Kyoto University decodes buckwheat genome and unravels the origins of a cultivated variety — Helping to solve food problems

Traditional crops such as buckwheat (grown and consumed in several regions, including Japan) and quinoa (grown in South America) are considered 'orphan crops' and have less commercial value than the three major grain crops (rice, wheat, and corn). This has meant that studies on breeding such orphan crops have not progressed. However, although these crops are inferior in energy content, they are superior in the amounts of vitamins, minerals, and other nutrients they contain, and they can even be grown on barren land. The world population is expected to reach 9.7 billion by 2050, and experts anticipate that it will be difficult to meet food demands through increased production of the three major grain crops alone, in part because of global warming and a shortage of arable land. 'Orphan crops' could help solve this problem.

Assistant Professor Yasuo Yasui of the Graduate School of Agriculture at Kyoto University, in collaboration with researchers at RIKEN, National Agriculture and Food Research Organization (NARO), Chiba University, Kyoto Prefectural University, Kazusa DNA Research Institute, Graduate University for Advanced Studies (SOKENDAI), Yunnan Agricultural University, and the University of Cambridge, have announced that they have succeeded in decoding the buckwheat genome and unraveling the origin of cultivated buckwheat. The self-fertile buckwheat variety was used to decipher the genome sequence with high precision at the chromosome level. The researchers found that buckwheat has undergone whole-genome duplication and that the current cultivated variety is closely related to the wild population in Tibet. The method used in this research study does not rely on genome editing, and its application to other orphan crops is expected to advance breeding efforts. The results were published in the 10 August 2023 issue of the international journal Nature Plants.

Buckwheat (Fagopyrum esculentum) is widely grown in Asia and Europe, creating a unique regional food culture. Most cultivated varieties are self-incompatible, which is a factor in the lack of breeding progress. In 2016, the research group was the first in the world to publish a draft (i.e., outline) genome sequence of buckwheat. However, accurate gene prediction and breeding from this information was difficult to achieve.

They selected a rare self-fertile buckwheat variety (Kyushu PL4) and used the latest genome sequencing technology to decode the entire set of chromosomes (2n=16), identifying a total of 30,608 genes. The chromosome base sequences have been confirmed to be a one-to-one match with the actual chromosomes. Next, the researchers focused on the fact that many gene pairs with similar sequences were found in the sequenced genome. By comparing the results of comparative genomic and molecular evolutionary analyses with whole-genome data from 10 other plant species, they found that whole-genome duplication had occurred twice in the common ancestor of the family Polygonaceae (which includes buckwheat) just before the Cretaceous mass extinction that occurred 65 million years ago.

To further explore the origin of the cultivated buckwheat variety, its genome was compared with those of ancestral buckwheat varieties growing wild along the borders of Yunnan, Sichuan, and the Tibet Autonomous Region in China. A population of ancestral wild species from southeastern Tibet was found to be most closely related to the cultivated variety. Chromosome 1 of the cultivated variety has the same characteristics as those of the cultivated varieties currently grown around the world. Furthermore, most grains have a chewy, mochi-like texture, whereas buckwheat does not.

In rice, the mochi-like property is caused by dysfunction of the granule-bound starch synthase (GBSS) gene. Therefore, considering that the genome had been duplicated, the researchers theorized that several GBSS genes would have to lose their function to gain the mochi-like property. Using a large-scale mutation detection system, they detected mutations in 5,801 individuals that had been treated with the mutation-inducing compound ethyl methanesulfonate (EMS).

The researchers selected buckwheat individuals deficient in either GBSS1 or GBSS2, which play a major role in granule-bound starch synthesis, and then crossed both individuals to produce offspring deficient in both genes.

Subsequently, only the individuals that had functional defects in both genes acquired the mochi-like texture. Additionally, individuals deficient in the S-LOCUS EARLY FLOWERING 3 (S-ELF3) gene, previously thought to be important for buckwheat self-incompatibility, were selected using the same method.

Common buckwheat cultivars have flowers with either a short or a long pistil on each plant and are self-incompatible; that is, an individual with short pistils cannot produce seeds with another individual with short pistils from the same cultivar, and likewise for individuals with long pistils. Selection results showed that buckwheat individuals with loss of function of the S-ELF3 gene had longer pistils and were capable of self-fertilization. The gene was found to regulate both the length of the pistil and the self-incompatibility of the short-pistil flower. The decoded buckwheat genome has been published in the database of the Kazusa DNA Research Institute.

The new buckwheat cultivar has an unprecedented texture and is currently being grown on a trial basis at the Experimental Farm at Kyoto University, with the aim of it eventually being registered as a breeding variety.

Yasui said, "We do not believe that buckwheat will solve the world's food problems, but we believe that some people will try the methods we used in this project with various crops. As a result, we expect the breeding of orphan crops, which have been abandoned but have great potential, to advance and provide the missing piece of the requisite 1.7-fold increase in food production by 2050 that cannot be achieved by the major crops alone."

Journal Information
Publication: Nature Plants
Title: Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat
DOI: 10.1038/s41477-023-01474-1