

Arabidopsis thaliana is an important model organism with a robust network of resources that has been of enormous value to the plant science research community. The use of isogenic material as a reference point or control is critical for many types of experiments in plant molecular biology and genetics. Recently, we noticed that some seed from a common source of the widely-used Columbia-0 (Col-0) strain gave rise to plants showing features atypical for this strain. Whole genome DNA-sequencing and allele-specific PCR assays confirmed that the abnormal individuals contain multiple introgressions from the ecotype Wassilewskija-2 (Ws-2), as described below. This emphasizes the importance of practices necessary to maintain the integrity of seed stocks and other biological collections. We urge research groups to evaluate whether they may have been affected and to revisit their materials if needed

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods