Sound Agriculture, a pioneer in sustainable crop production solutions, has introduced a groundbreaking software package, sounDMR. This innovative tool is set to transform how epigenetic variations in plant populations are understood, offering high-resolution epigenetic profiling of plants without costly equipment or intricate library preparations. This development paves the way for novel opportunities in plant breeding.
Key Insights from the Release:
- Understanding Epigenetics: Epigenetics delves into the heritable changes in gene expression that don’t alter the underlying DNA sequence. DNA methylation, a primary mechanism for epigenetic variation, plays a pivotal role in gene expression regulation across all life forms, especially in plants. Recent advancements in long and ultra-long-read sequencing technologies have facilitated the study of methylation patterns in intricate genomic regions.
- The Power of Nanopore Technology: Leveraging Oxford Nanopore technology, researchers can now study methylation patterns in non-model organisms, such as crops, even without extensive sequencing facilities.
- Research Findings: Led by Dr. Travis Bayer and Dr. Jack Colicchio, the research team utilized sounDMR to replicate results from the recognized gold-standard method for methylation sequencing, whole genome bisulfite sequencing (WGBS). Furthermore, the team harnessed Oxford Nanopore’s “adaptive sampling” to target approximately 400 specific genome regions. This data unveiled the impact of the known demethylating agent, zebularine, on the Arabidopsis thaliana genome, enhancing the comprehension of its effects.
- A New Era in Breeding: “Epigenetic variations exist in all plant systems, but they’ve been overlooked in breeding due to challenges in pinpointing these subtleties,” commented Dr. Travis Bayer, co-founder and CTO of Sound Agriculture. “With nanopore sequencing technology, we’ve gained deeper insights to inform breeding decisions, enhancing agricultural outcomes.”
- Endorsement from Oxford Nanopore: Gordon Sanghera, CEO of Oxford Nanopore Technologies, expressed enthusiasm about the application of nanopore sequencing in enhancing plant breeding outcomes. He emphasized the technology’s capability to provide in-depth genomic insights, especially in DNA methylation.
This development signifies a monumental stride in epigenetics, offering a holistic, cost-effective, and user-friendly method to explore the intricacies of plant populations at the epigenetic level. This breakthrough will empower plant breeders and researchers to decode epigenomic data in plant populations, leading to the precise and swift creation of desired crop varieties.
Researchers keen on exploring the sounDMR software can access it on Github.
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Photo by Beth Macdonald on Unsplash
