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Ohsumi A.,Japan National Agricultural Research Center | Takai T.,Japan National Agriculture and Food Research Organization | Ida M.,Kumiai Chemical Industry Co. | Yamamoto T.,Japan National Institute of Agrobiological Science | And 4 more authors.
Field Crops Research | Year: 2011

Rice yield potential is determined by the balance between sink size and source capacity. To clarify the factors that limit yield in temperate japonica cultivars, we compared the yield performance of Sasanishiki, a temperate japonica cultivar, with those of three near-isogenic lines (NILs) of Sasanishiki with introgression of quantitative trait loci (QTL) derived from a high-yielding indica cultivar, Habataki: qSBN1, which increases the number of secondary rachis branches; qPBN6, which increases the number of primary rachis branches; and a pyramid line that combines these two QTLs. NIL (SBN1), NIL (PBN6), and NIL (SBN1+. PBN6) produced 28-37%, 9-16%, and 62-65% more spikelets per panicle than Sasanishiki, respectively. However, the NILs with increased spikelet number per panicle did not increase grain yield significantly, because compensation is taken place among different yield components. The pyramid line nevertheless had 4-12% higher yield than Sasanishiki due to greater translocation of carbohydrates from stem to panicle. There was no difference in carbohydrate accumulation before heading or in biomass production among Sasanishiki and the three NILs. The results indicate that increasing sink size does not substantially improve yield in Sasanishiki, which lacks sufficient substrate supply to fully satisfy the increased sink demand that results from the spikelet-number QTLs. © 2010 Elsevier B.V.

Hayashi N.,Japan National Institute of Agrobiological Science | Inoue H.,Japan National Institute of Agrobiological Science | Kato T.,Aichi Agricultural Research Center | Funao T.,Aichi Agricultural Research Center | And 8 more authors.
Plant Journal | Year: 2010

Rice blast is one of the most widespread and destructive plant diseases worldwide. Breeders have used disease resistance (R) genes that mediate fungal race-specific gene-for-gene resistance to manage rice blast, but the resistance is prone to breakdown due to high pathogenic variability of blast fungus. Panicle blast 1 (Pb1) is a blast-resistance gene derived from the indica cultivar Modan. Pb1-mediated resistance, which is characterized by durability of resistance and adult/panicle blast resistance, has been introduced into elite varieties for commercial cultivation. We isolated the Pb1 gene by map-based cloning. It encoded a coiled-coilnucleotide-binding-siteleucine-rich repeat (CCNBSLRR) protein. The Pb1 protein sequence differed from previously reported R-proteins, particularly in the NBS domain, in which the P-loop was apparently absent and some other motifs were degenerated. Pb1 was located within one of tandemly repeated 60-kb units, which presumably arose through local genome duplication. Pb1 transcript levels increased during the development of Pb1+ cultivars; this expression pattern accounts for their adult/panicle resistance. Promoter:GUS analysis indicated that genome duplication played a crucial role in the generation of Pb1 by placing a promoter sequence upstream of its coding sequence, thereby conferring a Pb1-characteristic expression pattern to a transcriptionally inactive sleeping resistance gene. We discuss possible determinants for the durability of Pb1-mediated blast resistance. © 2010 Blackwell Publishing Ltd.

Ishikawa S.,Japan National Institute for Agro - Environmental Sciences | Abe T.,Japan National Institute for Agro - Environmental Sciences | Kuramata M.,Japan National Institute for Agro - Environmental Sciences | Yamaguchi M.,Akita | And 3 more authors.
Journal of Experimental Botany | Year: 2010

Large phenotypic variations in the cadmium (Cd) concentration of rice grains and shoots have been observed. However, the genetic control of Cd accumulation remains poorly understood. Quantitative trait loci (QTLs) determining the grain Cd concentration of rice grown in a Cd-polluted paddy field were identified. Using a mapping population consisting of 85 backcross inbred lines derived from a cross between the low-Cd-accumulating cultivar Sasanishiki (japonica) and high-Cd-accumulating cultivar Habataki (indica), two QTLs for increasing grain Cd concentration were found on chromosomes 2 and 7. A major-effect QTL, qGCd7 (QTL for grain Cd on chromosome 7), was detected on the short arm of chromosome 7. It accounted for 35.5% of all phenotypic variance in backcross inbred lines. qGCd7 was not genetically related to any QTLs for concentrations of essential trace metals (Cu, Fe, Mn, and Zn) or those for agronomic traits such as heading date, suggesting that this QTL is specific to Cd. Furthermore, the existence of qGCd7 was confirmed using chromosome segment substitution lines (CSSLs) and an F2 population from a cross between the target CSSL and Sasanishiki grown in a Cd-polluted paddy soil. To our knowledge, qGCd7 is a novel QTL with major effects for increasing grain Cd concentrations.

Kikuchi R.,Japan National Institute of Agrobiological Science | Kikuchi R.,Yokohama City University | Kawahigashi H.,Japan National Institute of Agrobiological Science | Oshima M.,University of Tsukuba | And 4 more authors.
Journal of Experimental Botany | Year: 2012

HvCO9 was characterized to elucidate the barley flowering control mechanisms and to investigate the functional diversification of the barley CONSTANS-like (CO-like) genes in flowering. HvCO9 was located on the same chromosome, 1HL, as Ppd-H2 (HvFT3), which is a positive regulator of short-day (SD) flowering. A phylogenetic analysis showed that HvCO9 was located on the same branch of the CO-like gene tree as rice Ghd7 and the barley and wheat VRN2 genes, which are all negative regulators of flowering. High level HvCO9 expressions were observed under SD conditions, whereas its expression levels were quite low under long-day (LD) conditions. HvCO9 expression correlated with HvFT1 and HvFT2 expression under SD conditions, although no clear effect of HvCO9 on HvFT3 expression, or vice versa, under SD conditions was observed. The over-expression of HvCO9 in rice plants produced a remarkable delay in flowering. In transgenic rice, the expression levels of the flowering-related Ehd1 gene, which is a target gene of Ghd7, and its downstream genes were suppressed, causing a delay in flowering. These results suggest that HvCO9 may act as a negative regulator of flowering under non-inductive SD conditions in barley; this activity is similar to that of rice Ghd7 under non-inductive LD conditions, but the functional targets of these genes may be different. Our results indicate that barley has developed its own pathways to control flowering by using homologous genes with modifications for the timing of expression. Further, it is hypothesized that each pathway may target different genes after gene duplication or species diversification. © 2011 The Author.

Itoh H.,Japan National Institute of Agrobiological Science | Nonoue Y.,Institute of the Society for Techno innovation of Agriculture | Yano M.,Japan National Institute of Agrobiological Science | Izawa T.,Japan National Institute of Agrobiological Science
Nature Genetics | Year: 2010

The critical day length triggering photoperiodic flowering is set as an acute, accurate threshold in many short-day plants, including rice 1,2. Here, we show that, unlike the Arabidopsis florigen gene FT 3, the rice florigen gene Hd3a (Heading date 3a) is toggled by only a 30-min day-length reduction. Hd3a expression is induced by Ehd1 (Early heading date 1) expression when blue light coincides with the morning phase set by OsGIGANTEA(OsGI)-dependent circadian clocks. Ehd1 expression is repressed by both night breaks under short-day conditions and morning light signals under long-day conditions. Ghd7 (Grain number, plant height and heading date 7) was acutely induced when phytochrome signals coincided with a photosensitive phase set differently by distinct photoperiods and this induction repressed Ehd1 the next morning. Thus, two distinct gating mechanismsof the floral promoter Ehd1 and the floral repressor Ghd7could enable manipulation of slight differences in day length to control Hd3a transcription with a critical day-length threshold. © 2010 Nature America, Inc. All rights reserved.

Ogiso E.,University of Tsukuba | Takahashi Y.,Institute of the Society for Techno innovation of Agriculture | Takahashi Y.,Nagoya University | Sasaki T.,Japan National Institute of Agrobiological Science | And 4 more authors.
Plant Physiology | Year: 2010

Casein kinase II (CK2) is a protein kinase with an evolutionarily conserved function as a circadian clock component in several organisms, including the long-day plant Arabidopsis (Arabidopsis thaliana). The circadian clock component CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is a CK2 target in Arabidopsis, where it influences photoperiodic flowering. In rice (Oryza sativa), a shortday plant, Heading date6 (Hd6) encodes a CK2α subunit that delays flowering time under long-day conditions. Here, we demonstrate that control of flowering time in rice by the Hd6 CK2a subunit requires a functional Hd1 gene (an Arabidopsis CONSTANS ortholog) and is independent of the circadian clock mechanism. Our findings from overexpressing the dominantnegative CK2 allele in rice support the independence of CK2 function from the circadian clock. This lack of control of the circadian clock by Hd6 CK2α might be due to the presence of glutamate in OsLHY (a CCA1 ortholog in rice) instead of the serine at the corresponding CK2 target site in CCA1. However, this glutamate is critical for the control of the OsPRR1 gene (a rice ortholog of the Arabidopsis TOC1/PRR1 gene) by OsLHY for regulation of the circadian clock. We also demonstrated that the other conserved CK2 target sites in OsLHY conferred robust rhythmic expression of OsLHY-LUC under diurnal conditions. These findings imply that the role of CK2 in flowering-time regulation in higher plants has diversified during evolution. © 2009 American Society of Plant Biologists.

Ookawa T.,Tokyo University of Agriculture and Technology | Hobo T.,Nagoya University | Yano M.,Japan National Institute of Agrobiological Science | Murata K.,Agricultural Research Institute | And 11 more authors.
Nature Communications | Year: 2010

The use of fertilizer results in tall rice plants that are susceptible to lodging and results in reduced plant yields. In this study, using chromosome segment substitution lines, we identified an effective quantitative trait loci (QTL) for culm strength, which was designated STRONG CULM2 (SCM2). Positional cloning of the gene revealed that SCM2 was identical to ABERRANT PANICLE ORGANIZATION1 (APO1), a gene previously reported to control panicle structure. A near-isogenic line carrying SCM2 showed enhanced culm strength and increased spikelet number because of the pleiotropic effects of the gene. Although SCM2 is a gain-of-function mutant of APO1, it does not have the negative effects reported for APO1 overexpression mutants, such as decreased panicle number and abnormal spikelet morphology. The identification of lodging-resistance genes by QTL analysis combined with positional cloning is a useful approach for improving lodging resistance and overall productivity in rice. © 2010 Macmillan Publishers Limited. All rights reserved.

Shibaya T.,Japan National Institute of Agrobiological Science | Nonoue Y.,Institute of the Society for Techno innovation of Agriculture | Ono N.,Institute of the Society for Techno innovation of Agriculture | Yamanouchi U.,Japan National Institute of Agrobiological Science | And 2 more authors.
Theoretical and Applied Genetics | Year: 2011

Heading date is the one of the most important traits in rice breeding, because it defines where rice can be cultivated and influences the expression of various agronomic traits. To examine the inhibition of heading by Heading date 2 (Hd2), previously detected on the distal end of chromosome 7's long arm by quantitative trait locus (QTL) analysis, we developed backcross inbred lines (BILs) from Koshihikari, a leading Japanese cultivar, and Hayamasari, an extremely early heading cultivar. The BILs were cultivated under natural field conditions in Tsukuba Japan, and under long-day (14.5 h), extremely long-day (18 h), and short-day (10 h) conditions. Combinations of several QTLs near Hd1, Hd2, Ghd7, Hd5, and Hd16 were detected under these four conditions. Analysis of advanced backcross progenies revealed genetic interactions between Hd2 and Hd16 and between Hd2 and Ghd7. In the homozygous Koshihikari genetic background at Hd16, inhibition of heading by the Koshihikari allele at Hd2 was smaller than that with the Hayamasari Hd16 allele. Similarly, in the homozygous Koshihikari genetic background at Ghd7, the difference in heading date caused by different alleles at Hd2 was smaller than in plants homozygous for the Hayamasari Ghd7 allele. Based on these results, we conclude that Hd2 and its genetic interactions play an important role in controlling heading under long-day conditions. In addition, QTLs near Hd2, Hd16, and Ghd7, which are involved in inhibition of heading under long-day conditions, function in the same pathway that controls heading date. © 2011 Springer-Verlag.

Kawahigashi H.,Japan National Institute of Agrobiological Science | Kasuga S.,Shinshu University | Ando T.,Institute of the Society for Techno innovation of Agriculture | Kanamori H.,Institute of the Society for Techno innovation of Agriculture | And 4 more authors.
Theoretical and Applied Genetics | Year: 2011

Target leaf spot is one of the major sorghum diseases in southern Japan and caused by a necrotrophic fungus, Bipolaris sorghicola. Sorghum resistance to target leaf spot is controlled by a single recessive gene (ds1). A high-density genetic map of the ds1 locus was constructed with simple sequence repeat markers using progeny from crosses between a sensitive variety, bmr-6, and a resistant one, SIL-05, which allowed the ds1 gene to be genetically located within a 26-kb region on the short arm of sorghum chromosome 5. The sorghum genome annotation database for BTx623, for which the whole genome sequence was recently published, indicated a candidate gene from the Leucine-Rich Repeat Receptor Kinase family in this region. The candidate protein kinase gene was expressed in susceptible plants but was not expressed or was severely reduced in resistant plants. The expression patterns of ds1 gene and the phenotype of target leaf spot resistance were clearly correlated. Genomic sequences of this region in parental varieties showed a deletion in the promoter region of SIL-05 that could cause reduction of gene expression. We also found two ds1 alleles for resistant phenotypes with a stop codon in the coding region. The results shown here strongly suggest that the loss of function or suppression of the ds1 protein kinase gene leads to resistance to target leaf spot in sorghum. © 2011 Springer-Verlag.

Fukuoka S.,Japan National Institute of Agrobiological Science | Nonoue Y.,Institute of the Society for Techno innovation of Agriculture | Yano M.,Japan National Institute of Agrobiological Science
Breeding Science | Year: 2010

Genetic dissection of a wide range of naturally occurring variations in rice has significantly progressed by means of quantitative trait locus analysis. This genetic dissection has resulted in molecular cloning of genes and loci with biological and agronomic interest. The success of these analyses depends strongly on the plant materials used. In the last decade, many kinds of plant materials, and particularly advanced backcross populations, have been developed for the genetic analysis of traits of interest. Some of those materials have been deposited in the public domain in order to facilitate further analyses of rice genetics and molecular biology. In this review, we describe how such plant materials, including chromosome segment substitution lines (CSSLs) and introgression lines, could be used in genetic analysis, as well as the kinds of plant materials that could be developed and that are now available to the rice research community. Furthermore, we introduce our current activities related to large-scale development of CSSLs using diverse Asian rice accessions as donors.

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