Seiji Yanagihara

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

Significance This work reports discovery of a unique gene important for rice agriculture. A significant yield enhancement in rice modern cultivar was achieved by identification of a gene, SPIKELET NUMBER (SPIKE) in Indonesian rice landrace. The SPIKE increased grain yield of an indica cultivar IR64, which is widely grown in the tropics, over four seasons at the field level and improved plant architecture without changing grain quality or growth period, which are important for regional adaptability. These results indicate finding of SPIKE will be extremely valuable for contributing to increase grain production of indica rice cultivars. Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13–36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.

Phosphorus deficiency-induced root elongation and its QTL in rice (Oryza sativa L.)

A significant level of root elongation was induced in rice (Oryza sativa) grown under phosphorus-deficient conditions. The root elongation clearly varied among a total of 62 varieties screened under two different phosphorus levels. Two contrasting varieties, ‘Gimbozu’, with a low elongating response and ‘Kasalath’, with a high elongating response, were chosen and crossed to produce a hybrid population for QTL analyses. QTLs for the phosphorus deficiency-induced root elongation were detected by two linkage maps, i.e., one with 82 F3 families constructed by 97 simple sequence repeat (SSR) and sequence-tag site markers and another with 97 F8 lines by 790 amplified fragment length polymorphism and SSR markers. A single QTL for the elongation response was detected on chromosome 6, with a LOD score of 4.5 in both maps and explained about 20% of total phenotypic variance. In addition, this QTL itself, or a region tightly linked with it, partly explained an ability to reduce accumulation of excess iron in the shoots. The identified QTL will be useful to improve rice varieties against a complex nutritional disorder caused by phosphorus deficiency and iron toxicity.

Effect of NaCl on the Photosynthesis, Water Relations and Free Proline Accumulation in the Wild Oryza Species

Summary The physiological responses of wild Oryza species (Oryza latifolia Desv., a salt-tolerant species and O. rufipogon Griff., a salt-susceptible species) to salinity stress were investigated by comparing with check varieties of cultivated rice (O. sativa L.), SR26B (salt-tolerant) and IR28 (salt-susceptible). As the NaCl concentration of water culture solution was raised to 12 dS m–1 (about 113mM), leaf Na+ content per dry matter in wild Oryza species increased from 4 to 17 times as compared with the control (no NaCl treatment), whereas the accumulation was lower in cultivated rice varieties. The increased concentration of leaf Na+ resulted in the decrease in leaf water potential (Ψw) in all rice species, although the degree of decline in photosynthetic rate was different among the varieties. It was notable that the photosynthetic rate was cdmost constant in O. latifolia though Ψw decreased to – 2.0 MPa with the increased NaCl concentration in the water culture solution. A significant negative correlation between free-proline content and osmotic potential (Ψs) of leaf blade was found in both salt tolerant entries, SR26B and O. latifolia. In spite of higher leaf Na+ storage, the survival rate of O. latifolia was higher than that of SR26B, indicating that the mechanism of salt tolerance in O. latifolia may be different from that in SR26B.

Genetic characterization of rainfed upland New Rice for Africa (NERICA) varieties

A total of 18 rainfed upland New Rice for Africa (NERICA) varieties were categorized as the heavy panicle and low tillering types and early heading, in compared with 32 different varieties. These chromosome components were clarified using 243 SSR markers which showed polymorphism among NERICA varieties and their parents, CG 14 (O. glaberrima Steud.) and one of the recurrent parents, WAB-56-104 (O. sativa L.). NERICA varieties were classified into three groups, which corresponded with these parents’ continuation including two exceptions, NERICAs 14 and 17, by a cluster analysis using polymorphism data of SSR markers and 14 differential markers among them were selected to classify NERICA varieties. However, three groups: NERICAs, 3 and 4, NERICAs, 8, 9 and 11 and NERICAs, 15 and 16 were not distinguishable. Association analysis was carried out for characterization of NERICA varieties by using SSR markers genotype and phenotype of agronomic traits. A total of 131 quantitative trait loci between SSR markers and 11 agronomic traits were detected. The characteristics of early maturity and heavy panicle of upland NERICA varieties were succeeded from Asian rice varieties and the characteristics of high dry matter production and late heading were introduced from CG 14 and the other varieties.

Genetic variation in blast resistance in rice germplasm from West Africa

The genetic variation in resistance to blast (Pyricularia oryzae Cavara) in 195 rice accessions comprising 3 species of the AA genome complex (Asian rice [Oryza sativa L.], African rice [Oryza glaberrima Steud.] and wild rice [Oryza barthii]) was investigated based on their patterns of reaction to standard differential blast isolates (SDBIs) and SSR marker polymorphism data. Cluster analysis of the polymorphism data of 61 SSR markers identified 3 major clusters: cluster A (mainly Japonica Group or upland accessions), cluster B (mainly Indica Group or lowland accessions) and cluster C (O. glaberrima and O. barthii). The accessions were classified again into 3 resistance groups based on reactions to SDBIs: group Ia (susceptible), group Ib (middle resistance) and group II (high resistance). Group Ia included only a few differential varieties, susceptible controls and the Japonica Group cultivar Nipponbare. Accessions in clusters A and B included all 3 resistance groups and showed a wide variation in blast resistance, but cluster C contained only group Ib. These results demonstrated that variations in Asian rice (O. sativa) accessions in West Africa were skewed toward high resistance and that variations in O. glaberrima and O. barthii were limited and lower than the Asian rice accessions.

Identification of a low tiller gene from a new plant type cultivar in rice (Oryza sativa L.)

We characterized a rice introgression line, YTH34, harboring a chromosome segment from a New Plant Type (NPT) cultivar, IR65600-87-2-2-3, in the genetic background of an Indica Group elite rice cultivar, IR 64, under upland and irrigated lowland conditions in Japan. The number of panicles (as an indicator of tiller number) and number of spikelets per panicle of YTH34 were lower than those of IR 64 under irrigated lowland conditions, but both of those as well as culm length, panicle length, seed fertility, panicle weight, whole plant weight, and harvest index were dramatically reduced under upland conditions. And the low tiller of YTH34 was confirmed to start after the maximum tiller stage. In particular, the decrease of panicle number was remarkable in upland, so we tried to identify the chromosome location of the relevant gene. Through segregation and linkage analyses using F3 family lines derived from a cross between IR 64 and YTH34, and SSR markers, we found that low tiller number was controlled by a single recessive gene, ltn2, and mapped with the distance of 2.1 cM from SSR marker RM21950, in an introgressed segment on chromosome 7. YTH34 harboring ltn2 and the genetic information for DNA markers linked will be useful for genetic modification of plant architectures of Indica Group rice cultivar.

Genetic variation of rice (Oryza sativa L.) germplasm in Myanmar based on genomic compositions of DNA markers

The genetic diversity of 175 rice accessions from Myanmar, including landraces and improved types from upland and lowland ecosystems in five different areas—Western (hilly), Northern (mountainous), North and South-eastern (plateau), and Southern (plain)—was evaluated on the basis of polymorphism data for 65 DNA markers and phenol reactions. On the basis of the DNA polymorphism data, high genetic diversity was confirmed to conserve in the accessions from each ecosystem and area. And the accessions were classified into two cluster groups I and II, which corresponded to Indica Group and Japonica Group, respectively. Cluster group I accessions were distributed mainly in upland ecosystems; group II were distributed in lowland in the Southern area, and the distributions of dominant groups differed among areas. Rice germplasm in Myanmar has maintained high genetic diversity among ecosystems and areas. This information will be used for advanced studies in germplasm and rice breeding in Myanmar.