Background Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. Results We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. Conclusions We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

BACKGROUND: Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. RESULTS: We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. CONCLUSIONS: Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

The objective of this study was to evaluate the allelopathic responses of rice seedlings under submergence stress at different temperatures (10, 25, 32, and 37 °C). The results showed that a wide range of allelopathic responses of rice seedlings depended on varieties and stress conditions, with temperature was being a key factor. It showed that the extracts of rice seedlings induced significant suppression on lettuce and radish seedling germination, but had negligible allelopathic effects on growth of barnyardgrass, whilst the emergence and growth of natural weeds was stimulated. In contrast, the root exudates of Koshihikari rice seedlings (K32) at 32 °C reduced the number of total weeds by ≈60.0% and the total dry weight of weeds by 93.0%; i.e., to a greater extent than other root exudates. Among the 13 identified phenolic acids, p-hydroxybenzoic, vanillic, syringic, sinapic and benzoic acids—at concentrations of 0.360, 0.045, 3.052, 1.309 and 5.543 μg/mL might be involved in allelopathic responses of K32, inhibiting the growth of barnyardgrass and natural weeds. Findings of the present study may provide useful information on allelopathic responses of rice under environmental stresses and thus further understand of the competitive relationships between rice and weeds under natural conditions.

In recent decades, phenolic compounds derived from plants have been considered as potential weed inhibitors due to their environmentally friendly properties, which are profitable regarding sustainable development targets. While experiments indicated that phenolic compounds exhibited significant inhibition on weeds via various biological pathways, none of these natural compounds have been efficiently applied in practical agricultural production. This paper provides an overview of the phenolic allelochemicals (and their plant sources) that have been reported to have the most potential for weed growth inhibition as well as their modes of action. The biosynthetic pathway, classification, distribution, release, degradation, extraction, and isolation of these allelochemicals are also discussed. In addition, the advantages and limitations of applying these allelochemicals in weed management and sustainable agricultural development are indicated. Accordingly, there are three promising strategies to deal with the present problems and improve the effectiveness of future studies, including: (a) to discover a new approach combining phenolic allelochemicals and other prospective phytochemicals in the development of natural herbicides; (b) to modify the chemical structure for strengthening the stability and activity of the target compound; and (c) to generate resistant crops against weed stress related to the proliferation of phenolic allelochemicals through genetic engineering approaches. Conceivably, the information on phenolic allelochemicals that is assembled in this paper may provide a useful dataset for future studies on the application of artificial intelligence in the design and production of efficient natural herbicides for weed management and sustainable agricultural development.

Analysis of genetic diversity of 90 Vietnamese local-colored rice accessions was evaluated by using 40 SSR markers. The numbers of polymorphic alleles ranged from 3 to 12 alleles per locus and average of 7.1 alleles per locus. The similarity coefficients of the rice landraces fluctuated from 0.76 to 0.93; at a genetic correlation level of 0.78. Ninety accessions of rice landraces were divided into five groups based on analysis of genetic relationships. The results have indicated that 11 markers included: M250, RM302, RM10926, RM208, RM227, RM17231, RM23251, RM5647, RM1376, RM339 and RM228 which gave the unique allele. These markers can be used effectively for genetic diversity of colored rice and provided a specific database and useful materials for landraces identification, local germplasm conservation for further colored rice improvement on rice quality via rice breeding programs in Vietnam.