Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.
Mol Plant. 2023 Sep 4;16(9):1427-1444. doi: 10.1016/j.molp.2023.08.013. Epub 2023 Aug 30.
Common buckwheat (Fagopyrum esculentum) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of F. esculentum var. homotropicum, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (F. esculentum) and Tartary buckwheat (F. tataricum), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including FhFAR genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.
普通荞麦（Fagopyrum esculentum）是一种分布广泛的古老作物。由于其优异的营养价值和高经济及生态价值，普通荞麦在全球范围内变得越来越重要。高质量参考基因组序列和群体基因组数据的可用性将加速普通荞麦的育种，但由于其异交性质导致的高度杂合性极大地阻碍了基因组组装。在这里，我们报告了普通荞麦同源自交变体 F. esculentum var. homotropicum 的染色体级高质量参考基因组的组装。比较基因组学表明，两种栽培荞麦，普通荞麦（F. esculentum）和鞑靼荞麦（F. tataricum）经历了代谢组学分化和生态型分化。普通荞麦中包括 FhFAR 基因在内的几个基因家族的扩张与其分布范围比鞑靼荞麦更广有关。参与类黄酮代谢的基因的拷贝数变异与普通荞麦和鞑靼荞麦之间芦丁含量的差异有关。此外，我们基于普通荞麦 572 个品种的全基因组重测序，提供了一个全面的基因组变异图谱。群体和进化基因组学揭示了与中国和非中国栽培群体之间环境适应性和花发育相关的遗传变异。对多年农艺性状与类黄酮含量的全基因组关联分析表明，Fh05G014970 是控制异交作物产量的开花期这一关键农艺性状的潜在主要调控因子，而 Fh06G015130 是决定风味相关类黄酮的关键基因。有趣的是，我们发现 FhS-ELF3 的基因易位和序列变异导致了普通荞麦的同形自交。总之，我们的研究结果阐明了普通荞麦物种形成、生态适应、育性和独特风味的遗传基础，并为未来该具有重要经济价值作物的基因组辅助育种提供了新资源。
