Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Effects of environmental factors on the germination and seedling emergence of glyphosate‐resistant (R) and ‐susceptible (S) biotypes of Eleusine indica (L.) Gaertn. were examined under laboratory and greenhouse conditions. The R biotype exhibited a higher germination percentage compared with the S biotype at constant temperatures of 20 and 35°C under dark conditions, and alternating temperatures of 30/25°C, and 35/25°C during a 12 h photo period. For both biotypes, germination was optimal at alternating temperatures of 30/20°C and 35/20°C. However, there was no significant difference (P > 0.05) in the germination between the R and S biotypes at these temperature regimes. The germination of both biotypes was inhibited by osmotic stress imposed by a water potential of −0.80 MPa. When the moisture stress was released and the seeds were subsequently transferred to distilled water, the germination was enhanced to approximately 90% and 16% for the R and S biotype seeds, respectively. Higher emergence rates were obtained in shallow seed depths (0 or 2 cm) compared to deep depths. Emergence percentage of the R biotype was higher than that of the S biotype at 0 cm and 2 cm depths. The maximum emergence percentage of the R biotype was higher than that of S biotype when seeds were sown on the surface of either loamy or clay loam soil taken from three different sites.

Weedy rice is one of the most dominant and competitive weed species found throughout rice planting areas worldwide. In Malaysia, a combination of agricultural practices such as direct seeding and shared use of machinery has contributed to the rapid proliferation of weedy rice across paddy fields in recent decades. Here, we report on the morphological characterization of weedy rice populations and inferred origin(s) of different morphotypes present in Peninsular Malaysia. Eight weedy rice morphotypes were distinguished based on a combination of traits such as awn presence/absence and hull color, from 193 accessions collected in 17 locations. Results showed a high proportion of awnless accessions (strawhull-, intermediate strawhull-, and brownhull-colored morphotypes, together composing 65% of sampled accessions), with awned accessions represented by strawhull, brownhull, and blackhull forms. Clustering and PCA analyses revealed four major clusters: (1) O. rufipogon and the majority of awned, blackhull, and brownhull—suggestive of a type of weedy rice originating from wild Oryza populations; (2) elite indica cultivar rice and the majority of strawhull weeds—supporting a previous proposal that weedy rice from Malaysia mainly evolved from indirect selection on cultivars for easy-shattering feral forms; (3) the majority of brownhull; and (4) a mixture of other weedy morphotypes—potentially reflecting multiple origins and subsequent admixture. The combination of key morphological descriptors will be useful for advising farmers appropriately in strategies for controlling the spread of weedy rice, including periodic manual weeding to reduce buildup of the seed bank in the fields.

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