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Dryad

Data from: Analysis of evolutionary relationships provides new clues to the origins of weedy rice

Data files

Dec 01, 2019 version files 4.90 MB

Abstract

Weedy rice (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 weedy rice, landrace rice, improved rice 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 weedy rice populations have the highest level of genetic diversity (He=0.8386), and can be divided into two groups (japonica-type and indica-type). The japonica-type weedy rice accessions from HLJ, JL, LN, and NX provinces clustered with the landraces grown in these same provinces. The indica-types from JS province also clustered with the indica-type landraces from JS province. Comparative transcriptome analysis of weedy rice populations, improved rice populations. and landrace rice from HLJ, JL and LN provinces showed that the weedy rice still clustered with the landrace rice, and that the improved rice lines comprise a single population. Thirty-two differentially expressed genes were shared by the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Using GO analysis, we identified 19 shared GO terms in the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Our results suggest that weedy rice populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN  suggests that improved rice populations have become a medium or end point in the evolution of weedy rice, which provides a new perspective for the study of weedy rice origins and lays a solid foundation for rice breeding.