Takayuki Kashiwagi

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.

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.

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.

Identification of quantitative trait loci for resistance to bending-type lodging in rice (Oryza sativa L.)

Abstract Bending-type lodging is one of the most important factors affecting the yield and grain quality of rice. This study identified quantitative trait loci (QTLs) for physical strength of the upper culms, and evaluated QTL effects on lodging resistance. In 2010 and 2011, QTLs for breaking strength, length, and diameter of the top three internodes were identified by analyzing chromosomal segment substitution lines (CSSLs) developed from ‘Koshihikari’ and ‘Kasalath’. The QTL analysis indicated that ‘Kasalath’ had two types of QTLs: one to strengthen specific internodes and one to simultaneously improve the physical strengths of plural internodes or the top three internodes. A QTL for breaking strengths of the top three internodes (bsuc11) was detected on chromosome 11 in both years. This QTL did not overlap with that for internode length. To evaluate the effects of bsuc11 on lodging resistance, this study selected three CSSLs with bsuc11 and analyzed the breaking strengths of the top three internodes after heading and the pushing resistance of the lower part. Internodes of ‘Koshihikari’ showed decreased breaking strengths after grain filling, while those of CSSLs with bsuc11 did not show this decrease in breaking strength. The pushing resistance of the lower part at the fully ripe stage was the same in ‘Koshihikari’ and CSSLs with bsuc11. These results suggested that bsuc11 could be a target to improve the physical strength of the upper culms to resist bending-type lodging, and that the physical strengths of upper and lower parts are controlled by different genetic factors in rice.

Time-related identification of chromosome regions affecting plant elongation in rice (Oryza sativa L.).

We investigated the time-related changes of Chromosome Regions that Affect Traits (CRATs) for elongation rate in rice (Oryza sativa L.) using chromosome segment substitution lines (CSSLs) carrying a single chromosome segment of the cultivar Kasalath (indica) in a Koshihikari (japonica) genetic background. The growth period of rice was partitioned into eight stages (each lasting 5-7days) from 18days after transplanting, and the elongation rate was determined as the increase of total plant height per time at each growth stage. CRATs for plant elongation rate were determined based on graphical genotype data of CSSLs that showed a significantly higher or lower elongation rate than Koshihikari. In total, 23 CRATs for plant elongation rate were detected, and different CRATs acted at different growth stages. Fifteen CRATs increased the elongation rate through Kasalath alleles, and eight increased it through Koshihikari alleles. These results suggest that plant height in rice is regulated in a stage-specific manner by a variety of genetic mechanisms that control plant elongation rate. Kasalath alleles of PE1-9 increased the elongation rate at an early growth stage (18-25days after transplanting), while Koshihikari alleles of PE8-3 decreased the elongation rate at a late growth stage (68-74days after transplanting). In a line that contained both of these CRATs, the elongation rate at the early growth stage was increased without affecting plant height at harvesting. We conclude that stage-specific optimization of plant height in rice may be achieved by combining CRATs that control plant elongation at specific stages.

Identification of a locus for asynchronous heading in rice, Oryza sativa L.

We have identified a locus for asynchronous heading in rice. The length of heading period in a plant was measured as the indicator of asynchronous heading in 98 backcross inbred lines (BILs). These lines were derived using a single-seed descent method from a backcross of (japonica Nipponbare/indica Kasalath)/Nipponbare, and we used this mapping population in quantitative trait locus (QTL) analysis. We located a single QTL related to asynchronous heading (qah7) in the region of R2401–C39 on chromosome 7, and its contribution to the total variation was 0.14 (r2), with the positive effect due to the Kasalath allele. A near isogenic line (NILah7) that carries a Kasalath chromosomal segment corresponding to qah7 in the Nipponbare genetic background was selected and analyzed to identify a locus for asynchronous heading. The length of heading period in NILah7 was significantly longer (P < 0.001) than that in Nipponbare.