MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO2 levels.

Improving crop yield potential through an enhanced response to rising atmospheric CO2 levels is an effective strategy for sustainable crop production in the face of climate change. Large-sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high-yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO2 levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high-yielding indica cultivar with large-sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free-air CO2 enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO2 levels. Our findings show that the moderately increased panicle number combined with large-sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO2 levels.

Alternate wetting and drying modulated physio-biochemical attributes, grain yield, quality, and aroma volatile in fragrant rice.

Alternate wetting and drying (AWD) has been recognized as a water-saving technology in rice production systems; however, pre- and post-flowering AWD could induce changes in yield, quality and aroma biosynthesis in fragrant rice. In the present study, two fragrant rice cultivars (Guixiangzhan and Nongxiang-18) were subjected to AWD till soil water potential reached -25 to -30 kPa during vegetative stage (VS), reproductive stage (RS), and both stages (VS + RS). The AWD did not affect net photosynthesis and gas exchange significantly, while malondialdehyde (MDA), H2 O2 and electrolyte leakage (EL) were higher than in control plants. The AWD treatments variably affected soluble sugars, proline and protein accumulation as well as the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), and reduced glutathione (GSH) contents. Moreover, filled grain percentage and 1000-grain weight in AWD treatments were found to be statistically similar (p > 0.05) to control, except grains panicle-1 under AWD-VS + RS that was reduced by 11% and 14% for Guixiangzhan and Nongxiang-18, respectively. On average, yield and related attributes in Guixiangzhan remained higher than in Nongxiang-18. In addition, the grain aroma volatile (2-acetyl-1-pyrroline, 2-AP) content increased by 8.79%, 14.45%, and 6.87% and 7.95%, 14.02%, and 5.04% under AWD-VS, AWD-RS, and AWD-VS + RS treatments, for Guixiangzhan and Nongxiang-18, respectively. Overall, AWD treatments, either at VS or RS, could promote rice aroma in terms of accumulation of 2AP, which might be linked with enhanced endogenous proline contents (a precursor for 2AP biosynthesis) without any severe consequences on rice yield and quality.

Laser microdissection transcriptome data derived gene regulatory networks of developing rice endosperm revealed tissue- and stage-specific regulators modulating starch metabolism.

KEY MESSAGE: Laser microdissection applied on the developing rice endosperm revealed tissue- and stage-specific regulators modulating programmed cell death and desiccation tolerance mechanisms in the central starchy endosperm following starch metabolism. Rice (Oryza sativa L.) filial seed tissues are heterozygous in its function, which accumulate distinct storage compounds spatially in starchy endosperm and aleurone. In this study, we identified the 18 tissue- and stage-specific gene co-regulons in the developing endosperm by isolating four fine tissues dorsal aleurone layer (AL), central starchy endosperm (CSE), dorsal starchy endosperm (DSE), and lateral starchy endosperm (LSE) at two developmental stages (7 days after flowering, DAF and 12DAF) using laser microdissection (LM) coupled with gene expression analysis of a 44 K microarray. The derived co-expression regulatory networks depict that distinct set of starch biosynthesis genes expressed preferentially at first in CSE at 7 DAF and extend its spatial expression to LSE and DSE by 12 DAF. Interestingly, along with the peak of starch metabolism we noticed accumulation of transcripts related to phospholipid and glycolipid metabolism in CSE during 12 DAF. The spatial distribution of starch accumulation in distinct zones of starchy endosperm contains specific transcriptional factors and hormonal-regulated genes. Genes related to programmed cell death (PCD) were specifically expressed in CSE at 12DAF, when starch accumulation was already completed in that tissue. The aleurone layer present in the outermost endosperm accumulates transcripts of lipid, tricarboxylic acid metabolism, several transporters, while starch metabolism and PCD is not pronounced. These regulatory cascades are likely to play a critical role in determining the positional fate of cells and offer novel insights into the molecular physiological mechanisms of endosperm development from early to middle storage phase.

Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content.

Enhancement of the nitrogen-fixing ability of endophytic bacteria in rice is expected to result in improved nitrogen use under low-nitrogen conditions. Endophytic nitrogen-fixing bacteria require a large amount of energy to fix atmospheric nitrogen. However, it is unknown which carbon source and bacteria would affect nitrogen-fixing activity in rice. Therefore, this study examined genotypic variations in the nitrogen-fixing ability of rice plant stem as affected by non-structural carbohydrates and endophytic bacterial flora in field-grown rice. In the field experiments, six varieties and 10 genotypes of rice were grown in 2017 and 2018 to compare the acetylene reduction activity (nitrogen-fixing activity) and non-structural carbohydrates (glucose, sucrose, and starch) concentration in their stems at the heading stage. For the bacterial flora analysis, two genes were amplified using a primer set of 16S rRNA and nitrogenase (NifH) gene-specific primers. Next, acetylene reduction activity was correlated with sugar concentration among genotypes in both years, suggesting that the levels of soluble sugars influenced stem nitrogen-fixing activity. Bacterial flora analysis also suggested the presence of common and genotype-specific bacterial flora in both 16S rRNA and nifH genes. Similarly, bacteria classified as rhizobia, such as Bradyrhizobium sp. (Alphaproteobacteria) and Paraburkholderia sp. (Betaproteobacteria), were highly abundant in all rice genotypes, suggesting that these bacteria make major contributions to the nitrogen fixation process in rice stems. Gammaproteobacteria were more abundant in CG14 as well, which showed the highest acetylene reduction activity and sugar concentration among genotypes and is also proposed to contribute to the higher amount of nitrogen-fixing activity.

Analysis of carbon flow at the metabolite level reveals that starch synthesis from hexose is a limiting factor in a high-yielding rice cultivar.

Understanding the limiting factors of grain filling is essential for the further improvement of grain yields in rice (Oryza sativa). The relatively slow grain growth of the high-yielding cultivar 'Momiroman' is not improved by increasing carbon supply, and hence low sink activity (i.e. the metabolic activity of assimilate consumption/storage in sink organs) may be a limiting factor for grain filling. However, there is no metabolic evidence to corroborate this hypothesis, partly because there is no consensus on how to define and quantify sink activity. In this study, we investigated the carbon flow at a metabolite level from photosynthesis in leaves to starch synthesis in grains of three high-yielding cultivars using the stable isotope 13C. We found that a large amount of newly fixed carbon assimilates in Momiroman was stored as hexose instead of being converted to starch. In addition, the activity of ADP-glucose pyrophosphorylase and the expression of AGPS2b, which encodes a subunit of the ADP-glucose pyrophosphorylase enzyme, were both lower in Momiroman than in the other two cultivars in grains in superior positions on panicle branches. Hence, slower starch synthesis from hexose, which is partly explained by the low expression level of AGPS2b, may be the primary metabolic reason for the lower sink activity observed in Momiroman.

Identification of Quantitative Trait Loci for the Concentrations of Phenylpropanoid Glycosides in Brown Rice.

Rice (Oryza sativa L.) is a staple food for most of the world's population, as it is eaten by nearly half of its inhabitants. Phenylpropanoid glycosides derived from plants have various biomedical effects. The comparison of the concentrations of the four major phenylpropanoid glycosides in brown rice, i.e., 6-O-feruloylsucrose (1), 3',6-di-O-sinapoylsucrose (2), 3'-O-sinapoyl-6-O-feruloylsucrose (3), and 3',6-di-O-feruloylsucrose (4), between a conventional japonica-type cultivar Koshihikari and a high-yielding indica-type cultivar Takanari revealed that they were 57-162% higher in Koshihikari than in Takanari. To identify quantitative trait loci (QTLs) for the concentrations of these compounds (1-4), reciprocal chromosome segment substitution lines derived from a cross between Koshihikari and Takanari were analyzed. We identified QTLs for the concentrations of compound 1 on chromosome 2 and of compound 2 on chromosome 4 in the reciprocal genetic background. The concentrations of these compounds were increased by the Koshihikari alleles and decreased by the Takanari alleles. Therefore, the favorable alleles of Koshihikari are available to ameliorate the lower concentrations of compounds 1 and 2 in Takanari. The combinations of QTLs identified in the present study together with those of other biologically active compounds make it possible to breed health beneficial cultivars.

QTL analysis for carbon assimilate translocation-related traits during maturity in rice (Oryza sativa L.).

Problems with carbon assimilate translocation from source organs to sink (grains) during ripening cause yield losses in rice (Oryza sativa L.), especially in high-sink-capacity varieties. We conducted a genetic analysis of traits related to such translocation by using recombinant inbred lines. Shoot weight (SW) of T65, a japonica parent, was retained from heading to late maturity, whereas that of DV85, an aus parent, was greater than that of T65 at 5 days after heading (DAH) and then decreased until 20 DAH. This difference was observed clearly under standard-fertilizer but not low-fertilizer conditions. Non-structural carbohydrate (NSC) contents in the parents showed a tendency similar to that for SW. QTL analysis revealed pleiotropic QTLs on chromosomes 5 and 10, probably by associations with heading date QTLs. A QTL associated with harvest index and NSC at 5 DAH was detected on chromosome 1. By considering the temporal changes of the traits, we found a QTL for decrease in SW on chromosome 11; the DV85 allele of this QTL facilitated assimilate translocation and suppressed biomass growth. A suggestive QTL for NSC decrease was located on chromosome 2. These QTLs could represent potential targets for controlling carbon assimilate translocation in breeding programs.

Mass-producible disposable needle-type ion-selective electrodes for plant research.

Easily mass-producible needle-type Na+ and K+ ion-selective electrodes (ISEs) were developed for the direct and indirect measurement of Na+ and K+ ion concentrations in live plants. A polyimide strip with a silver layer on one side and Ag/AgCl formed at one end was used to construct two types of ISEs. For the type I ISE, an electrolyte layer was formed on the layer of silver and Ag/AgCl, which was then covered with a protecting layer. Subsequently, an ion-selective membrane (ISM) was formed at the truncated end with Ag/AgCl. For the type II ISE, a syringe needle was used as a container and an ISM was formed at the sharp end. Then, the polyimide strip with Ag/AgCl at one end was inserted and an electrolyte solution was injected to complete the ISE. Reference electrodes (REs) with similar structures were fabricated by forming a liquid junction instead of the ISM. The electrode responses and the relationship between the ISE potential and the Na+/K+ ion concentration agreed with those predicted by the Nernst equation. The Na+ and K+ ion concentrations in different parts of the rice plant (Oryza sativa L.) were measured using the Na+ and K+ ISEs, respectively. The results obtained using these devices agreed well with those obtained using inductively coupled plasma atomic emission spectrometry, thus confirming the practical applicability of the developed ISEs.

Internal transport of CO2 from the root-zone to plant shoot is pH dependent.

We investigated the fate of carbon dioxide (CO2 ) absorbed by roots or internally produced by respiration using gas exchange and stable isotopic labeling. CO2 efflux from detached leaves supplied with bicarbonate/CO2 solutions was followed over six cycles. CO2 effluxes were detected when bicarbonate solution at high pH was used, corresponding to 71-85% of the expected efflux. No CO2 efflux was detected when CO2 solutions at low pH were used but CO2 efflux was subsequently detected as soon as bicarbonate solutions at high pH were supplied. By sealing the leaf and petiole in a plastic bag to reduce diffusion to the atmosphere, a small CO2 efflux signal (14-30% of the expected efflux) was detected suggesting that CO2 in the xylem stream can readily escape to the atmosphere before reaching the leaf. When the root-zones of intact plants were exposed to CO2 solutions, a significant efflux from leaf surface was observed (13% of the expected efflux). However, no signal was detected when roots were exposed to a high pH bicarbonate solution. Isotopic tracer experiments confirmed that CO2 supplied to the root-zone was transported through the plant and was readily lost to the atmosphere. However, little 13 C moved to the shoot when roots were exposed to bicarbonate solutions at pH 8, suggesting that bicarbonate does not pass into the xylem.

Laser Microdissection-Based Tissue-Specific Transcriptome Analysis Reveals a Novel Regulatory Network of Genes Involved in Heat-Induced Grain Chalk in Rice Endosperm.

Heat stress occurrence during seed filling leads to the formation of a chalky portion in the limited zone of the starchy endosperm of rice grains. In this study, isolation of aleurone, dorsal, central and lateral tissues of developing endosperm by laser-microdissection (LM) coupled with gene expression analysis of a 44 K microarray was performed to identify key regulatory genes involved in the formation of milky-white (MW) and white-back (WB) grains during heat stress. Gene regulatory network analysis classified the genes changed under heat stress into five modules. The most distinct expression pattern was observed in modules where most of the small heat shock proteins and cellular organization genes were changed under heat stress in dorsal aleurone cells and dorsal starchy endosperm zones. The histological observation supported the significant increase in cell number and size of dorsal aleurone cells in WB grains. With regard to the central starchy endosperm zone, preferential down-regulation of high molecular weight heat shock proteins (HMW HSPs), including a prominent member encoding endoplasmic reticulum (ER) chaperones, by heat stress was observed, while changes in expression of starch biosynthesis genes were minimal. Characterization of transgenic plants suppressing endosperm lumenal binding protein gene (BiP1), an ER chaperone preferentially down-regulated at the MW zone under heat stress, showed evidence of forming the chalky grains without disturbing the expression of starch biosynthesis genes. The present LM-based comprehensive expression analysis provides novel inferences that HMW HSPs play an important role in controlling redox, nitrogen and amino acid metabolism in endosperm leading to the formation of MW and WB chalky grains under heat stress.

Draft Genome Sequence of Burkholderia vietnamiensis Strain RS1, a Nitrogen-Fixing Endophyte Isolated from Sweet Potato.

Burkholderia vietnamiensis strain RS1 is an endophytic bacterium with nitrogen-fixing ability that was isolated from tuberous roots of sweet potato. Here, we present its draft genome of 6,542,727 bases that contains a cluster of genes associated with nitrogen fixation. This genome sequence will provide important insights into the plant growth-promoting potential of endophytic bacteria.

Detection and validation of QTLs for milky-white grains caused by high temperature during the ripening period in Japonica rice.

The occurrence of chalky rice (Oryza sativa L.) grains caused by high temperature is a serious problem in rice production. Of the several kinds of chalky grains, milky-white grains are not well analyzed. The milky-white rice grain phenomenon is caused by genetic factors as well as environmental and nutritional conditions. To analyze the genetic control system for rice grain quality, we raised recombinant inbred lines from progeny produced from 'Tsukushiroman' (high temperature sensitive) and 'Chikushi 52' (high temperature tolerant) cultivars. Quantitative trait locus (QTL) analysis revealed that the QTL on chromosome 4, linked to the simple sequence repeat marker RM16424, contributed substantially to the occurrence of milky-white grains, as it was detected over two experimental years. To validate the effect of the QTL, we developed near isogenic lines that have the 'Chikushi 52' segment on the short arm of chromosome 4 in the 'Tsukushiroman' genetic background, and that had a lower milky-white grain ratio than that of 'Tsukushiroman' when exposed to high temperatures during the ripening period. These results suggest that the 'Chikushi 52' allele on chromosome 4 suppresses the occurrence of milky-white grains and improves rice grain quality under heat stress during the grain ripening period.

Quantitative trait loci for large sink capacity enhance rice grain yield under free-air CO2 enrichment conditions.

The global atmospheric CO2 concentration has been increasing annually. To determine the trait that effectively increases rice (Oryza sativa L.) grain yield under increased atmospheric CO2 concentrations, as predicted in the near future, we grew a chromosome segment substitution line (CSSL) and a near-isogenic line (NIL) producing high spikelet numbers per panicle (CSSL-GN1 and NIL-APO1, respectively) under free-air CO2 enrichment (FACE) conditions and examined the effects of a large sink capacity on grain yield, its components, and growth-related traits under increased atmospheric CO2 concentrations. Under ambient conditions, CSSL-GN1 and NIL-APO1 exhibited a similar grain yield to Koshihikari, as a result of the trade-off between increased spikelet number and reduced grain filling. However, under FACE conditions, CSSL-GN1 and NIL-APO1 had an equal or a higher grain yield than Koshihikari because of the higher number of spikelets and lower reduction in grain filling. Thus, the improvement of source activity by increased atmospheric CO2 concentrations can lead to enhanced grain yield in rice lines that have a large sink capacity. Therefore, introducing alleles that increase sink capacity into conventional varieties represents a strategy that can be used to develop high-yielding varieties under increased atmospheric CO2 concentrations, such as those predicted in the near future.

Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice.

There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, 'Tsukushiroman' (sensitive to heat stress) and 'Chikushi 52' (tolerant of heat stress). The F7 and F8 lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from 'Chikushi 52' on chromosome 8 with the genetic background of 'Tsukushiroman', showed relatively lower ratios of white-back grains than 'Tsukushiroman'. Therefore, insertion of the 'Chikushi 52' genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions.

Laser microdissection-based gene expression analysis in the aleurone layer and starchy endosperm of developing rice caryopses in the early storage phase.

BACKGROUND: Rice endosperm is composed of aleurone cells in the outermost layers and starchy endosperm cells in the inner part. The aleurone layer accumulates lipids, whereas starchy endosperm mainly accumulates starch. During the ripening stage, the starch accumulation rate is known to be asynchronous, depending on the position of the starchy endosperm. Different physiological and molecular mechanisms are hypothesized to underlie the qualitative and quantitative differences in storage products among developing rice endosperm tissues. RESULTS: Target cells in aleurone layers and starchy endosperm were isolated by laser microdissection (LM), and RNAs were extracted from each endosperm tissue in the early storage phase. Genes important for carbohydrate metabolism in developing endosperm were analyzed using qRT-PCR, and some of the genes showed specific localization in either tissue of the endosperm. Aleurone layer-specific gene expression of a sucrose transporter, OsSUT1, suggested that the gene functions in sucrose uptake into aleurone cells. The expression levels of ADP-glucose pyrophosphorylase (AGPL2 and AGPS2b) in each endosperm tissue spatially corresponded to the distribution of starch granules differentially observed among endosperm tissues. By contrast, expressions of genes for sucrose cleavage-hexokinase, UDP-glucose pyrophosphorylase, and phosphoglucomutase-were observed in all endosperm tissues tested. Aleurone cells predominantly expressed mRNAs for the TCA cycle and oxidative phosphorylation. This finding was supported by the presence of oxygen (8 % concentration) and large numbers of mitochondria in the aleurone layers. In contrast, oxygen was absent and only a few mitochondria were observed in the starchy endosperm. Genes for carbon fixation and the GS/GOGAT cycle were expressed highly in aleurone cells compared to starchy endosperm. CONCLUSIONS: The transcript level of AGPL2 and AGPS2b encoding ADP-glucose pyrophosphorylase appears to regulate the asynchronous development of starch granules in developing caryopses. Aleurone cells appear to generate, at least partially, ATP via aerobic respiration as observed from specific expression of identified genes and large numbers of mitochondria. The LM-based expression analysis and physiological experiments provide insight into the molecular basis of the spatial and nutritional differences between rice aleurone cells and starchy endosperm cells.

qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa.

A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5-2.0 h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource.

Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines.

BACKGROUND: Increasing rice yield potential is a major objective in rice breeding programs, given the need for meeting the demands of population growth, especially in Asia. Genetic analysis using genomic information and high-yielding cultivars can facilitate understanding of the genetic mechanisms underlying rice yield potential. Chromosome segment substitution lines (CSSLs) are a powerful tool for the detection and precise mapping of quantitative trait loci (QTLs) that have both large and small effects. In addition, reciprocal CSSLs developed in both parental cultivar backgrounds may be appropriate for evaluating gene activity, as a single factor or in epistatic interactions. RESULTS: We developed reciprocal CSSLs derived from a cross between Takanari (one of the most productive indica cultivars) and a leading japonica cultivar, Koshihikari; both the cultivars were developed in Japan. Forty-one CSSLs covered most of the Takanari genome in the Koshihikari background and 39 CSSLs covered the Koshihikari genome in the Takanari background. Using the reciprocal CSSLs, we conducted yield trials under canopy conditions in paddy fields. While no CSSLs significantly exceeded the recurrent parent cultivar in yield, genetic analysis detected 48 and 47 QTLs for yield and its components in the Koshihikari and Takanari backgrounds, respectively. A number of QTLs showed a trade-off, in which the allele with increased sink-size traits (spikelet number per panicle or per square meter) was associated with decreased ripening percentage or 1000-grain weight. These results indicate that increased sink size is not sufficient to increase rice yield in both backgrounds. In addition, most QTLs were detected in either one of the two genetic backgrounds, suggesting that these loci may be under epistatic control with other gene(s). CONCLUSIONS: We demonstrated that the reciprocal CSSLs are a useful tool for understanding the genetic mechanisms underlying yield potential in the high-yielding rice cultivar Takanari. Our results suggest that sink-size QTLs in combination with QTLs for source strength or translocation capacity, as well as careful attention to epistatic interactions, are necessary for increasing rice yield. Thus, our findings provide a foundation for developing rice cultivars with higher yield potential in future breeding programs.

Deep rooting conferred by DEEPER ROOTING 1 enhances rice yield in paddy fields.

To clarify the effect of deep rooting on grain yield in rice (Oryza sativa L.) in an irrigated paddy field with or without fertilizer, we used the shallow-rooting IR64 and the deep-rooting Dro1-NIL (a near-isogenic line homozygous for the Kinandang Patong allele of DEEPER ROOTING 1 (DRO1) in the IR64 genetic background). Although total root length was similar in both lines, more roots were distributed within the lower soil layer of the paddy field in Dro1-NIL than in IR64, irrespective of fertilizer treatment. At maturity, Dro1-NIL showed approximately 10% higher grain yield than IR64, irrespective of fertilizer treatment. Higher grain yield of Dro1-NIL was mainly due to the increased 1000-kernel weight and increased percentage of ripened grains, which resulted in a higher harvest index. After heading, the uptake of nitrogen from soil and leaf nitrogen concentration were higher in Dro1-NIL than in IR64. At the mid-grain-filling stage, Dro1-NIL maintained higher cytokinin fluxes from roots to shoots than IR64. These results suggest that deep rooting by DRO1 enhances nitrogen uptake and cytokinin fluxes at late stages, resulting in better grain filling in Dro1-NIL in a paddy field in this study.

Detection and verification of QTLs associated with heat-induced quality decline of rice (Oryza sativa L.) using recombinant inbred lines and near-isogenic lines.

Decline in the apparent quality of rice (Oryza sativa L.) grain due to high temperatures during ripening recently became a major concern in many areas in Japan. The occurrence of white-back kernels (WBK) is one of the main problems of heat-induced quality decline. We identified QTLs associated with the occurrence of WBK using recombinant inbred lines (RILs) and verified their effects using near-isogenic lines (NILs). The QTL analysis used F7 and F8 RILs derived from 'Hana-echizen' (HE), which is tolerant to high temperature, × 'Niigata-wase' (NW), which is sensitive to high temperature. Four QTLs were identified on chromosomes 3, 4, 6, and 9 (qWB3, qWB4, qWB6 and qWB9). To verify the effects of qWB6 and qWB9, we developed two NILs in which qWB6 or both were introduced from HE into the NW background. The HE allele at qWB6 significantly decreased WBK under multiple environments. The combination of qWB6 and qWB9 in an F2 population derived from a cross between a NIL and NW showed that the NW allele at qWB9 significantly decreased WBK if the qWB6 allele was HE. These results will be of value in marker-assisted selection for the breeding of rice with tolerance to heat-induced quality decline.