Weedomes

The genus Echinochloa (Poaceae) includes approximately 250 annual and perennial species (Bajwa et al. 2015). Kraehmer et al. (2016) made systematic frequency assessments for rice weeds based on phytosociological studies, and found that Echinochloa species tops the most frequent rice weeds globally. Among Echinochloa species, E. crus-galli (annual, 2n = 6x = 54) (Aoki & Yamaguchi. 2008; Yabuno. 1966) is reported to be the most prevalent species which is followed by E. colona and the tetraploid E. oryzicola. (Kraehmer et al. 2016). While artificial selection for useful agronomical traits drove changes in early rice species during domestication, wild barnyardgrass in paddy fields under natural and unintentionally selections has been driven to evolve some adaptive and invasive characteristics to evade removal from rice fields. In paddy fields, E. crus-galli morphologically resembles rice (Oryza sativa) at the seedling stage, which increase the difficulty of manual weeding (Barrett el al. 1983). Nowadays, in addition, E. crus-galli is included among the most dangerous herbicide resistant weeds of the world, which has evolved both target-site and non-target-site herbicide resistance (Norsworthy et al. 2014). The losses of yield in rice due to E. crus-galli competition across the world are estimated about 35% (Oerke and Dhene. 2004).

In the absence of human intervention, the world-wide notorious weed Echinochloa crus-galli come to dominate agricultural fields and the molecular mechanism underlying its success over crops is unclear. We have sequenced the genome of E. crus-galli recently and yielded a genomic assembly of 1.2 Gb, representing 85.7% of the predicted genome size (Guo et al., 2017). Based on the genome, two biosynthetic gene clusters were found to be employed by E. crus-galli against stresses from paddy field such as rice and pathogenic fungi. Our results provide new insights on molecular mechanisms for the extreme adaptation of the weed. More important, the genome provide a good reference for Echinochloa weeds.

Here, we try to set up an international cooperative group or consortium to focus on genetic diversity of global Echinochloa weeds via genome re-sequencing approach. We hope to shed light on the genetic diversity, origin, evolution and population structures of Echinochloa weeds at the global level and figure out some key functional genomic regions or genes which regulate important phenotypes of Echinochloa weeds. It is important to estimate genetic diversity and elucidate the origin and evolution of Echinochloa weeds, not only we can understand their adaptive evolution under human influences, but also for the effective management of this weed. Based on this global investigation, we can collect global samples and mix together as a phenotypic and genetic pool to lay the foundation for the taxonomy of Echinochloa weeds, which is not clear yet. Based on the project’s results, we can seek for some targeted approaches to prevent and control the rampancy of Echinochloa weeds in field, which will increase rice yield and resolve food crisis to some extent.

Aoki, D. & Yamaguchi, H. Genetic relationship between Echinochloa crus-galli and Echinochloa oryzicola accessions inferred from internal transcribed spacer and chloroplast DNA sequences. Weed Biol. Manag. 8, 233–242 (2008).

Bajwa, A. A. et al. Eco-biology and management of Echinochloa crus-galli. Crop Prot. 75, 151–162 (2015).

Barrett, S. C. H. Crop Mimicry in Weeds. Econ. Bot. 37, 255–282 (1983).

Norsworthy, J. K., Wilson, M. J., Scott, R. C. & Gbur, E. E. Herbicidal activity on acetolactate synthase-resistant barnyardgrass (Echinochloa crus-galli) in Arkansas, USA. Weed Biol. Manag. 14, 50–58 (2014).

Guo L, Qiu J, Ye C, Jin G, Mao L, Zhang H, Yang X, Peng Q, Wang Y and Jia L, Chulong Zhang, Yonggen Lou, Qian Qian, Hirofumi Yamaguchi, Hisakazu Yamane, Chui-Hua Kong, Michael P. Timko, Lianyang Bai, Longjiang Fan. Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nature Commu. 8: 1031 (2017)

Kraehmer, H., Jabran, K., Mennan, H. & Chauhan, B. S. Global distribution of rice weeds A review. Crop Prot. 80, 73–86 (2016).

Oerke, E. C. & Dehne, H. W. Safeguarding production - losses in major crops and the role of crop protection. Crop Prot. 23, 275–285 (2004).

Yabuno, T. Biosystematic study of the genus Echinochloa. Jap. J. Bot. 19, 277–323 (1966).

Prof. Longjiang Fan

Institute of Crop Science & Institute of Bioinfromatics, Zhejiang University, China

Mobile: 0086-13738010968

E-mail: fanlj@zju.edu.cn

Lab homepage: bioinplant