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

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. K E Y W O R D Scomparative transcriptome analysis, genetic diversity, haplotype analysis, weedy rice

Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit

“…These cellular reactions have been documented in several cultivated plants such as barley, in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates ( Hong, Ni & Zhang, 2020 ; Qiu et al, 2020 ). Furthermore, evidence of selection of drought-resistance genes has been documented in cultivated plants such as weedy rice ( Han et al, 2022 ), cotton ( Shim, Bandillo & Angeles-Shim, 2021 ) and moth bean ( Yundaeng et al, 2019 ). Thus, the enrichment of genes found in the cultivated plants of pitahaya might be related to the response to drought.…”

“…Previous research discovered that variation in organs such as the roots and shoots of useful plants can be attributed to management for adaptation to intermittent drought ( e.g. Agave : Huang et al, 2018 ; Phaseolus : Berny Mier y Teran et al, 2019 ; Rice: Han et al, 2022 ).…”

Kam Sweet Rice (Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis

“…Sorting the peak values obtained by capillary electrophoresis. Method of molecular marker data conversion, statistical analysis, Nei’s genetic distance calculation, analysis of molecular variance (AMOVA) and population differentiation coefficient calculation refer to Han et al (2019) .…”

“…The DNA sequences of parts of six rice genes ( SKC1 , SAP8 , Pid3 , Xa23 , GS5 , and Ehd1 ) were obtained from the NCBI database, and oligonucleotide primers were designed using primer5. PCR amplifications are the same as Han et al (2019) . PCR products were Sanger sequenced, and data were retained for later analyses.…”

The complete chloroplast genome of japonica type weedy rice (Oryza sativa f. spontanea)

“…In addition, previous studies showed that the indica - japonica differentiation of de-domesticated weedy rice is closely associated with the indica - japonica differentiation of cultivated rice in genetic structure (Han, Ma, Cui, Wang, et al. 2020 ; Zhu et al. 2021 ).…”