Genome data rewrite the story of oat domestication in China

Oat is among the top ten cereal crop species in terms of global production. It can adapt to different climates, and farmers can grow it successfully even in harsh environments where other crops such as rice and corn fail. However, not all oat plants are the same. Based on their grains, two major oak varieties can easily be distinguished: hulled, grains that are covered in a non-edible husk, and naked, grains that have a soft outer casing that easily separates from the edible grain during threshing. To gain information on the origins of these different varieties, researchers in China have sequenced the genomes of over 100 oat plants from around the world. Their analyses indicate that, unlike what is the current belief — that the two varieties came from one domestication event, the hulled and naked oat were domesticated independently. The work is published in the Open Science journal GigaScience.

It is believed that the common oat (Avena sativa), which today is grown all over the world, was domesticated in Europe around 3,000 years ago. In contrast, the origins of naked oat, which today is grown mainly in China, remain unclear. Many researchers regard naked oat as a variant of hulled oat, speculating that a mutation occurred after hulled oat was introduced into China. However, new population genomic data generated and analyzed by the laboratory of Prof. Bing Han at Inner Mongolia Agricultural University (IMAU) tell a different story. 

Rather than being a variant of common oat that separated relatively recently, the authors estimate that hulled oat and naked oat diverged around 51,000 years ago. They therefore speculate that the two varieties were domesticated independently a long time ago, rather than one being a recent derivative of the other. The analyses in the study include a set of whole genome sequences, including 89 naked oat and 22 hulled oat plants, as well as four other closely related hexaploid species from around the world.

Additional findings in this study arising from a deeper analysis of this large data set support this view. For example, if naked oat split recently from hulled oat, geneticists expected to see traces of a population bottleneck in the naked oat, which would have reduced the genetic diversity in the naked oat population. However, the scientists found the opposite: in their data, the genetic diversity of naked oat is higher than that of hulled oat, not the other way around.

The overall picture emerging from the data still remains rather complex, Prof. Bing Han explains: “The breeding of naked oat in China has gone through phases, including the direct collection and utilization of landraces, cross-breeding between naked oat varieties, and cross-breeding of naked oat with hulled oat.” All of this can increase the intricacy of the findings, leaving a great deal more to discover about the genetic history of naked oat.

The findings in this work demonstrate the power of large-scale genome sequencing to better understand the domestication history of one of the major crop species that is feeding the world today.

Further Reading:

Nan J; Ling Y; An J; Wang T; Chai M; Fu J; Wang G; Yang C; Yang Y; Han: B (2023): "Genome resequencing reveals independent domestication and breeding improvement of naked oat" GigaScience;  https://doi.org/10.1093/gigascience/giad061

Article URL: https://academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/giad061

Data Availability:

Nan J; Ling Y; An J; Wang T; Chai M; Fu J; Wang G; Yang C; Yang Y; Han: B (2023): Supporting data for "Genome resequencing reveals independent domestication and breeding improvement of naked oat" GigaScience Database. http://dx.doi.org/10.5524/102412

About GigaScience

GigaScience is co-published by GigaScience Press and Oxford University Press. Winner of the 2018 PROSE award for Innovation in Journal Publishing (Multidisciplinary), the journal covers research that uses or produces 'big data' from the full spectrum of the biological and biomedical sciences. It also serves as a forum for discussing the difficulties of and unique needs for handling large-scale data from all areas of the life and medical sciences. The journal has a completely novel publication format -- one that integrates manuscript publication with complete data hosting, and analyses tool incorporation. To encourage transparent reporting of scientific research as well as enable future access and analyses, it is a requirement of manuscript submission to GigaScience that all supporting data and source code be made available in the GigaScience database, GigaDB, as well as in publicly available repositories. GigaScience will provide users access to associated online tools and workflows, and has integrated a data analysis platform, maximizing the potential utility and re-use of data.

About GigaScience Press

GigaScience Press is BGI's Open Access Publishing division, which publishes scientific journals and data. Its publishing projects are carried out with international publishing partners and infrastructure providers, including Oxford University Press and River Valley Technologies. It currently publishes two award-winning data-centric journals: its premier journal GigaScience (launched in 2012), which won the 2018 American Publishers PROSE award for innovation in journal publishing, and its new journal GigaByte (launched 2020), which won the 2022 ALPSP Award for Innovation in Publishing. The press also publishes data, software, and other research objects via its GigaDB.org database. To encourage transparent reporting of scientific research and to enable future access and analyses, it is a requirement of manuscript submission to all GigaScience Press journals that all supporting data and source code be made openly available in GigaDB or in a community approved, publicly available repository.