Genetic diversity in Japanese aromatic rice (Oryza sativa L.) as revealed by nuclear and organelle DNA markers

Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.     

水稻产量形成的生理生态研究进展

水稻产量形态规律是水稻育种和栽培的基础理论，已成为作物学研究的热点课题。从产量构成、光合生产和源库结构方面简介了水稻产量形成规律的生理生态研究进展，分析了3个方面的研究特点和构成产量形成过程的网络关系。同时水稻产量形成是一个动态过程，水稻产量性状的最终表现决定于其生长发育过程中众多基因的表达、调控和相互作用，提出应用现代发育遗传学与分子生态学的理论和方法，深入研究水稻产量的形成规律。     

Variation and correlation analysis of flavonoids and carotenoids in Korean pigmented rice (Oryza sativa L.) cultivars

Flavonoids and carotenoids of pigmented rice ( Oryza sativa L.), including five black cultivars and two red cultivars, from Korea were characterized to determine the diversity among the phytochemicals and to analyze the relationships among their contents. Black cultivars were higher in flavonoids and carotenoids than the red and white cultivars. The profiles of eight phytochemicals identified from the rice grains were subjected to principal component analysis (PCA) to evaluate the differences among cultivars. PCA could fully distinguish between these cultivars. The Heugjinjubyeo (BR-1) and Heugseolbyeo (BR-2) cultivars were separated from the others based on flavonoid and carotenoid concentrations. Flavonoid contents had a positive correlation with carotenoid contents among all rice grains. The BR-1 and BR-2 cultivars appear to be good candidates for future breeding programs because they have simultaneously high flavonoid and carotenoid contents.     

Uptake and metabolism of isouron in rice (Oryza sativa L.) seedlings

Summary Isouron, a pre-emergence herbicide, inhibited the growth of rice seedlings in a nutrient solution; the critical concentration was about 0.10 mg l^-1. Isotope studies showed that isouron, added to the nutrient solution, was observed by the rice roots and translocated rapidly to the shoot. In rice seedlings, isouron was converted to six known metabolites, 3-(5-(1-dimethyl-2-hydroxy-ethy)-3-isoxazolyl]urea, 3-(5-tert-butyl-3-isoxazolyl)-1-methylurea, 3-(5-tert-butyl-3-isoxazolyl)ure, 3-amino-5-tert-butylisoxazole, 3-[5-(1,1-dimethyl-2-hydroxyethyl)-3-isoxazolyl]-1-dimethylurea, and 3-[5-(1,1-dimethyl-2-hydroxyethyl)-3-isoxazolyl]-1-methylurea, and two unknown metabolites.     

Morphological and molecular evaluation of Turkish rice (Oryza sativa L.) landraces

Genetic Resources and Crop Evolution - This study was carried out to evaluate Turkish rice landraces, in 2016 and 2017. Twenty-nine morphological traits were used for morphological evolution and 10...     

Selection of efficient vesicular-arbuscular mycorrhizal fungi for wetland rice (Oryza sativa L.)

Summary We tested the response of the wetland rice cultivar Prakash to inoculation with ten vescular-arbucular mycorrhizal (VAM) fungi (three selected from the first screening and seven isolated from local paddy fields) in a pot experiment under flooded conditions in order to select the most efficient mycorrhizal fungi to inoculate the rice nursery. A sandy clay loam soil was used as the substrate, fertilized with the recommended N and K levels (100 kg N ha^–1 as ammonium sulphate and 50 kg K ha^–1 as muriate of potash) and half the recommended level of P (25 kg ha^–1 as super phosphate). The inoculation was made into dry nursery beds and the beds were flooded when the seedlings were about 25 cm high, in 15 days. Twenty-eight-day old seedlings were transferred to pots filled with well puddled soil flooded with 5 cm of standing water. Based on the increase in grain yield and total biomass, Glomus intraradices and Acaulospora sp. were considered efficient and suitable for inoculation into rice nurseries.     

籼稻2个杂种F1种子活力和劣变处理后生化性状的比较

为明确杂交稻种子在储藏过程中品种间抗老化能力的差异,采用人工老化方法研究了杂交籼稻“汕优63”F1;和“特优559”F1种子活力,比较了2品种劣变后9个生化性状的变化。结果表明：种子活力,SOD、POD、CAT、脱氢酶活性,可溶性蛋白含量随种子老化而降低,种子浸出液电导率、可溶性糖和MDA含量随种子老化增加。劣变后“特优559”的SOD、POD、CAT、脱氢酶活性降低程度及可溶性糖和MDA含量增加程度比“汕优63”低,说明“特优559”抗老化能力比“汕优63”强。SOD、POD、CAT、脱氢酶活性和可溶性蛋白含量与种子活力极显著正相关,电导率、可溶性糖、MDA含量与种子活力极显著负相关。     

Nitrogen acquisition and its relation to growth and yield in recent high-yielding cultivars of rice (Oryza sativa L.) in Japan

During the last two decades, high-yielding cultivars for multipurpose use of rice have been bred and released in Japan. Some of them have repeatedly recorded high yields of over 9?t?ha^?1 of brown rice (about 11.25?t?ha^?1 of rough rice). Here, characteristic features of nitrogen (N) acquisition and its relation to formation of yield components, dry matter production and grain yield at yield levels over 9?t?ha^?1 of brown rice in recent high-yielding cultivars, a large grain type of japonica variety, “Akita 63,” extra-panicle weight types of indica variety, “Takanari” and “Saikai 198,” and a panicle weight type of japonica variety, “Fukuhibiki,” are described as compared with those in the standard japonica cultivars, “Toyonishiki” and “Nipponbare.” The grain yield of the recent high-yielding cultivars was 9.4 to 11.6?t?ha^?1 of brown rice; that is 1.2?1.7 times greater than those of the standard cultivars. Sink capacity (1000-grain weight?×?spikelet number per unit land area) was 47?62% greater in the recent high-yielding cultivars, largely due to their 1.3?1.5 times greater N-use efficiency for sink formation (sink capacity per unit amount of total plant N in the aboveground part at maturity), although major component(s) responsible for their greater sink capacity differ among the cultivars. The ratio of grain yield to total dry matter was 1.1?1.4 times greater in the recent high-yielding cultivars than in the standard cultivars, indicating that the former efficiently translocate dry matter into spikelets during the grain-filling period. N-use efficiency for dry matter production (total dry matter per unit amount of total plant N) was comparable between “Akita 63,” “Fukuhibiki” and “Toyonishiki,” and slightly greater in “Takanari” and “Saikai 198” than in “Nipponbare.”

These results indicate that greater N-use efficiency for sink formation and efficient translocation of dry matter into spikelets contribute greatly to the high-yielding potential of the recent high-yielding cultivars.     

A retrotransposon-based probe for fingerprinting and evolutionary studies in rice (Oryza sativa)

A genomic DNA fragment (pAA7-2) amplified by a random amplified polymorphic DNA primer from the rice cultivar IR68 was used to assess the genetic variation and genetic relationships among the species of genus Oryza. A Southern hybridization experiment of diverse upland rice accessions using a single restriction enzyme HindIII generated unique DNA fingerprint for each accession. The differential hybridization pattern reflecting the copy number variation of pAA7-2 in a collection of wild species and cultivated species of rice provided insight about the genetic relationships among them. All AA genome species exhibited clear banding pattern suggesting presence of fewer copies of this sequence. Strongest hybridization signal was obtained in species belonging to BB, CC, GG, BBCC, CCDD genomes, whereas weakest hybridization signal was visible in EE, FF, and HHJJ genome species. Oryza brachyantha was the most divergent species. Clear difference in banding pattern was evident between Oryza schlechteri and Oryza coarctata belonging to HHKK genome. Although pAA7-2 had no repetitive sequences often associated with hypervariable loci, homology to a putative unclassified expressed retrotransposon distributed over several rice chromosomes was responsible for the complex banding patterns. There were more sites homologous to pAA7-2 sequence in corn and sorghum genome compared with the rice genome. The study demonstrates the potential of pAA7-2 as a powerful molecular tool for DNA fingerprinting, genetic diversity, phylogenetic, and evolutionary studies in Oryza sativa and its wild relatives and other grasses.     

Ecogeographic and genetic diversity based on morphological characters of indigenous rice (Oryza sativa L.) in Yunnan, China

Yunnan is one of the largest centres of genetic ecological diversity and the richest area for elite germplasm of rice (O. sativa L.) resources in the world. Its indigenous rice average diversity index of six ecological groups are, in turn, javanica (1.2319) > aman (1.1738) > communis (1.1726) > nuda (1.1618) > aus (1.1371) > boro (0.9889), and there are great differences between indica (1.1454) and japonica (1.2081). The indigenous rice in Yunnan can be divided into 58 varieties, almost the total number found in China, and the cultivars account for 8.6% of the total cultivars in China. A great difference in ecological diversity index of rice resources between prefectures or counties in Yunnan province also exists, with the southwest part (Lincang, Xishuangbanna, Dehong, Simao) and southeast part (Wenshan) having been found to be the largest centre of genetic diversity, as their average genetic diversity index ranges from 1.2735 to 1.2036, especially. The average diversity index of the Cangyuan, Gengma, Zhenkang, Yongde, Yingjiang, Jinghong, Menghai, Shuangjiang, Ruili, Longchuan, Mojiang, Wenshan and Guangnan counties, in particular, have an average diversity index ranging from 0.8 to1.0. On the contrary, in Diqing, Dongchuan, Kunming, Lijiang, Qujing, Chuxiong, it is comparatively low, i.e., 0.7843–1.1075. Differences in the ecological diversity index of rice resources between rice regions are small, only 1.1322 to 1.2849.     

Effect of elevated nitrogen levels on endogenous gibberellin and jasmonic acid contents of three rice (Oryza sativa L.) cultivars

Three rice (Oryza sativa L.) cultivars ( cv. Daesanbyeo, cv. Dongjinbyeo, cv. Junambyeo) were analyzed for endogenous gibberellin (GA) and jasmonic acid (JA) contents and their changes in response to elevated nitrogen (N) levels. The N fertilizer was applied in the form of urea [(NH₂)₂CO] at three rates (0, 36.8, 73.6 kg N ha^–1). Plant growth (height and dry weight) was enhanced by the first N rate but not further enhanced by the highest rate. The endogenous GA contents were analyzed through high‐performance liquid chromatography (HPLC) and gas chromatography–mass spectrometry–selected ion monitoring (GC‐MS‐SIM) while that of JA with GC‐MS‐SIM. They were analyzed one week after N application and were significantly increased with elevated N levels in all rice cultivars. The bioactive GA₁ markedly increased, but its concentration differed in different rice cultivars. Similar fluctuations were observed for endogenous GA₈, GA₁₂, GA₁₉, GA₂₀, and GA₅₃ in response to elevated N levels, showing that the rates of biosynthesis of GAs were differently affected by elevated N levels within different rice cultivars. The level of GA₂₀, a precursor of GA₁ biosynthesis, was not significantly increased, though GA₁₉, a precursor of GA₂₀, was found to be the most abundant GA type in all rice cultivars. Jasmonic acid content in the plants increased with the basic urea application (36.8 kg N ha^–1), but significantly decreased with the double urea level (73.6 kg N ha^–1). The results demonstrate that GA and JA are differentially affected in response to elevated N application in rice.     

Changing sink and source relations in rice (Oryza sativa L.) using carbon dioxide enrichment in the field

Rice plants in the field were enclosed in chambers covered with mylar film and subjected to CO² enrichment for 30 days before or after flowering. The CO² enrichment was intended to increase grain number (sink size) befiore flowering, and to increase photosynthesis of a canopy (source) after flowering.

The CO² enrichment before flowering increased grain number per unit land area and grain weight. The enrichment after flowering did not affect grain number but increased filled-grain percentage and grain weight. As a result, both treatments increased grain yield. Analysis of yield components indicates that a major factor responsible for the yield differences is grain number. It was also shown that the increase in yield was directly proportional to the dry matter increase after panicle initiation.

The CO² enrichment before flowering increased grain number per unit land area and grain weight. The enrichment after flowering did not affect grain number but increased filled-grain percentage and grain weight. As a result, both treatments increased grain yield. Analysis of yield components indicates that a major factor responsible for the yield differences is grain number. It was also shown that the increase in yield was directly proportional to the dry matter increase after panicle initiation.     

Silicon‐induced cadmium resistance in rice (Oryza sativa)

Silicon (Si)‐induced cadmium (Cd) tolerance in rice (Oryza sativa L.) was investigated by analyzing Cd uptake, growth, and physiological parameters. Silicon treatments (0.0, 0.2, or 0.6 mM) were added to 6 d–old seedlings, and Cd treatments (0.0 or 5.0 μM) were added to 20 d–old seedlings. Parameters determined included: maximum net CO₂ assimilation (A_max), stomatal conductance (g_smax), and transpiration (E_max) rates at varying intercellular CO₂ concentrations (C_i). Also measured were chlorophyll fluorescence, growth, and Cd‐uptake parameters. Results showed a Si‐induced inhibition of Cd uptake. However, 0.2 mM or 0.6 mM Si treatment concentrations did not differentially inhibit Cd uptake or differentially alleviate Cd‐induced growth inhibition, despite a significant increase in tissue Si concentration due to 0.6 mM Si treatment compared to 0.2 mM Si treatment. Additionally, photosynthesis and chlorophyll‐fluorescence analysis showed that treatment with Cd significantly inhibited photosynthetic efficiency. Interestingly, the addition of 0.2 mM Si, more so than the addition of 0.6 mM Si, significantly alleviated the inhibitory effects of Cd toxicity on photosynthesis and chlorophyll‐fluorescence parameters. Our results suggest that 0.2 mM Si could be close to an optimum Si‐dose requirement for the alleviation of toxicity symptoms mediated by moderate (5 μM) Cd exposure.     

Asymmetric warming effects on N dynamics and productivity in rice (Oryza sativa L.)

Climate warming exhibits strong diurnal variations, with higher warming rates being observed at nighttime, which significantly affects rice (Oryza sativa L.) growth and grain yield. The objective of this study was to determine the effects of asymmetric warming (all-day warming, AW; daytime warming from 07:00 to 19:00, DW; nighttime warming from 19:00 to 07:00, NW, and a control, CK) on rice nitrogen (N) dynamics and productivity. Two rice bucket warming experiments were performed in Nanjing in Jiangsu Province, China, using the free air temperature increase (FATI) technique. The daily mean temperatures in the rice canopy in the AW, DW and NW plots were 2.0, 1.1 and 1.3ºC higher than those in the rice canopy in the CK plots, respectively. The results indicated that the total N accumulation of rice was 8.27–40.53% higher in the warming treatment than in the control during the jointing, anthesis and maturity stages. However, there was no significant difference detected among the three warming treatments. The warming treatment substantially decreased N translocation efficiency, leading to the retention of more N in the plant stems during grain filling. The warming treatment also decreased the N harvest index, N utilization efficiency based on grain yield and N utilization efficiencies based on biomass in both growing seasons. The warming treatment significantly increased the aboveground biomass (9.26–16.18%) in the jointing stage but decreased it (2.75–9.63%) in the maturity stage. Although DW increased the carbon (C) gain by photosynthesis and NW increased the C loss by night respiration, the daytime higher-temperature treatment affected rice photosynthesis and reduced its photosynthetic rate and product. This effect may be one of the primary reasons for the insignificant difference in the aboveground biomass between the DW and NW treatments. In the AW, DW and NW plots, the grain yield was reduced by an average of 10.07, 5.05 and 7.89%, respectively, across both years. The effective panicles and grains per spike tended to decrease in the warmed plots, whereas irregular changes in the 1000-grain weight were observed. Our results suggest that under the anticipated climate warming, rice productivity would further decline in the Yangtze River Basin.     

Crop growth and nitrogen transformations in wheat (Triticum aestivum L.) planted after wetland rice (Oryza sativa L.)

Summary A field study was undertaken to examine the effects of various management strategies on wheat (Triticum aestivum L.) performance and N cycling in an intensively cropped soil. Microplots receiving 100 kg N ha^–1 as¹⁵NH₄ ^{+ 15}NO₃ ^– at sowing, tillering or stem elongation were compared with unfertilized microplots. Stubble from the previous rice crop was either incorporated, burnt without tillage, burnt then tilled or retained on the surface of untilled soil. Wheat grain yield ranged from 1.5 to 5.1 t ha^– and was closely related to N uptake. Plant accumulation of soil N averaged 36 kg N ha^–1 (LSD 5% = 10) on stubble-incorporation plots and 54 kg N ha^–1 on stubble-retention plots. Fertilizer N accumulation averaged 18 kg N ha^–1 (LSD 51% = 6) on stubble-incorporation plots and 50 kg N ha^–1 on stubble-retention plots. Tillage had little effect on burnt plots. Delaying N application from sowing until stem elongation increased average fertilizer N uptake from 26 to 39 kg N ha^–1 (LSD 5% = 6), but reduced soil N uptake from 50 to 37 kg N ha^– (LSD 5% = 10).Immobilization and leaching did not vary greatly between treatments and approximately one-third of the fertilizer was immobilized. Less than 1% of the fertilizer was found below a depth of 300 mm. Incorporating 9 t ha^–1 of rice stubble 13 days before wheat sowing reduced net apparent mineralization of native soil N from 37 to 3 kg ha^–1 between tillering and maturity. It also increased apparent denitrification of fertilizer N from an average 34 to 53 kg N ha^–1 (LSD 5% = 6). N loss occurred over several months, suggesting that denitrification was maintained by continued release of metabolizable carbohydrate from the decaying rice stubble. The results demonstrate that no-till systems increase crop yield and use of both fertilizer and soil N in intensive rice-based rotations.