Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice.

Yong-Qing Zhu,Ying Wang,Jia Fang,Bao-Rong Lu,Li-Hao Pang

doi:10.3390/biology10090828

Abstract

Simple SummaryWeedy rice is a noxious weed infesting rice fields worldwide and causing tremendous losses of rice yield and quality. The control of this conspecific weed is difficult owing to abundant genetic diversity associated with its complex origins and evolution. Applying different molecular methods, we demonstrate the multiple origins of weedy rice with the major pathway from its cultivar progenitors. The origin and diversification of weedy rice are also closely associated with differentiation of indica-japonica rice varieties. In addition, novel mutations are identified, which may promote continued evolution and genetic diversity of weedy rice. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.

Highlights

Agricultural weeds post great threats to global food security because of their extensive and strong competition with cooccurring crops for resources such as water, nutrients, and solar energy [1–3]
As one of the most noxious weeds infesting rice fields worldwide, weedy rice poses great challenges for global food security by reducing the production of cultivated rice, a staple food consumed by one half of the world’s population. This conspecific weed has complex origins and abundant genetic diversity, which makes the control of weedy rice extremely difficult
We demonstrated in this study that most weedy rice had the de-domestication origins from cultivated progenitors and only a very small proportion of weedy rice had wild-introgression origins from its wild progenitor

Summary

Introduction

Agricultural weeds post great threats to global food security because of their extensive and strong competition with cooccurring crops for resources such as water, nutrients, and solar energy [1–3]. Statistical analyses by the Food and Agricultural Organization (FAO) of the United Nations indicated that yield losses caused by the infestation of weeds are much greater than the total losses of crop yields caused by diseases and insect pests [8]. Weeds encompass abundant genetic diversity and wide adaptation, which is more likely associated with their complex origins and evolutionary processes [9–11], such genetic diversity and adaptation harbored by weeds can be utilized in crop breeding as valuable germplasm [12,13]. This may be true for conspecific weeds that belong to the same species of their crops biologically [13,14]. Our knowledge of the de-domestication process is still very limited

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