Ken Ishimaru

Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield

Increases in the yield of rice, a staple crop for more than half of the global population, are imperative to support rapid population growth. Grain weight is a major determining factor of yield. Here, we report the cloning and functional analysis of THOUSAND-GRAIN WEIGHT 6 (TGW6), a gene from the Indian landrace rice Kasalath. TGW6 encodes a novel protein with indole-3-acetic acid (IAA)-glucose hydrolase activity. In sink organs, the Nipponbare tgw6 allele affects the timing of the transition from the syncytial to the cellular phase by controlling IAA supply and limiting cell number and grain length. Most notably, loss of function of the Kasalath allele enhances grain weight through pleiotropic effects on source organs and leads to significant yield increases. Our findings suggest that TGW6 may be useful for further improvements in yield characteristics in most cultivars.

Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags

Abstract We have constructed a rice function map by collating the results on quantitative trait loci (QTLs) for 23 important physiological and agronomic characters (including 13 newly measured traits) obtained using backcross inbred lines of japonica Nipponbare×indica Kasalath. Using these materials, The Rice Genome project (RGP) has developed a high-density genetic map. QTLs controlling yield did not overlap with those controlling the morphological and physiological traits supposed to relate to yield, such as photosynthetic ability. This result suggests that these traits do not influence yield, at least in this genetic background and environment. QTLs controlling yield also did not overlap with the structural genes controlling carbon metabolism (rbcS, cytosolic or plastidic fructose-1,6-bisphosphate, R-enzyme, and sucrose synthase).The combination of a function map and results from the RGP can be advantageous. The utility of this map is discussed.

Identification and functional analysis of a locus for improvement of lodging resistance in rice

We identified a new locus responsible for increased pushing resistance of the lower part of rice (Oryza sativa) and analyzed its physiological function to understand how to improve lodging resistance in rice. Quantitative trait loci (QTLs) controlling pushing resistance of the lower part were analyzed in a population of backcross inbred lines of japonica Nipponbare × indica Kasalath plants cut out at 40 cm to exclude the effect of the weight of the upper parts. Five QTLs for pushing resistance were detected; only one QTL from Kasalath on chromosome 5 (prl5) had a positive effect. The likelihood odds ratio curve of prl5 echoed that for lodging resistance by typhoon. We selected three near-isogenic lines (NILs) in which the chromosomal region of prl5 was substituted with that of Kasalath in the Nipponbare background. The dry weights and densities and the contents of accumulated carbohydrate in stems below 40 cm (lower stems) in each NIL were significantly higher than those of Nipponbare. There was no difference between Nipponbare and the NILs in yield, root characteristics, or the weights of the upper parts. Pushing resistance of the lower part and lodging resistance in the NILs were up to twice as high as in Nipponbare. These results suggest that prl5 might affect the characteristics of the lower stems of the NILs, thus increasing lodging resistance.

Improvement of lodging resistance with QTLs for stem diameter in rice ( Oryza sativa L.)

Varietal differences among ten rice cultivars showed that stem diameter is a key factor in lodging resistance (measured in terms of pushing resistance). Two near-isogenic lines (NILs) were selected from a series of chromosome segment substitution lines developed between cultivars Nipponbar and Kasalath, one containing a single stem diameter QTL (sdm8; NIL114), and another with four stem diameter QTLs (sdm1, sdm7, sdm8, sdm12; NIL28). Compared with the Nipponbare control, stem diameters were larger in NIL114 and NIL28 by about 7 and 39%, respectively. Pushing resistance in NIL28 was significantly greater than in Nipponbare, but NIL114 was similar to Nipponbare. The two NILs had greater weight of lower stem and culm wall thickness than Nipponbare. NIL28 had higher plant height, which is a negative effect on lodging resistance, than Nipponbare. The non-structural carbohydrate contents of NIL stems were higher than that of Nipponbare, whereas the silicon contents were lower in the NILs, and cellulose contents were lower only in NIL28. The basal internodes of the two NILs were significantly stiffer than those of Nipponbare. These results suggest that increasing stem diameter in rice breeding programs would improve lodging resistance, although the combination of multiple QTLs would be necessary to produce thicker stems with higher pushing resistance, whereas the higher plant height could also result from the combination of multiple QTLs.

Factors Responsible for Decreasing Sturdiness of the Lower Part in Lodging of Rice (Oryza sativa L.)

Abstract Here, we propose new improvement targets capable of decreasing loss of the sturdiness of the lower part in the rice plant (Oryza sativa L.), thereby improving lodging resistance. In nine rice cultivars with various plant lengths, we analyzed the factors responsible for sturdiness of the lower part and, thus, for resistance to lodging. The ratio of lodging resistance to sturdiness of the lower part (RLS) was calculated. The difference in pushing resistance between the lower part and the whole plant varied among cultivars. Among the morphological traits, plant length and the weight of the upper part of plant were not correlated with RLS, but the difference between plant length and length from the ground to the ear (DPE), as well as the weight of the lower stem, were positively correlated with RLS. DPE and the weight of the lower stem were not significantly correlated with ear weight. These results suggest that improvements in DPE and in the weight of the lower stem could be primary targets for improving RLS, thus increasing lodging resistance, without affecting yield.

Overexpression of a Maize SPS Gene Improves Yield Characters of Potato under Field Conditions

Abstract We analyzed the yield characters of field-grown transgenic potato plants (Solanum tuberosum) carrying a maize gene for sucrose-phosphate synthase (SPS), the key enzyme in sucrose synthesis. The SPS activity in the leaves of transgenic plants (line Ag1203) was 2 times that of the control (cv. May Queen). There was no difference in the photosynthetic CO2 uptake rates between Ag1203 and May Queen plants, and the leaf starch content of Ag1203 was lower. These observations indicate that the introduction of a foreign SPS gene improved the supply of photosynthate from source (leaves) to sink (tubers). Additionally, leaf senescence of the transgenic potato plants was delayed relative to that of May Queen. The average tuber weight and total yield of Ag1203 plants were at least 20% higher, and the tuber sucrose content, which is related to eating quality, was also higher. Increased translocation of photosynthate and longer period of photosynthetic activity in the leaves may have increased the yield of Ag1203. These results suggest that introduction of the SPS gene improved the yield characters and quality of potato tubers under field conditions.

Effect of CO2 Enrichment on the Translocation and Partitioning of Carbon at the Early Grain-filling Stage in Rice (Oryza sativa L.)

Abstract Rice plants (Oryza sativa L.) were grown under normal (350 µL L-1 CO2) and CO2-enriched (660 µ L L-1 CO2) conditions, and 13CO2 was supplied to the rice plants after heading to examine the translocation and partitioning of photosynthate at the early grain-filling stage. At 2 days after supplying 13CO2, no difference in the 13C content of the whole plant was observed between the plants grown under normal and CO2-enriched conditions, but translocation of 13C from the leaf blade to other plant organs seemed to be accelerated by CO2 enrichment. Up to 9 days after supplying, 13CO2 fixed into sucrose was mainly used to synthesize starch in the stem rather than translocated to the ear in plants grown under normal conditions. In contrast, the supplied 13C was rapidly translocated to the ear, and 13C stored as starch in the stem was also translocated to the ear in plants grown under CO2-enriched conditions. Therefore, we concluded that CO2 enrichment accelerated the translocation of carbohydrates to the ear.

Identification and functional analysis of alleles for productivity in two sets of chromosome segment substitution lines of rice

Using two sets of chromosome segment substitution lines (CSSLs) of crosses between cvs. ‘Koshihikari’ and ‘Kasalath’ (Ko/Ka) and between ‘Koshihikari’ and ‘Nona Bokra’ (Ko/NB), respectively, we have identified alleles for ten traits related to productivity (e.g., harvest index and biomass) in rice (Oryza sativa L.). A total of 43 chromosome regions affecting traits (CRATs) in Ko/Ka CSSLs and 40 in Ko/NB CSSLs were detected. Among them, ten and 18 CRATs in Ko/Ka and Ko/NB CSSLs, respectively, had positive effects. A CRAT for harvest index (HI) with a positive allele from ‘Kasalath’ on chromosome 6 (tentatively named HI6) increased the HI by 25 % relative to ‘Koshihikari’, raising it to the theoretical upper limit in rice (0.6). Functional analysis using CSSLs with HI6 indicated that HI6 reduced the size of the lower parts of the plant, which is not important for production, while maintaining the size of the other organs related to production (e.g., flag leaf and panicle), resulting in improved nitrogen (N) use efficiency. These results suggest an ‘ideal plant type’ with improved N use efficiency that can sustain higher yields. A CRAT for the SPAD (soil plant analysis development) value, which is a chlorophyll meter value commonly used as an indicator of leaf N content and strongly associated with the source ability of a leaf, with a ‘Nona Bokra’ allele on chromosome 4 increased the value by 13 % relative to ‘Koshihikari’ with no loss of leaf area. These CRATs can be used for the improvement of rice productivity.

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria

A number of studies have shown that elevated atmospheric CO2 ([CO2]) affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE) experiment (ambient + 200 μmol.mol−1) using three rice cultivars (Akita 63, Takanari, and Koshihikari) and two experimental lines of Koshihikari [chromosome segment substitution and near-isogenic lines (NILs)] to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient) and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA) gene and increased methyl coenzyme M reductase (mcrA) in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields.

Effects of Elevated CO2 Concentration on Photosynthetic Carbon Metabolism in Flag-Leaf Blades of Rice before and after Heading

Abstract We monitored the effects of elevated atmospheric C02 concentrations on the photosynthetic carbon metabolism in the flag leaves of rice plant (Oryza sativaL. cv. Akitakomachi) before and after heading. The plants were grown under ambient (350 ppm : control) or elevated (650 ppm) C02 conditions. Flag-leaf blades grown under high C02 accumulated more starch than control leaf blades before heading, but the level of starch declined to almost zero under both C02 concentrations as soon as the development of ears began. Before heading, the transcript level of sucrose-phosphate synthase (SPS) (EC 2.4.1.14), a key enzyme in the sucrose synthesis in flag-leaf blades was significantly higher under elevated C02 conditions than under elevated C02 (P<0.01). The difference in the expression of SPS decreased after heading, coinciding with a change in starch contents in both groups. These results showed that the effects of elevated C02 concentration on rice plants might vary with the growth stage of the leaf blades. We also discussed the influence of the changes in the carbohydrate metabolism of rice plants caused by elevated C02 concentration on yield.