Weedomes

Weedy rice (Oryza sativa f. spontanea Rosh.), which harbors phenotypes of both wild and domesticated rice, has become one of the most notorious weeds in rice fields worldwide (Qiu et al. 2014). Weedy rice emerged as an agricultural weed over the past 20 years, and had severe impacts for a much longer time in the regions that have relied on direct seeding for a long time, such as the United States. It has been reported that weedy rice causes an annual loss of over $50 million in southern parts of the United States (Gealy et al. 2002). The area affected by weedy rice in China exceeds three million ha, and the total crop yield has been reduced by 3.4 billion kilograms (Liang and Qiang 2011). Moreover, other crops, including jute, maize and soybean, are also influenced by weedy rice (Baki et al. 2000). The invasive success of this weed is mainly owing to its mixture of domesticated and undomesticated traits. It possesses features of undomesticated Oryza species, including seed dispersal mechanisms and seed dormancy. On the other hand, it also harbors traits of domesticated rice, such as rapid growth, and resembles domesticated rice during the seedling stage, which promotes the invasiveness in the agroecosystem (Sun et al. 2013).

Phylogenetic relationships and long-term sympatric distributions lead to biological and developmental similarities between weedy and cultivated rice (Cao et al. 2006). As a result, weedy rice becomes a very effective competitor against cultivates rice rapidly. Although multiple origins for weedy rice have been proposed, currently de-domestication from cultivated varieties has been acknowledged as one of the main routes for the origin of weedy rice all over the world (Ishikawa et al. 2005; Sun et al. 2013; Qiu et al. 2014; Song et al. 2014; Qiu et al. 2017; Li et al. 2017).

Here, we initiated an international cooperative group or consortium to focus on genetic diversity of global weedy rice via genome re-sequencing approach. We hope to shed light on the origin of weedy rice at the global level and dig out some key functional genomic regions or genes which regulate important phenotypes of weedy rice, such as pericarp color, shattering etc. It is important to elucidate the origin of weedy rice, not only we can understand the adaptive evolution of a plant taxon under human influences, but also for the effective management of this weed. Now there is still no clear definition of weedy rice and systematic descriptions of its characteristic features. Based on this global investigation, we can collect global samples and mix together as a phenotypic and genetic pool to lay the foundation for weedy rice taxonomy. Also, for field prevention and control of weedy rice, the exploration of key functioning regulatory genes will provide us with more ideas to distinguish weedy rice and cultivated rice and thus we can seek for some targeted approaches to prevent and control the rampancy of weedy rice in field, which will increase rice yield and resolve food crisis to some extent.

Baki B B, Chin D V, Mortimer M. Wild and weedy rice in rice ecosystems in Asia - A Review. International Rice Research Institute Repository, 2013.

Cao Q, Bao-Rong L U, Xia H, et al. Genetic Diversity and Origin of Weedy Rice (Oryza sativa f. spontanea) Populations Found in North-eastern China Revealed by Simple Sequence Repeat (SSR) Markers. Annals of Botany, 2006, 98(6):1241-1252.

Gealy D R, Tai T H, Sneller C H. Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Science, 2002, 50(3):333-339.

Li L F, Li Y L, Jia Y, et al. Signatures of adaptation in the weedy rice genome. Nature Genetics, 2017, 49(5):811.

Liang DY, Qiang S. Current situation and control strategy of weedy rice in China. China Plant Protection, 2011, 31:21–24 (in Chinese).

Ishikawa R, Toki N, Imai K, et al. Origin of Weedy Rice Grown in Bhutan and the Force of Genetic Diversity. Genetic Resources & Crop Evolution, 2005, 52(4):395-403.

Qiu J, Zhou Y, Mao L, et al. Genomic variation associated with local adaptation of weedy rice during de-domestication. Nature Communications, 2017, 8:15323.

Qiu J, Zhu J, Fu F, et al. Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China. Planta, 2014, 240(6):1353.

Song B, Chuah T, Tam S M, et al. Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia. Molecular Ecology, 2014, 23(20):5003-17.

Sun J, Qian Q, Ma D R, et al. Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. New Phytologist, 2013, 197(1):290.

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

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