Seed World

Sound Agriculture Releases New Software Package to Aid in Plant Breeding

Sound Agriculture researchers have announced the release of a new software package called sounDMR according to a release. sounDMR will show epigenetic variation in plant populations.

Scientific Reports published the findings show casing the software. It enables “high-resolution epigenetic profiling of plants without the need for expensive equipment or complex library preparations, fostering new opportunities in plant breeding.”

Travis Bayer  and Jack Colicchio led the research team using sounDMR to reproduce findings from the standard method for methylation sequencing, whole genome bisulfite sequencing (WGBS). The team expanding on the findings by utilizing Oxford Nanopore’s “adaptive sampling.” This allowed for targeted sequencing of around 400 specific genome regions. The study found that zebularine, a known demethylating agent, “decreased methylation across the Arabidopsis thaliana genome and induced epigenetic variation,” allowing for a better understanding of the effects.

“There are epigenetic variations in all plant systems that haven’t been considered in breeding because of the difficulty in identifying these nuances,” said Bayer, co-founder and chief technology officer of Sound Agriculture. “With nanopore sequencing technology, we now have an added level of insight to support breeding decisions that can improve agriculture outcomes.”

“We are really pleased to see nanopore sequencing being used to improve outcomes in plant breeding. Oxford Nanopore technology offers more comprehensive genomic insights, especially in DNA methylation,” said Gordon Sanghera, CEO of Oxford Nanopore Technologies. “This is a great example of high-accuracy epigenetic insights in biological analyses being used to support new genomic discoveries for the benefit of agriculture.”

This research is a milestone in the epigenetic field, as it offers a more affordable yet comprehensive approach to understanding complex plant populations at an epigenetic level.

To learn more, visit Github.