Analysis of evolutionary relationships provides new clues to the origins of weedy rice.

Bing Han,Hee‐Jong Koh,Hui Zhang,Yanjie Wang,Guilan Cao,Xiaoding Ma,Di Cui,Leiyue Geng,Longzhi Han

doi:10.1002/ece3.5948

Abstract

Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (H e = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.

Highlights

Rice (Oryza sativa L.) is one of the most important food crops worldwide because it provides daily sustenance for one-third of the world's population
Between Weedy rice (WR) and improved rice (IR), gene expression was significantly different in 130 genes; 73 genes were up-regulated and 57 were down-regulated (Figure 7b, Table S4 see Dryad upload)
There were fewer differentially expressed genes (DEGs) between the weedy and landrace rice (LR) groups than between the weedy and IR groups under the same experimental conditions, which explains why the WR collections clustered with LR in the PCA

Summary

| INTRODUCTION

Rice (Oryza sativa L.) is one of the most important food crops worldwide because it provides daily sustenance for one-third of the world's population. Wild rice and elite cultivars shaped agricultural WR evolution in Southeast Asia (Song, Chuah, Tam, & Olsen, 2014), while Qiu et al (2014) suggest that WR originated from hybridization of domesticated indica/japonica varieties based on a case study from southern China. A series of exceptional dwarf varieties were developed through hybridization with natural dwarf mutants This is the only time in the history of rice domestication that a superior landrace was cultivated at a large scale for the purposes of rice breeding. Wild rice cannot be grown in HLJ, JL, and LN provinces due to unsuitable environmental conditions For this reason, genes from wild rice cannot have been transferred into modern IR varieties via natural hybridization. Our results will provide a new perspective on the origins of WR and will allow strategies for weed control and management in rice paddy fields

| MATERIALS AND METHODS

| DISCUSSION