New advances in the comparative genome resolution of buckwheat and its closely related wild species, golden buckwheat

Buckwheat, a genus of buckwheat (Fagopyrum Mill) in the family Polygonaceae, is an important cereal crop that originated in China, with a short reproductive life, adaptability, tolerance to infertile, balanced nutrition and rich in active ingredients such as rutin, which is an important health food for people with diabetes and three highs. Buckwheat is widely distributed around the world, but also in China's arid, high-altitude poor mountainous areas and Yi and other minorities of important food crops and disaster relief and leisure crops. Buckwheat flowers are large and bright and long cycle, but also rural tourism and tourism, multi-product integration and the development of recreation industry is an indispensable and important carrier.

The genus buckwheat is widely cultivated as a food crop, including annual buckwheat (Fagopyrum tataricum) and sweet buckwheat (F. esculentum), and as a medicinal perennial golden buckwheat (F. dibotrys or F. cymosum). Buckwheat is a traditional medicinal plant with antibacterial, anti-inflammatory, cancer-preventing and anti-tumour properties, and is a key ingredient in medicines such as rush syrup, golden buckwheat flakes and Weimaranin. Golden buckwheat is a wild relative of buckwheat, but the two agronomic traits differ significantly, for example, compared with buckwheat, golden buckwheat with large seeds and rutin and other active ingredients more abundant, underground expansion of the stem, long flowering period, cold tolerance and other characteristics, and golden buckwheat is also considered to be an important distant hybrid material for genetic improvement of buckwheat. In terms of use, golden buckwheat is mainly used as a medicinal and forage, buckwheat is mainly used as food and functional food, resulting in the genetic mechanism of the divergence between the two is not clear. In order to fully exploit the excellent genetic resources of golden buckwheat and to accelerate the identification of buckwheat-golden buckwheat hybrid progeny of excellent material, it is necessary to carry out comparative genomic studies of golden buckwheat and buckwheat.

Recently, Zhou Meiliang's team at the Institute of Crop Science, Chinese Academy of Agricultural Sciences, published an online paper in New phytologist entitled "Comparison of buckwheat genomes reveals the genetic basis of metabolomic divergence and ecotype differentiation". The paper, entitled "Comparison of buckwheat genomes reveals the genetic basis of metabolomic divergence and ecotype differentiation", reveals the important reasons for the differences between buckwheat and buckwheat traits at the genomic level, as well as a preliminary delineation and comparison of buckwheat ecotypes.

A diploid buckwheat genome of 1.08 G in size was assembled based on diploid-trisgenic and Hi-C techniques, and 38,919 protein-coding genes were annotated. Comparison with the buckwheat genome revealed that the golden buckwheat genome was twice the size of the buckwheat genome (0.48G), mainly due to amplification of repetitive sequences. It was found that there are two large inversions on chromosomes 3 and 4, and the genes are closely related to metabolism, cell wall formation and root morphogenesis, which are presumed to be related to the unique quality and agronomic traits of golden buckwheat. Genomic evolutionary analysis found that golden buckwheat and buckwheat have diverged in recent times, and that genes associated with metabolism in golden buckwheat have been strongly selected for.

In the study, the underground expanded stems and roots of golden buckwheat and buckwheat roots were selected for metabolomic analysis, and it was found that golden buckwheat contained much higher levels of catechins, proanthocyanidins, rutin, quercetin and other flavonoids than buckwheat, which is an important reason why golden buckwheat can be used for medicinal purposes. The genomic level further revealed an amplification of flavonoid synthesis-related genes in buckwheat, especially the FdCHI, FdF3H, FdDFR and FdLAR gene families. In addition, the team collected 34 diploid wild buckwheat from the Yunnan-Guizhou plateau in both the upright and oblique ecotypes and evaluated the traits, finding that the agronomic traits of the upright ecotype were better than those of the oblique ecotype, while the quality traits of the oblique ecotype were better than those of the upright ecotype. To investigate the genetic mechanisms underlying the divergence of traits between the two ecotypes, the team resequenced these samples and calculated the genetic divergence coefficients between them, uncovering a series of genes associated with quality and agronomic traits, including FdMYB44 and FdCRF4. The research laid the theoretical foundation for trait improvement and quality breeding of golden buckwheat, as well as for molecular breeding of interspecific crosses between buckwheat and golden buckwheat.

Ming He (now an assistant researcher at the Institute of Vegetable and Flower Research, Chinese Academy of Agricultural Sciences), Yuqi He (a postdoctoral fellow), Kaixuan Zhang (an associate researcher), Xiang Lu (a PhD student) and Xuemei Zhang (a PhD student) were the first authors of the paper, and Meiliang Zhou was the corresponding author. Wang Junzhen, Senior Agronomist, Institute of Alpine Agriculture, Liangshan Yi Autonomous Prefecture, Sichuan Province; Professor Tang Yu, Sichuan Institute of Tourism; Professors Cheng Jianping and Ruan Jinjun, Guizhou University; Dr Ehsan Dulloo and Professor Zhang Zongwen, International Biodiversity Centre; Professor Yan Mingli, Institute of Crop Research, Hunan Academy of Agricultural Sciences; Professor Mark A. Chapman, Director, Centre for Mixed Crop Research, University of Southampton, UK; and Professor Milton M. Chapman, Bulgarian Academy of Sciences. Professor Chapman and Professor Milen I. Georgiev of the Bulgarian Academy of Sciences were also involved in the research. The research is supported by the National Key R&D Programme - Efficient Breeding Technology and Variety Creation for Dicotyledonous Grains, the EU Horizon 2020 project, and the National Natural Science Foundation of China Key International Cooperation Project.