Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice.

Enhancing leaf photosynthetic capacity is essential for improving the yield of rice (Oryza sativa L.). Although the exploitation of natural genetic resources is considered a promising approach to enhance photosynthetic capacity, genomic factors related to the genetic diversity of leaf photosynthetic capacity have yet to be fully elucidated due to the limitation of measurement efficiency. In this study, we aimed to identify novel genomic regions for the net CO2 assimilation rate (A) by combining genome-wide association study (GWAS) and the newly developed rapid closed gas exchange system MIC-100. Using three MIC-100 systems in the field at the vegetative stage, we measured A of 168 temperate japonica rice varieties with six replicates for three years. We found that the modern varieties exhibited higher A than the landraces, while there was no significant relationship between the release year and A among the modern varieties. Our GWAS scan revealed two major peaks located on chromosomes 4 and 8, which were repeatedly detected in the different experiments and in the generalized linear modelling approach. We suggest that high-throughput gas exchange measurements combined with GWAS is a reliable approach for understanding the genetic mechanisms underlying photosynthetic diversities in crop species.

Metabolomic analysis of rice brittle culm mutants reveals each mutant- specific metabolic pattern in each organ.

INTRODUCTION: Plant cell walls play an important role in providing physical strength and defence against abiotic stress. Rice brittle culm (bc) mutants are a strength-decreased mutant because of abnormal cell walls, and it has been reported that the causative genes of bc mutants affect cell wall composition. However, the metabolic alterations in each organ of bc mutants have remained unknown. OBJECTIVES: To evaluate the metabolic changes in rice bc mutants, comparative analysis of the primary metabolites was conducted. METHODS: The primary metabolites in leaves, internodes, and nodes of rice bc mutants and wild-type control were measured using CE- and LC-MS/MS. Multivariate analyses using metabolomic data was performed. RESULTS: We found that mutations in each bc mutant had different effects on metabolism. For example, higher oxalate content was observed in bc3 and bc1 bc3 mutants, suggesting that surplus carbon that was not used for cell wall components might be used for oxalate synthesis. In addition, common metabolic alterations such as a decrease of sugar nucleotides in nodes were found in bc1 and Bc6, in which the causative genes are involved in cellulose accumulation. CONCLUSION: These results suggest that metabolic analysis of the bc mutants could elucidate the functions of causative gene and improve the cell wall components for livestock feed or bioethanol production.

Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions.

How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Expression quantitative trait loci (eQTL) analysis is frequently used to find genomic regions underlying gene expression polymorphisms. This approach requires transcriptome data for the complete set of the QTL mapping population under the given conditions. Therefore, only a limited range of environmental conditions is covered by a conventional eQTL analysis. We sampled sparse time series of field-grown rice from chromosome segment substitution lines (CSSLs) and conducted RNA sequencing (RNA-Seq). Then, by using statistical analysis integrating meteorological data and the RNA-Seq data, we identified 1,675 eQTLs leading to polymorphisms in expression dynamics under field conditions. A genomic region on chromosome 11 influences the expression of several defense-related genes in a time-of-day- and scaled-age-dependent manner. This includes the eQTLs that possibly influence the time-of-day- and scaled-age-dependent differences in the innate immunity between Koshihikari and Takanari. Based on the eQTL and meteorological data, we successfully predicted gene expression under environments different from training environments and in rice cultivars with more complex genotypes than the CSSLs. Our novel approach of eQTL identification facilitated the understanding of the genetic architecture of expression dynamics under field conditions, which is difficult to assess by conventional eQTL studies. The prediction of expression based on eQTLs and environmental information could contribute to the understanding of plant traits under diverse field conditions.

High-yielding rice Takanari has superior photosynthetic response to a commercial rice Koshihikari under fluctuating light.

Leaves within crop canopies experience variable light over the course of a day, which greatly affects photosynthesis and crop productivity. Little is known about the mechanisms of the photosynthetic response to fluctuating light and their genetic control. Here, we examined gas exchange, metabolite levels, and chlorophyll fluorescence during the photosynthetic induction response in an Oryza sativa indica cultivar with high yield (Takanari) and a japonica cultivar with lower yield (Koshihikari). Takanari had a faster induction response to sudden increases in light intensity than Koshihikari, as demonstrated by faster increases in net CO2 assimilation rate, stomatal conductance, and electron transport rate. In a simulated light regime that mimicked a typical summer day, the faster induction response in Takanari increased daily CO2 assimilation by 10%. The faster response of Takanari was explained in part by its maintenance of a larger pool of Calvin-Benson cycle metabolites. Together, the rapid responses of electron transport rate, metabolic flux, and stomatal conductance in Takanari contributed to the greater daily carbon gain under fluctuating light typical of natural environments.

Metabolic diversity analysis and genome wide assessment of oxalate accumulation in the leaves of rice (Oryza sativa) cultivars.

Soluble oxalate accumulates in rice leaves, and it causes mineral deficiency and urinary syndrome in livestock that consume the leaves. In our previous study, we found that the oxalate content was higher in the leaves of Koshihikari (japonica type cultivar) than in those of Takanari (indica type cultivar). This difference was seen even when the two cultivars were grown under a high CO2 concentration, which inhibits oxalate synthesis via photorespiration, suggesting that the difference resulted from genetic factors rather than environmental factors. To clarify whether genetic factors affect the oxalate content of rice leaves, we measured the contents of oxalate and oxalate-related organic acids in the leaves of various rice cultivars the Rice Core Collection (WRC) and Japan Rice Core Collection (JRC) by capillary electrophoresis-mass spectrometry. Results showed that japonica type cultivars tended to accumulate more oxalate than aus or indica type cultivars. Correlation analysis revealed a positive correlation between oxalate accumulation and the citrate content, suggesting that the isocitrate pathway is involved in oxalate accumulation. On the other hand, a genome-wide association study for the oxalate content of the WRC and JRC cultivars did not reveal significant loci directly related to oxalate accumulation. This indicates that the combination of various loci may affect the oxalate contents of rice leaves.

Draft Genome Sequence of the Cyanobacterium Synechococcus sp. Strain Nb3U1.

We report the 3.5-Mb draft genome sequence of the cyanobacterium Synechococcus sp. strain Nb3U1, which was isolated from a microbial mat sample collected from Nakabusa Hot Spring, Nagano, Japan.

Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication.

Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is triggered by NopP (type III secretion system [T3SS]-dependent effector), encoded by symbiosis island A (SymA) in B. diazoefficiens USDA122. This immunity was overcome by many mutants with large SymA deletions that encompassed T3SS (rhc) and N2 fixation (nif) genes and were bounded by insertion sequence (IS) copies in direct orientation, indicating homologous recombination between ISs. Similar deletion events were observed in B. diazoefficiens USDA110 and B. japonicum J5. When we cultured a USDA122 strain with a marker gene sacB inserted into the rhc gene cluster, most sucrose-resistant mutants had deletions in nif/rhc gene clusters, similar to the mutants above. Some deletion mutants were unique to the sacB system and showed lower competitive nodulation capability, indicating that IS-mediated deletions occurred during free-living growth and the host plants selected the mutants. Among 63 natural bradyrhizobial isolates, 2 possessed long duplications (261-357 kb) harboring nif/rhc gene clusters between IS copies in direct orientation via homologous recombination. Therefore, the structures of symbiosis islands are in a state of flux via IS-mediated duplications and deletions during rhizobial saprophytic growth, and host plants select mutualistic variants from the resultant pools of rhizobial populations. Our results demonstrate that homologous recombination between direct IS copies provides a natural mechanism generating deletions and duplications on symbiosis islands.

Maintaining higher leaf photosynthesis after heading stage could promote biomass accumulation in rice.

Leaf photosynthetic rate changes across the growing season as crop plants age. Most studies of leaf photosynthesis focus on a specific growth stage, leaving the question of which pattern of photosynthetic dynamics maximizes crop productivity unanswered. Here we obtained high-frequency data of canopy leaf CO2 assimilation rate (A) of two elite rice (Oryza sativa) cultivars and 76 inbred lines across the whole growing season. The integrated A value after heading was positively associated with crop growth rate (CGR) from heading to harvest, but that before heading was not. A curve-smoothing analysis of A after heading showed that accumulated A at > 80% of its maximum (A80) was positively correlated with CGR in analyses of all lines mixed and of lines grouped by genetic background, while the maximum A and accumulated A at ≤ 80% were less strongly correlated with CGR. We also found a genomic region (~ 12.2 Mb) that may enhance both A80 and aboveground biomass at harvest. We propose that maintaining a high A after heading, rather than having high maximum A, is a potential target for enhancing rice biomass accumulation.

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons.

It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms. As a result, the landraces were found to have higher structural culm strength and greater diversity than the breeding varieties. Genetic loci associated with strong culms were identified, and it was demonstrated that haplotypes with positive effects of those loci were present in a high proportion of these landraces. These results indicated that the utilization of the strong culm-associated loci present in Japanese rice landraces may further improve the lodging resistance of modern breeding varieties that have relied on semi-dwarfism.

Rice Cultivar Takanari Has Higher Photosynthetic Performance Under Fluctuating Light Than Koshihikari, Especially Under Limited Nitrogen Supply and Elevated CO2.

Plants in the field experience dynamic changes of sunlight rather than steady-state irradiation. Therefore, increasing the photosynthetic rate of an individual leaf under fluctuating light is essential for improving crop productivity. The high-yielding indica rice (Oryza sativa L.) cultivar Takanari is considered a potential donor of photosynthesis genes because of its higher steady-state photosynthesis at both atmospheric and elevated CO2 concentrations than those of several Japanese commercial cultivars, including Koshihikari. Photosynthetic induction after a sudden increase in light intensity is faster in Takanari than in Koshihikari, but whether the daily carbon gain of Takanari outperforms that of Koshihikari under fluctuating light in the field is unclear. Here we report that Takanari has higher non-steady-state photosynthesis, especially under low nitrogen (N) supply, than Koshihikari. In a pot experiment, Takanari had greater leaf carbon gain during the initial 10 min after a sudden increase in irradiation and higher daily CO2 assimilation under simulated natural fluctuating light, at both atmospheric (400 ppm) and elevated (800 ppm) CO2 concentrations. The electron transport rate during a day under field conditions with low N supply was also higher in Takanari than in Koshihikari. Although the advantages of Takanari were diminished under high N supply, photosynthetic N use efficiency was consistently higher in Takanari than in Koshihikari, under both low and high N supply. This study demonstrates that Takanari is a promising donor parent to use in breeding programs aimed at increasing CO2 assimilation in a wide range of environments, including future higher CO2 concentrations.

Objective assessment of tumor regression in post-neoadjuvant therapy resections for pancreatic ductal adenocarcinoma: comparison of multiple tumor regression grading systems.

Neoadjuvant therapy is increasingly used to control local tumor spread and micrometastasis of pancreatic ductal adenocarcinoma (PDAC). Pathology assessments of treatment effects might predict patient outcomes after surgery. However, there are conflicting reports regarding the reproducibility and prognostic performance of commonly used tumor regression grading systems, namely College of American Pathologists (CAP) and Evans' grading system. Further, the M.D. Anderson Cancer Center group (MDA) and the Japan Pancreas Society (JPS) have introduced other grading systems, while we recently proposed a new, simple grading system based on the area of residual tumor (ART). Herein, we aimed to assess and compare the reproducibility and prognostic performance of the modified ART grading system with those of the four grading systems using a multicenter cohort. The study cohort consisted of 97 patients with PDAC who had undergone post-neoadjuvant pancreatectomy at four hospitals. All patients were treated with gemcitabine and S-1 (GS)-based chemotherapies with/without radiation. Two pathologists individually evaluated tumor regression in accordance with the CAP, Evans', JPS, MDA and ART grading systems, and interobserver concordance was compared between the five systems. The ART grading system was a 5-tiered system based on a number of 40× microscopic fields equivalent to the surface area of the largest ART. Furthermore, the final grades, which were either the concordant grades of the two observers or the majority grades, including those given by the third observer, were correlated with patient outcomes in each system. The interobserver concordance (kappa value) for Evans', CAP, MDA, JPS and ART grading systems were 0.34, 0.50, 0.65, 0.33, and 0.60, respectively. Univariate analysis showed that higher ART grades were significantly associated with shorter overall survival (p = 0.001) and recurrence-free survival (p = 0.005), while the other grading systems did not show significant association with patient outcomes. The present study revealed that the ART grading system that was designed to be simple and more objective has achieved high concordance and showed a prognostic value; thus it may be most practical for assessing tumor regression in post-neoadjuvant resections for PDAC.

A niche for cyanobacteria producing chlorophyll f within a microbial mat.

Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR). In the same mat, two ecotypes of Synechococcus and two ecotypes of Chl f-producing Leptolyngbya were detected in the upper and deeper layers, respectively. Only the Leptolyngbya strains could grow when FR was the sole light source. These results suggest that the deeper layer of the microbial mat was a habitat for Chl f-producing cyanobacteria, and Chl f enabled them to survive in a habitat with little PAR.

Temperature change affected groundwater quality in a confined marine aquifer during long-term heating and cooling.

Global warming and urbanization together with development of subsurface infrastructures (e.g. subways, shopping complexes, sewage systems, and Ground Source Heat Pump (GSHP) systems) will likely cause a rapid increase in the temperature of relatively shallow groundwater reservoirs (subsurface thermal pollution). However, potential effects of a subsurface temperature change on groundwater quality due to changed physical, chemical, and microbial processes have received little attention. We therefore investigated changes in 34 groundwater quality parameters during a 13-month enhanced-heating period, followed by 14 months of natural or enhanced cooling in a confined marine aquifer at around 17 m depth on the Saitama University campus, Japan. A full-scale GSHP test facility consisting of a 50 m deep U-tube for circulating the heat-carrying fluid and four monitoring wells at 1, 2, 5, and 10 m from the U-tube were installed, and groundwater quality was monitored every 1-2 weeks. Rapid changes in the groundwater level in the area, especially during the summer, prevented accurate analyses of temperature effects using a single-well time series. Instead, Dual-Well Analysis (DWA) was applied, comparing variations in subsurface temperature and groundwater chemical concentrations between the thermally-disturbed well and a non-affected reference well. Using the 1 m distant well (temperature increase up to 7 °C) and the 10 m distant well (non-temperature-affected), the DWA showed an approximately linear relationships for eight components (B, Si, Li, dissolved organic carbon (DOC), Mg(2+), NH4(+), Na(+), and K(+)) during the combined 27 months of heating and cooling, suggesting changes in concentration between 4% and 31% for a temperature change of 7 °C.

Selective detection and phylogenetic diversity of Acaryochloris spp. that exist in association with didemnid ascidians and sponge.

Acaryochloris spp. are unique cyanobacteria which contain chlorophyll d as the predominant pigment. The phylogenetic diversity of Acaryochloris spp. associated with 7 Prochloron- or Synechocystis-containing didemnid ascidians and 1 Synechococcus-containing sponge obtained from the coast of the Republic of Palau was analyzed; we established a PCR primer set designed to selectively amplify the partial 16S rRNA gene of Acaryochloris spp. even in DNA samples containing a large amount of other cyanobacterial and algal DNAs. Polymerase chain reaction-denaturing gradient gel electrophoresis with this primer set enabled detection of the phyogenetic diversity of Acaryochloris spp. All the ascidian and sponge samples contained Acaryochloris spp. Fourteen phylotypes that were highly homologous (98-100%) with A. marina MBIC11017 were detected, while only 2 phylotypes were detected with our previously developed method for detecting cyanobacteria. The results also revealed that many uncultured phylotypes of Acaryochloris spp. were associated with those didemnid ascidians, since a clonal culture of only 1 phylotype has been established thus far. No specific relationship was found among the Acaryochloris phylotypes and the genera of the ascidians even when sample localities were identical; therefore, these invertebrates may provide a favorable habitat for Acaryochloris spp. rather than hosts showing any specific symbiotic relationships.

Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae).

The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats.

Molecular detection of epiphytic Acaryochloris spp. on marine macroalgae.

A molecular method for detecting the epiphyte community on marine macroalgae was developed by using PCR-denaturing gradient gel electrophoresis. Selective amplification of 16S rRNA gene fragments from either cyanobacteria or algal plastids improved the detection of minor epiphytes. Two phylotypes of Acaryochloris, a chlorophyll d-containing cyanobacterium, were found not only on red macroalgae but also on green and brown macroalgae.

Preparation of refractive index matching polymer film alternative to oil for use in a portable surface-plasmon resonance phenomenon-based chemical sensor method.

In order to simplify the procedure for assembling a surface-plasmon resonance (SPR) sensor, a refractive index matching polymer film was prepared as an alternative to the conventionally used matching oil. The refractive index matching polymer film, the refractive index of which was nearly equal to the prism and sensor chip material (a cover glass) of the SPR sensor, was prepared by casting a tetrahydrofuran solution of poly (vinyl chloride) (PVC) containing equal weights of dioctyl phthalate and tricresyl phosphate. The refractive index matching polymer film was found to have a refractive index of 1.516, which is identical to that of the prism and the cover glass used for the present SPR sensor. The utility of the matching polymer film for the SPR sensor was confirmed by the detection of anti-human albumin, based on an antigen-antibody reaction.