Genomic insights into the evolution of Echinochloa species as weed and orphan crop

Dongya Wu,Qinghong Qian,Beng-Kah Song,Yu Feng,Ying‐Xiong Qiu ,Congsong Dong ,Luan Cutti,Jie Qiu,Longbiao Guo,Michael P Timko,Feng Lin,Sangting Lao,Longjiang Fan,Huajun Chen,Xifang Weng,Aldo Merotto,Jia Lu ,Shuiguang Deng,Huabing Lu,Lihong Xie ,Qian Zhu ,Tse Seng Chuah ,Hanyang Lin ,Laura Scarabel,Wei Tang,Haiming Xu,Enhui Shen,Kenneth M Olsen,Bowen Jiang,Hirofumi Yamaguchi,Qin Yu,Chu-Yu Ye

doi:10.1038/s41467-022-28359-9

Abstract

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Highlights

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems
Herbicides are widely used for the control of barnyard grasses, which has resulted in resistance evolution to herbicides of multiple sites-of-action in many barnyard grass populations across the world[11,12,13,14]
Owing to the nature of hexaploidy, the sequence similarity among the three subgenomes severely reduced the accuracy of the chromosome scaffolding using regular Hi-C-assisted methods (Supplementary Fig. 1a)

Summary

Introduction

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Herbicides are widely used for the control of barnyard grasses, which has resulted in resistance evolution to herbicides of multiple sites-of-action in many barnyard grass populations across the world[11,12,13,14]. These mainly include resistance to the auxin mimic quinclorac and inhibitors of acetolactate synthase (ALS) (e.g., penoxsulam and bispyribac-sodium), acetyl-CoA carboxylase (ACCase) (e.g., fenoxaprop-ethyl and cyhaloprop-butyl), 5-enolpyruvylshikimate-. Owing to their highly plastic plant architecture and morphological similarities across the genus, barnyard grass species are very difficult to delimit on the basis of morphological criteria

Methods

Results

Conclusion