Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations.

The improvement of leaf net photosynthetic rate (An) is a major challenge in enhancing crop productivity. However, the genetic control of An among natural genetic accessions is still poorly understood. The high-yielding indica cultivar Takanari has the highest An of all rice cultivars, 20-30% higher than that of the high-quality japonica cultivar Koshihikari. By using reciprocal backcross inbred lines and chromosome segment substitution lines derived from a cross between Takanari and Koshihikari, we identified three quantitative trait loci (QTLs) where the Takanari alleles enhanced An in plants with a Koshihikari genetic background and five QTLs where the Koshihikari alleles enhanced An in plants with a Takanari genetic background. Two QTLs were expressed in plants with both backgrounds (type I QTL). The expression of other QTLs depended strongly on genetic background (type II QTL). These beneficial alleles increased stomatal conductance, the initial slope of An versus intercellular CO2 concentration, or An at CO2 saturation. Pyramiding of these alleles consistently increased An. Some alleles positively affected biomass production and grain yield. These alleles associated with photosynthesis and yield can be a valuable tool in rice breeding programs via DNA marker-assisted selection.

QTLs maintaining grain fertility under salt stress detected by exome QTL-seq and interval mapping in barley.

Enhancing salt stress tolerance is a key strategy for increasing global food production. We previously found that long-term salinity stress significantly reduced grain fertility in the salt-sensitive barley (Hordeum vulgare) accession, 'OUC613', but not in the salt-tolerant accession, 'OUE812', resulting in large differences in grain yield. Here, we examined the underlying causes of the difference in grain fertility between these accessions under long-term treatment with 150 or 200 mM NaCl from the seedling stage to harvest and identified quantitative trait loci (QTLs) for maintaining grain fertility. In an artificial pollination experiment of the two accessions, grain fertility was significantly reduced only in OUC613 plants produced using pollen from plants grown under NaCl stress, suggesting that the low grain fertility of OUC613 was mainly due to reduced pollen fertility. Using QTL-seq combined with exome-capture sequencing and composite interval mapping of recombinant inbred lines derived from a cross between OUE812 and OUC613, we identified a QTL (qRP-2Hb) for grain fertility on chromosome 2H. The QTL region includes two genes encoding an F-box protein and a TIFY protein that are associated with male sterility, highlighting the importance of this region for maintaining grain fertility under salt stress.

Leaf photosynthetic rate and mesophyll cell anatomy changes during ontogenesis in backcrossed indica × japonica rice inbred lines.

The high-yielding indica rice variety, 'Takanari', has the high rate of leaf photosynthesis compared with the commercial japonica varieties. Among backcrossed inbred lines from a cross between 'Takanari' and a japonica variety, 'Koshihikari', two lines, BTK-a and BTK-b, showed approximately 20% higher photosynthetic rate than that of 'Takanari' for a flag leaf at full heading. This is a highest recorded rate of rice leaf photosynthesis. Here, the timing and cause of the increased leaf photosynthesis in the BTK lines were investigated by examining the photosynthesis and related parameters, as well as mesophyll cell anatomy during ontogenesis. Their photosynthetic rate was greater than that of 'Takanari' in the 13th leaf, as well as the flag leaf, but there were no differences in the 7th and 10th leaves. There were no consistent differences in the stomatal conductance, or the leaf nitrogen and Rubisco contents in the 13th and flag leaves. The total surface area of mesophyll cells per leaf area (TAmes) in the 13th and flag leaves increased significantly in the BTK lines due to the increased number and developed lobes of mesophyll cells compared with in 'Takanari'. The mesophyll conductance (g m) became greater in the BTK lines compared with 'Takanari' in the flag leaves but not in the 10th leaves. A close correlation was observed between TAmes and g m. We concluded that the increased mesophyll conductance through the development of mesophyll cells during the reproductive period is a probable cause of the greater photosynthetic rate in the BTK lines.

Time course of programmed cell death, which included autophagic features, in hybrid tobacco cells expressing hybrid lethality.

KEY MESSAGE: PCD with features of vacuolar cell death including autophagy-related features were detected in hybrid tobacco cells, and detailed time course of features of vacuolar cell death were established. A type of interspecific Nicotiana hybrid, Nicotiana suaveolens × N. tabacum exhibits temperature-sensitive lethality. This lethality results from programmed cell death (PCD) in hybrid seedlings, but this PCD occurs only in seedlings and suspension-cultured cells grown at 28 °C, not those grown at 36 °C. Plant PCD can be classified as vacuolar cell death or necrotic cell death. Induction of autophagy, vacuolar membrane collapse and actin disorganization are each known features of vacuolar cell death, but observed cases of PCD showing all these features simultaneously are rare. In this study, these features of vacuolar cell death were evident in hybrid tobacco cells expressing hybrid lethality. Ion leakage, plasma membrane disruption, increased activity of vacuolar processing enzyme, vacuolar membrane collapse, and formation of punctate F-actin foci were each evident in these cells. Transmission electron microscopy revealed that macroautophagic structures formed and tonoplasts ruptured in these cells. The number of cells that contained monodansylcadaverine (MDC)-stained structures and the abundance of nine autophagy-related gene transcripts increased just before cell death at 28 °C; these features were not evident at 36 °C. We assessed whether an autophagic inhibitor, wortmannin (WM), influenced lethality in hybrid cells. After the hybrid cell began to die, WM suppressed increases in ion leakage and cell deaths, and it decreased the number of cells containing MDC-stained structures. These results showed that several features indicative of autophagy and vacuolar cell death were evident in the hybrid tobacco cells subject to lethality. In addition, we documented a detailed time course of these vacuolar cell death features.

Accumulation of long-lived mRNAs associated with germination in embryos during seed development of rice.

Mature dry seeds contain translatable mRNAs called long-lived mRNAs. Early studies have shown that protein synthesis during the initial phase of seed germination occurs from long-lived mRNAs, without de novo transcription. However, the gene expression systems that generate long-lived mRNAs in seeds are not well understood. To examine the accumulation of long-lived mRNAs in developing rice embryos, germination tests using the transcriptional inhibitor actinomycin D (Act D) were performed with the Japonica rice cultivar Nipponbare. Although over 70% of embryos at 10 days after flowering (DAF) germinated in the absence of the inhibitor, germination was remarkably impaired in embryos treated with Act D. In contrast, more than 70% of embryos at 20, 25, 30 and 40 DAF germinated in the presence of Act D. The same results were obtained when another cultivar, Koshihikari, was used, indicating that the long-lived mRNAs required for germination predominantly accumulate in embryos between 10 and 20 DAF during seed development. RNA-Seq identified 529 long-lived mRNA candidates, encoding proteins such as ABA, calcium ion and phospholipid signalling-related proteins, and HSP DNA J, increased from 10 to 20 DAF and were highly abundant in 40 DAF embryos of Nipponbare and Koshihikari. We also revealed that these long-lived mRNA candidates are clearly up-regulated in 10 DAF germinating embryos after imbibition, suggesting that the accumulation of these mRNAs in embryos is indispensable for the induction of germination. The findings presented here may facilitate in overcoming irregular seed germination or producing more vigorous seedlings.

Introgression of two chromosome regions for leaf photosynthesis from an indica rice into the genetic background of a japonica rice.

Increases in rates of individual leaf photosynthesis (P n) are critical for future increases of rice yields. A previous study, using introgression lines derived from a cross between indica cultivar Habataki, with one of the highest recorded values of P n, and the Japanese elite cultivar Koshihikari, identified four QTLs (qCAR4, qCAR5, qCAR8, and qCAR11) that affect P n. The present study examined the combined effect of qCAR4 and qCAR8 on P n in the genetic background of Koshihikari. The pyramided near-isogenic line NIL(qCAR4+qCAR8) showed higher P n than both NIL(qCAR4) and NIL(qCAR8), equivalent to that of Habataki despite being due to only two out of the four QTLs. The high P n of NIL(qCAR4+qCAR8) may be attributable to the high leaf nitrogen content, which may have been inherited from NIL(qCAR4), to the large hydraulic conductance due to the large root surface area from NIL(qCAR4), and to the high hydraulic conductivity from NIL(qCAR8). It might be also attributable to high mesophyll conductance, which may have been inherited from NIL(qCAR4). The induction of mesophyll conductance and the high leaf nitrogen content and high hydraulic conductivity could not be explained in isolation from the Koshihikari background. These results suggest that QTL pyramiding is a useful approach in rice breeding aimed at increasing P n.

The mesophyll anatomy enhancing CO2 diffusion is a key trait for improving rice photosynthesis.

Increases in rates of individual leaf photosynthesis (P(n)) are critical for future increases in yields of rice plants. Although many efforts have been made to improve rice P(n) with transgenic technology, the desired increases in P(n) have not yet been achieved. Two rice lines with extremely high values of P(n) were identified among the backcrossed inbred lines derived from the indica variety Takanari, one of the most productive varieties in Japan, and the elite japonica variety Koshihikari (Koshihikari/Takanari//Takanari). The P(n) values of the two lines at an ambient CO(2) concentration of 370µmol mol(-1) as well as at a saturating concentration of CO(2) were 20-50% higher than those of the parental varieties. Compared with Takanari, these lines had neither a higher content nor a higher activity of ribulose 1,5-bisphosphate carboxylase/oxygenase when the leaf nitrogen contents were similar, but they did have high mesophyll conductance with respect to CO(2) flux due to their higher density and more highly developed lobes of mesophyll cells. These lines also had higher electron transport rates. The plant growth rates of these lines were higher than that of Takanari. The findings show that it is possible to increase P(n) significantly, both at the current atmospheric concentration of CO(2) and at the increased concentration of CO(2) expected in the future, using appropriate combinations of genetic resources that are available at present.

RNA-binding proteins associated with desiccation during seed development in rice.

Long-lived mRNAs stored in mature seeds can remain active for long periods even if seeds undergo severe desiccation. They are then translated at the initiation of germination. To clarify the mechanism for stabilization of long-lived mRNAs during seed desiccation, fluctuations in RNA-binding protein (RBP) profiles that occur during seed formation in rice were analyzed. Proteomic analysis revealed that glycine-rich RBP 1A (GRP1A) is a highly abundant RBP in mature rice seeds. In addition, real-time RT-PCR analysis showed that putative RBP RZ-1A (RZ-1A) is seed specific. Moreover, transcripts of these two RBPs were clearly up-regulated during desiccation in rice seeds. The features of these two RBPs resemble those of late embryogenesis abundant proteins that function as molecular chaperones in dry seeds. Therefore, GRP1A and RZ-1A may have important roles in the stability of long-lived mRNAs in rice seeds.

Proteomic analysis of embryonic proteins synthesized from long-lived mRNAs during germination of rice seeds.

Dry seeds contain translatable, long-lived mRNAs that are stored during seed maturation. Early studies using transcriptional inhibitors supported the view that protein synthesis during the initial phase of germination occurs on long-lived mRNA templates. Rice seeds were treated with the transcriptional inhibitor actinomycin D (Act D), and the embryonic proteins translated from long-lived mRNAs during germination were identified using a proteomic analysis. De novo transcription was not required for germination of rice seeds, since >80% of seeds germinated when transcription was prevented by treatment with Act D. In contrast, germination was completely inhibited in the presence of cycloheximide, an inhibitor of translation. Thus, de novo protein synthesis is necessary for germination of rice seeds. The proteomic analysis revealed that 20 proteins are up-regulated during germination, even after Act D treatment. Many of the up-regulated proteins are involved in carbohydrate metabolism and cytoskeleton formation. These results indicate that some of the germination-specific proteins involved in energy production and maintenance of cell structure in rice seeds are synthesized from long-lived mRNAs. The timing of translation of eight up-regulated proteins was clearly later than that of the other up-regulated proteins under conditions in which transcription was inhibited by Act D, suggesting that translation of long-lived mRNAs in rice seeds is regulated according to the germination phase.

Hydraulic conductance as well as nitrogen accumulation plays a role in the higher rate of leaf photosynthesis of the most productive variety of rice in Japan.

An indica variety Takanari is known as one of the most productive rice varieties in Japan and consistently produces 20-30% heavier dry matter during ripening than Japanese commercial varieties in the field. The higher rate of photosynthesis of individual leaves during ripening has been recognized in Takanari. By using pot-grown plants under conditions of minimal mutual shading, it was confirmed that the higher rate of leaf photosynthesis is responsible for the higher dry matter production after heading in Takanari as compared with a japonica variety, Koshihikari. The rate of leaf photosynthesis and shoot dry weight became larger in Takanari after the panicle formation and heading stages, respectively, than in Koshihikari. Roots grew rapidly in the panicle formation stage until heading in Takanari compared with Koshihikari. The higher rate of leaf photosynthesis in Takanari resulted not only from the higher content of leaf nitrogen, which was caused by its elevated capacity for nitrogen accumulation, but also from higher stomatal conductance. When measured under light-saturated conditions, stomatal conductance was already decreased due to the reduction in leaf water potential in Koshihikari even under conditions of a relatively small difference in leaf-air vapour pressure difference. In contrast, the higher stomatal conductance was supported by the maintenance of higher leaf water potential through the higher hydraulic conductance in Takanari with the larger area of root surface. However, no increase in root hydraulic conductivity was expected in Takanari. The larger root surface area of Takanari might be a target trait in future rice breeding for increasing dry matter production.

Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves.

DNA marker-assisted selection appears to be a promising strategy for improving rates of leaf photosynthesis in rice. The rate of leaf photosynthesis was significantly higher in a high-yielding indica variety, Habataki, than in the most popular Japanese variety, Koshihikari, at the full heading stage as a result of the higher level of leaf nitrogen at the same rate of application of nitrogen and the higher stomatal conductance even when the respective levels of leaf nitrogen were the same. The higher leaf nitrogen content of Habataki was caused by the greater accumulation of nitrogen by plants. The higher stomatal conductance of Habataki was caused by the higher hydraulic conductance. Using progeny populations and selected lines derived from a cross between Koshihikari and Habataki, it was possible to identify the genomic regions responsible for the rate of photosynthesis within a 2.1 Mb region between RM17459 and RM17552 and within a 1.2 Mb region between RM6999 and RM22529 on the long arm of chromosome 4 and on the short arm of chromosome 8, respectively. The designated region on chromosome 4 of Habataki was responsible for both the increase in the nitrogen content of leaves and hydraulic conductance in the plant by increasing the root surface area. The designated region on chromosome 8 of Habataki was responsible for the increase in hydraulic conductance by increasing the root hydraulic conductivity. The results suggest that it may be possible to improve photosynthesis in rice leaves by marker-assisted selection that focuses on these regions of chromosomes 4 and 8.

Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines.

BACKGROUND AND AIMS: The rate of photosynthesis in paddy rice often decreases at noon on sunny days because of water stress, even under submerged conditions. Maintenance of higher rates of photosynthesis during the day might improve both yield and dry matter production in paddy rice. A high-yielding indica variety, 'Habataki', maintains a high rate of leaf photosynthesis during the daytime because of the higher hydraulic conductance from roots to leaves than in the standard japonica variety 'Sasanishiki'. This research was conducted to characterize the trait responsible for the higher hydraulic conductance in 'Habataki' and identified a chromosome region for the high hydraulic conductance. METHODS: Hydraulic conductance to passive water transport and to osmotic water transport was determined for plants under intense transpiration and for plants without transpiration, respectively. The varietal difference in hydraulic conductance was examined with respect to root surface area and hydraulic conductivity (hydraulic conductance per root surface area, L(p)). To identify the chromosome region responsible for higher hydraulic conductance, chromosome segment substitution lines (CSSLs) derived from a cross between 'Sasanishiki' and 'Habataki' were used. KEY RESULTS: The significantly higher hydraulic conductance resulted from the larger root surface area not from L(p) in 'Habataki'. A chromosome region associated with the elevated hydraulic conductance was detected between RM3916 and RM2431 on the long arm of chromosome 4. The CSSL, in which this region was substituted with the 'Habataki' chromosome segment in the 'Sasanishiki' background, had a larger root mass than 'Sasanishiki'. CONCLUSIONS: The trait for increasing plant hydraulic conductance and, therefore, maintaining the higher rate of leaf photosynthesis under the conditions of intense transpiration in 'Habataki' was identified, and it was estimated that there is at least one chromosome region for the trait located on chromosome 4.

Proteomic analysis of RNA-binding proteins in dry seeds of rice after fractionation by ssDNA affinity column chromatography.

In proteomic analysis, one of the major limitations is the detection of low-abundance proteins. To detect low-abundance RNA-binding proteins in mature dry seeds of rice, fractionation by single stranded DNA (ssDNA) affinity column chromatography was carried out before analysis by two-dimensional gel electrophoresis (2-DE). Proteomic analysis of the ssDNA-binding fraction revealed the existence of three types of RNA-binding proteins, including a K homology (KH) domain containing protein, a putative RNA-binding protein and a glycine-rich RNA-binding protein, in mature seeds. In addition, decreases in the putative RNA-binding protein and glycine-rich RNA-binding protein after absorbing water in seeds appear to be associated with seed germination.

Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines.

BACKGROUND: In cereal crops, stem lodging can be classified into two types: stem-breaking type and stem-bending type. To improve stem-lodging resistance, the strong culm traits of superior lodging-resistant varieties must be characterized. The identification of quantitative trait loci (QTLs) and the corresponding genes associated with the parameters for bending moment at breaking (M) and flexural rigidity (FR) is expected to enable the efficient development of lodging-resistant varieties. A set of Chromosome Segment Substitution Lines (CSSLs) derived from the cross between Takanari and Koshihikari were used in this study to identify QTLs associated with lodging resistance. RESULTS: The indica variety Takanari possesses large M due to its large section modulus (SM) despite its small bending stress (BS), whereas Takanari also has large FR due to its large secondary moment of inertia (SMI) and Young's modulus (YM). The QTLs for BS were assigned to chromosomes 3, 5, 6, 8, 9, 10, 11, and 12. Koshihikari alleles increased BS in these QTLs. The YM was increased by substitution of the Koshihikari chromosomal segments on chromosomes 2, 10, and 11. Other QTLs mapped to chromosomes 7 and 12, such that the Koshihikari alleles contributed to the decrease of YM. QTLs for cellulose density were assigned to chromosomes 1, 3, and 5, which were replaced by substitutions of Koshihikari segments. The QTLs for hemicellulose, cellulose, and holocellulose densities identified on chromosome 5 overlapped with those for BS, indicating the positive effect of the Koshihikari segment on increasing BS. CONCLUSIONS: These results suggested that the QTLs for the densities of cell wall materials in japonica varieties contributed to increased BS and might be utilized for improving lodging resistance in indica varieties of rice.

Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice.

Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Oryza sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar. Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT-box-binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops.

Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance.

Dry matter production of crops is determined by how much light they intercept and how efficiently they use it for carbon fixation; i.e., photosynthesis. The high-yielding rice cultivar, Akenohoshi, maintains a high photosynthetic rate in the middle of the day owing to its high hydraulic conductance in comparison with the elite commercial rice cultivar, Koshihikari. We developed 94 recombinant inbred lines derived from Akenohoshi and Koshihikari and measured their exudation rate to calculate hydraulic conductance to osmotic water transport in a paddy field. A quantitative trait locus (QTL) for exudation rate was detected on the long arm of chromosome 2 at the heading and ripening stages. We developed chromosome segment substitution lines which carried Akenohoshi segments in the Koshihikari genetic background, and measured hydraulic conductance to both osmotic and passive water transport. The QTL was confirmed to be located within a region of about 4.2Mbp on the distal end of long arm of chromosome 2. The Akenohoshi allele increased root surface area and hydraulic conductance, but didn't increase hydraulic conductivity of a plant.

Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice.

Severe lodging has occurred in many improved rice varieties after the recent strong typhoons in East and Southeast Asian countries. The indica variety Takanari possesses strong culm characteristics due to its large section modulus, which indicates culm thickness, whereas the japonica variety Koshihikari is subject to substantial bending stress due to its thick cortical fibre tissue. To detect quantitative trait loci (QTLs) for lodging resistance and to eliminate the effects of genetic background, we used reciprocal chromosome segment substitution lines (CSSLs) derived from a cross between Koshihikari and Takanari. The oppositional effects of QTLs for section modulus were confirmed in both genetic backgrounds on chromosomes 1, 5 and 6, suggesting that these QTLs are not affected by the genetic background and are controlled independently by a single factor. The candidate region of a QTL for section modulus included SD1. The section modulus of NIL-sd1 was lower than that of Koshihikari, whereas the section modulus of NIL-SD1 was higher than that of Takanari. This result indicated that those regions regulate the culm thickness. The reciprocal effects of the QTLs for cortical fibre tissue thickness were confirmed in both genetic backgrounds on chromosome 9 using CSSLs.

Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism.

Lodging has been a major roadblock to attaining increased crop productivity. In an attempt to understand the mechanism for culm strength in rice, we isolated an effective quantitative trait locus (QTL), STRONG CULM3 (SCM3), the causal gene of which is identical to rice TEOSINTE BRANCHED1 (OsTB1), a gene previously reported to positively control strigolactone (SL) signaling. A near-isogenic line (NIL) carrying SCM3 showed enhanced culm strength and increased spikelet number despite the expected decrease in tiller number, indicating that SL also has a positive role in enhancing culm strength and spikelet number. We produced a pyramiding line carrying SCM3 and SCM2, another QTL encoding APO1 involved in panicle development. The NIL-SCM2+SCM3 showed a much stronger culm than NIL-SCM2 and NIL-SCM3 and an increased spikelet number caused by the additive effect of these QTLs. We discuss the importance of utilizing suitable alleles of these STRONG CULM QTLs without inducing detrimental traits for breeding.

Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism.

Lodging has been a major roadblock to attaining increased crop productivity. In an attempt to understand the mechanism for culm strength in rice, we isolated an effective quantitative trait loci (QTL), STRONG CULM3 (SCM3), the causal gene of which is identical to rice TEOSINTE BRANCHED1 (OsTB1), a gene previously reported to positively control strigolactone (SL) signaling. A near-isogenic line (NIL) carrying SCM3 showed enhanced culm strength and increased spikelet number despite the expected decrease in tiller number, indicating that SL also has a positive role in enhancing culm strength and spikelet number. We produced a pyramiding line carrying SCM3 and SCM2, another QTL encoding APO1 involved in panicle development. The NIL-SCM2+SCM3 showed a much stronger culm than NIL-SCM2 and NIL-SCM3 and an increased spikelet number caused by the additive effect of these QTLs. We discuss the importance of utilizing suitable alleles of these STRONG CULM QTLs without inducing detrimental traits for breeding.

Increased lodging resistance in long-culm, low-lignin gh2 rice for improved feed and bioenergy production.

Lignin modification has been a breeding target for the improvements of forage digestibility and energy yields in forage and bioenergy crops, but decreased lignin levels are often accompanied by reduced lodging resistance. The rice mutant gold hull and internode2 (gh2) has been identified to be lignin deficient. GH2 has been mapped to the short arm of chromosome 2 and encodes cinnamyl-alcohol dehydrogenase (CAD). We developed a long-culm variety, 'Leaf Star', with superior lodging resistance and a gh phenotype similar to one of its parents, 'Chugoku 117'. The gh loci in Leaf Star and Chugoku 117 were localized to the same region of chromosome 2 as the gh2 mutant. Leaf Star had culms with low lignin concentrations due to a natural mutation in OsCAD2 that was not present in Chugoku 117. However, this variety had high culm strength due to its strong, thick culms. Additionally, this variety had a thick layer of cortical fiber tissue with well-developed secondary cell walls. Our results suggest that rice can be improved for forage and bioenergy production by combining superior lodging resistance, which can be obtained by introducing thick and stiff culm traits, with low lignin concentrations, which can be obtained using the gh2 variety.