Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia.

High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.

Silicon application improves caryopsis development and yield in rice.

BACKGROUND: Caryopsis development consists of several processes in the production of grain yield in field crops. This study evaluated the effect of silicon (Si) on spikelet formation, spikelet fertility, and grain filling and its impact on grain yield in rice. RESULTS: Applying Si increased grain yield by 44% in Chainat 1( CNT1) and by 23% in Pathumthani 1 (PTT1). With no Si application, CNT1 had fewer total spikelets, and the fertilized and filled spikelets responded more strongly to Si than PTT1 did. Grain yield in both genotypes increased with increasing number of spikelets and filled fertilized grains. There were close relationships between Si concentration in the shoots, flag leaf, and the husk, which were positively correlated with grain yield, the number of spikelets, and fertilized and filled grains. Applying Si fertilizer also increased the expression level of Lsi6 in both CNT1 and PTT1 by 202% and 144% respectively compared with the expression of plants with no Si supplied. CONCLUSION: This study has shown how rice grain yield can be limited by Si deficiency through the spikelet formation, fertilization, and grain filling processes. Applying Si fertilizer could improve rice grain yield through increasing spikelet formation, fertilization, and grain filling, which is in parallel with Lsi6 gene expression. This information can be used for improving rice productivity by Si fertilization management. © 2020 Society of Chemical Industry.

Effect of zinc-biofortified seeds on grain yield of wheat, rice, and common bean grown in six countries.

Seeds enriched with zinc (Zn) are ususally associated with better germination, more vigorous seedlings and higher yields. However, agronomic benefits of high-Zn seeds were not studied under diverse agro-climatic field conditions. This study investigated effects of low-Zn and high- Zn seeds (biofortified by foliar Zn fertilization of maternal plants under field conditions) of wheat (Tritcum aestivum L.), rice (Oryza sativa L.), and common bean (Phaseolus vulgaris L.) on seedling density, grain yield and grain Zn concentration in 31 field locations over two years in six countries. Experimental treatments were: (1) low-Zn seeds and no soil Zn fertilization (control treatment), (2) low-Zn seeds + soil Zn fertilization, and (3) Zn-biofortified seeds and no soil Zn fertilization. The wheat experiments were established in China, India, Pakistan, and Zambia, the rice experiments in China, India and Thailand, and the common bean experiment in Brazil. When compared to the control treatment, soil Zn fertilization increased wheat grain yield in all six locations in India, two locations in Pakistan and one location in China. Zinc-biofortified seeds also increased wheat grain yield in all four locations in Pakistan and four locations in India compared to the control treatment. Across all countries over 2 years, Zn-biofortified wheat seeds increased plant population by 26.8% and grain yield by 5.37%. In rice, soil Zn fertilization increased paddy yield in all four locations in India and one location in Thailand. Across all countries, paddy yield increase was 8.2% by soil Zn fertilization and 5.3% by Zn-biofortified seeds when compared to the control treatment. In common bean, soil Zn application as well as Znbiofortified seed increased grain yield in one location in Brazil. Effects of soil Zn fertilization and high-Zn seed on grain Zn density were generally low. This study, at 31 field locations in six countries over two years, revealed that the seeds biofortfied with Zn enhanced crop productivity at many locations with different soil and environmental conditions. As high-Zn grains are a by-product of Zn biofortification, use of Zn-enriched grains as seed in the next cropping season can contribute to enhance crop productivity in a cost-effective manner.

Applying nitrogen fertilizer increased anthocyanin in vegetative shoots but not in grain of purple rice genotypes.

BACKGROUND: Anthocyanin is a major antioxidant compound in purple rice, with properties that can protect against oxidative damage in some human diseases. This study was undertaken to determine if nitrogen (N) fertilizer can enhance anthocyanin and antioxidant levels in four purple Thai rice genotypes. RESULTS: The anthocyanin concentration and antioxidant capacity were increased in the shoots of N120 plants compared with plants without N. The leaves had higher anthocyanin concentration and antioxidant capacity than the stem+leaf sheath. Maximum shoot anthocyanin concentrations occurred at tillering and then declined by 87-94% at maturity. Antioxidant capacity was high at tillering and panicle initiation and declined by 26% in leaves and by 98% in the stem+leaf sheath at maturity. Unlike in the vegetative shoot, grain anthocyanin was not affected by the addition of N fertilizer. The response of grain antioxidant capacity to N fertilizer was affected by genotype, increasing in KPY by 45% but decreasing in K19959 by 30% in N120 plants. CONCLUSION: Applying N fertilizer could be a promising way to improve the antioxidative properties in vegetative parts for use in rice-grass juice, cosmetics and other products, especially the young leaves, which contained high values of anthocyanin as well as antioxidant capacity. However, further field studies should be undertaken to optimize N utilization for anthocyanin and antioxidant capacity in purple rice genotypes. © 2018 Society of Chemical Industry.

Untapped Endophytic Colonization and Plant Growth-Promoting Potential of the Genus Novosphingobium to Optimize Rice Cultivation.

With the aim of searching for potent diazotrophic bacteria that are free of public health concerns and optimize rice cultivation, the endophytic colonization and plant growth-promoting activities of some endophytic diazotrophic bacteria isolated from rice were evaluated. Among these bacteria, the emerging diazotrophic strains of the genus Novosphingobium effectively associated with rice plant interiors and consequently promoted the growth of rice, even with the lack of a nitrogen source. These results suggest that diazotrophic Novosphingobium is an alternative microbial resource for further development as a safe biological enhancer in the optimization of organic rice cultivation.

Isolation and Characterisation of Endophytic Nitrogen Fixing Bacteria in Sugarcane.

Endophytic nitrogen fixing bacteria were isolated from the leaves, stems and roots of industrial variety (cv. U-Thong 3; UT3), wild and chewing sugarcane plants grown for 6 weeks in nitrogen (N)-free sand. Eighty nine isolates of endophytic bacteria were obtained on N-free agar. An acetylene reduction assay (ARA) detected nitrogenase activity in all 89 isolates. Three isolates from the chewing (C2HL2, C7HL1 and C34MR1) sugarcane and one isolate from the industrial sugarcane (UT3R1) varieties were characterised, and their responses to different yeast extract concentrations were investigated. Three different responses in nitrogenase activity were observed. Isolates C2HL2 and C7HL1 exhibited major increases with the addition of 0.005% yeast extract, C34MR1 exhibited no response, and UT3R1 exhibited a significant decrease in nitrogenase activity with 0.005% yeast extract. In all the isolates, nitrogenase activity decreased with further increase of the yeast extract to 0.05%. The highest nitrogenase activity was observed in isolates C2HL2 and C7HL1, which had 16S rRNA gene sequences that were closely related to Novosphingobium sediminicola and Ochrobactrum intermedium, respectively.

Responses of rice to Fe2+ in aerated and stagnant conditions: growth, root porosity and radial oxygen loss barrier.

Lowland rice (Oryza sativa L.) encounters flooded soils that are anaerobic and chemically reduced. Exposure of the roots to high soil Fe2+ concentrations can result in toxicity. Internal aeration delivering O2 to submerged roots via the aerenchyma is well understood, but the effect of Fe2+ on O2 transport in roots is less studied. We aimed to evaluate the effects of Fe2+ on growth and root aeration. O. sativa var. Amaroo was grown in aerobic and deoxygenated solutions with 0mM, 0.18mM, 0.36mM, 0.54mM or 0.72mM Fe2+ using FeSO4.7H2O and a control with 0.05mM Fe-EDTA. The treatments were imposed on 14-day-old plants (28-30 days old when harvested). Dry mass, shoot Fe concentration, root porosity and patterns of radial O2 loss (ROL) along roots were determined. In the aerobic solution, where Fe2+ was oxidised in the bulk medium, root dry mass increased with higher Fe2+; this was not the case in stagnant solutions, which had no significant root growth response, although Fe oxidation near the root surface was visible as a precipitate. In the highest Fe2+ treatment, shoot Fe concentrations in aerobic (667mgkg-1) and stagnant (433mgkg-1) solutions were below the level for toxicity (700mgkg-1). Rice responded to high Fe2+ in aerobic conditions by increasing root porosity and inducing strong barriers to ROL. In stagnant conditions, root porosity was already high and the ROL barrier induced, so these root aeration traits were not further influenced by the Fe2+ concentrations applied.

Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand.

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.

Genetic structure and isolation by distance in a landrace of Thai rice.

Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans.

Iron-fortified parboiled rice - A novel solution to high iron density in rice-based diets.

The present study pioneered an investigation of a novel and cost-effective approach to fortify Fe in rice and to greatly improve Fe nutrition in rice-based diets through parboiling, though it remains at its preliminary phase. Rice grains of seven cultivars were parboiled in deionised water containing different levels of Fe chelate made by mixing different proportions of Fe sulfate (FeSO4) with ethylenediaminetetra-acetic acid disodium salt (Na2EDTA). Adding Fe to the parboiling water resulted in an increased Fe concentration in the most grain, effectively where FeSO4 and Na2EDTA were mixed at 2:1 molar ratio (11.16g Fe per 100g raw paddy grain). This treatment resulted in Fe concentrations in white rice milled for 60s and 120s, which were 20-50 times higher than those in the unfortified milled raw rice grains. The Fe concentrations in milled rice grains were 50-150mg Fe kg(-1) in 60s milled grains with a slight reduction in 120s milled grains. Perls Prussian blue staining of the cross section of Fe-fortified parboiled rice grains suggested inward movement of added Fe into the endosperm through the apoplastic pathway in the dorsal region of the rice grain. The retention rates of fortified Fe varied among the different cultivars, possibly due to different physical-chemical properties of the grains. The percentages of soluble fraction of the total Fe were higher than 50% in all cultivars tested, indicating its high bioavailability potential, though it remains to be evaluated. The present findings provided a preliminary basis for further investigation of this innovative technique, before its adoption by parboiled rice industry, such as optimising the levels of Fe addition and industrial process and Fe bioavailability in Fe-fortified-parboiled rice.