J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (6): 1423-1441.DOI: 10.1111/jipb.13459

• Functional Omics and Systems Biology • Previous Articles     Next Articles

High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility

Qiang He1†, Dan Ma1†, Wei Li1, Longsheng Xing1, Hongyu Zhang1, Yu Wang1, Cailian Du1, Xuanzhao Li1, Zheng Jia1, Xiuxiu Li2, Jianan Liu1, Ze Liu1, Yuqing Miao1, Rui Feng1, Yang Lv1, Meijia Wang1, Hongwei Lu2,3, Xiaochen Li1, Yao Xiao1, Ruyu Wang1, Hanfei Liang1, Qinghong Zhou1, Lijun Zhang4*, Chengzhi Liang2,5* and Huilong Du1,2*   

  1. 1. School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
    2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
    3. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310000, China
    4. Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China
    5. University of Chinese Academy of Sciences, Beijing 100049, China
    These authors contributed equally to the work.
    *Correspondences:Lijun Zhang(15034054161@163.com);Chengzhi Liang(cliang@genetics.ac.cn);Huilong Du(huilongdu@hbu. edu.cn, Dr. Du is fully responsible for the distributions of all materials associated with this article)
  • Received:2022-08-02 Accepted:2023-01-20 Online:2023-01-21 Published:2023-06-01

Abstract: Common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), the two most widely cultivated buckwheat species, differ greatly in flavonoid content and reproductive mode. Here, we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb. Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat. Moreover, multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion (MATE) and chalcone synthase (CHS) underwent significant expansion in buckwheat, especially in common buckwheat. Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species. We also identified a candidate key rutin- degrading enzyme gene (Ft8.2377) that was highly expressed in Tartary buckwheat seed. In addition, we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen, which was potentially related to self-incompatibility in common buckwheat. Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and self- incompatibility in buckwheat.

Key words: buckwheat, comparative genomics, flavonoid biosynthesis, genome evolution, self-incompatibility

Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
No. 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: +86 10 6283 6133 Fax: +86 10 8259 2636 E-mail: jipb@ibcas.ac.cn
Copyright © 2022 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q