Genetic diversity of weedy rice and its potential application as a novel source of disease resistance

Authors: OSAKINA, ARON - Washington University; Jia, Yulin

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2023
Publication Date: 8/12/2023
Citation: Osakina, A., Jia, Y. 2023. Genetic diversity of weedy rice and its potential application as a novel source of disease resistance. Plants. https://doi.org/10.3390/plants12152850.
DOI: https://doi.org/10.3390/plants12152850

Interpretive Summary: Rice (Oryza sativa L.) is one of the most important staple foods for humanity. Rice production continues to be challenged by weedy rice infestation, as weedy rice competes for nutrients, water, sunlight and other crucial vital resources with cultivated rice, thus posing a great threat to food security. Apart from reducing rice yields each year, weedy rice causes significant economic loss in rice through reduction of grain quality. Selective elimination of weedy rice from cultivated rice fields through application of herbicide has had limited success, since weedy and cultivated rice share morphological and physiological traits at earlier stages of growth. However, weedy rice has features such as seed red pericarp pigmentation and heavy shattering that distinguishes them from cultivated rice. Understanding the genetics of weedy rice is therefore essential for weed management and can be beneficial for rice protection. Molecular markers such as simple sequence repeats (SSR), restriction fragment length polymorphism (RFLP) markers and whole genome sequencing and quantitative trait loci analysis (QTL) have been used to implore the genetic diversity of weedy rice at allelic and whole genome level globally. In these previous studies it was established weedy rice genotypes around the world were not similar but showed genetic differential at whole genome level and at individual allele that control salient weedy rice traits, these alleles include R for red pericarp pigmentation, Sh4 for seed shattering and Hd1 for flowering and heading time. Furthermore, pathological studies previously performed in weedy rice showed that some weedy rice germplasms were resistant to fungal pathogens such as Magnaporthe oryzae and Rhizoctonia solani. Sequencing of these weedy rice revealed those that were resistant to M. oryzae contained genes such as Ptr and Pi-ta, while those that showed resistance to R. solani had QTLs that control plant height. This mini review therefore describes the genetic diversity in weedy rice germplasm at allele and genome level and proposes weedy rice as a novel source for developing disease resistance in cultivated rice.

Technical Abstract: Weeds that infest crop fields are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allow it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for understanding noxious agricultural weed management but can also lead to the transfer of weedy rice competitive traits to cultivated rice. Molecular Studies using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP) and whole genome sequence performed on weedy rice in different regions have shown that great genetic variations in weedy rice population globally. These variations are evident both at whole genome and at single allele level including the Sh4 that is important in shattering, the Hd1 which is crucial for Heading and flowering, and the Rc important for pericarp pigmentation. The goal of this review is to describe the genetic diversity of current weedy rice germplasm both at the whole genome and individual locus level, and their significance as novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual locus that control important traits can be of great target to rice breeders.