Genomic advances reveal how similar weeds can dominate wheat fields that are geographically separated by over 5,000 miles
Two newly sequenced Alopecurus genomes, blackgrass and orange/shortawn foxtail, represent important advancements for plant breeders working to manage these challenging agricultural weeds. These genomes offer key insights into the genetic mechanisms that make these weeds such resilient survivors in modern farming systems, enabling breeders to develop more effective control strategies.
Blackgrass (Alopecurus myosuroides) and orange/shortawn foxtail (Alopecurus aequalis) are widespread across the Northern Hemisphere, with blackgrass becoming a dominant weed in Western European winter wheat and barley crops, and orange foxtail similarly affecting cereal crops in parts of China and Japan. Both species are notorious for out-competing crops, and despite changes in cropping practices, their prevalence persists. Moreover, both weeds have evolved resistance to multiple herbicides, further complicating control efforts.
For plant breeders, understanding the genetic factors driving resistance and resilience in these weeds is essential for developing sustainable crop protection strategies. High-quality genomic resources like these new genomes are crucial to fill this knowledge gap.
In December 2023, an annotated blackgrass genome was published, a collaboration between Rothamsted, Clemson University, and Bayer. The seeds were sourced from a population in the Broadbalk long-term experiment, which had never been treated with herbicides, ensuring susceptibility to chemical control. Comparing these seeds to resistant populations from other UK fields helped identify genetic mechanisms related to herbicide resistance.
In December 2024, an annotated orange foxtail genome was published, a joint effort between Rothamsted, the Earlham Institute, and the European Reference Genome Atlas (ERGA) initiative. The orange foxtail plants were sourced from seeds held at Kew’s Millennium Seed Bank, from a population collected in the UK. Since orange foxtail is not present in the UK’s agroecosystem, these plants have likely never been exposed to herbicides, making the genome a valuable reference for understanding the species without the influence of selective herbicide pressures.
Dr. Jon Wright, bioinformatician at the Earlham Institute and lead author of the study, emphasized the importance of genomic resources for breeders and producers facing increasing pressure to develop sustainable approaches to manage weeds.
“To understand how these weeds compete with the plants we want to cultivate and look inside the box of tricks they use to frustrate farmers, we absolutely need to have high-quality genomes. We’ve been able to start exploring the evolutionary story of these weeds, particularly their development of herbicide resistance. This could be used to develop effective herbicides or other strategies to better control these weeds.”
The orange foxtail genome is 2.83 Gb in size, smaller than the blackgrass genome (3.572 Gb), and contains over 33,750 protein-coding genes. It is assembled into seven chromosome-level scaffolds, most of which are complete with telomere sequences. Comparing the genomes of orange foxtail and blackgrass with barley revealed surprising structural similarities between the orange foxtail genome and barley, suggesting areas of functional conservation or divergence that drive adaptations to specific ecological niches.
Read more about the Current Status of Community Resources and Priorities for Weed Genomics Researchhere
