Kazutoshi Okuno

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions

The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.

Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice

Blast-Resistant Rice The durability of disease resistance for an agricultural crop reflects the extent to which the defense stands up to evolutionary dodges on the part of the pathogen. Pi21, which is a quantitative trait locus (QTL) of rice, contributes to a particularly durable resistance to a fungal rice blast disease: Rice plants carrying the resistant allele have been in cultivation for more than a century, and yet the pathogen has been unable to find a way through the defense. Fukuoka et al. (p. 998; see the news story by Normile) have now cloned the responsible Pi21 QTL allele and were able to separate Pi21 resistance from tightly linked reductions in grain quality, paving the way for more widespread use of this allele in rice breeding. Quantitative trait loci may offer a particularly durable strategy for disease resistance. Blast disease is a devastating fungal disease of rice, one of the world’s staple foods. Race-specific resistance to blast disease has usually not been durable. Here, we report the cloning of a previously unknown type of gene that confers non–race-specific resistance and its successful use in breeding. Pi21 encodes a proline-rich protein that includes a putative heavy metal–binding domain and putative protein-protein interaction motifs. Wild-type Pi21 appears to slow the plant’s defense responses, which may support optimization of defense mechanisms. Deletions in its proline-rich motif inhibit this slowing. Pi21 is separable from a closely linked gene conferring poor flavor. The resistant pi21 allele, which is found in some strains of japonica rice, could improve blast resistance of rice worldwide.

Genetic studies of speciation in cultivated rice. 5. Inter- and intraspecific differentiation in the waxy gene expression of rice

SummaryTo get an insight in the gene regulation at the waxy locus of rice, the Wx gene product (Wx protein) controlling the synthesis of amylose was examined by electrophoretic techniques. Among nonwaxy rice strains, two different alleles, Wxa and Wxb, were found at the waxy locus. Wxa drastically enhanced the quantitative level of Wx protein as well as the amylose content in endosperm starch as compared with Wxb. The alleles acted additively in triploid endosperms. This implies that regulatory elements responsible for the Wx gene expression are on the same chromosome. The distribution patterns of Wxa and Wxb in five species of Oryza revealed that the regulatory changes are closely related to racial differentiation within a common rice species (O. sativa), suggesting that Wxb might have been selected for through the difference in grain quality during domestication.

Development of SSR-based sorghum (Sorghum bicolor (L.) Moench) diversity research set of germplasm and its evaluation by morphological traits

Assessment and utilization of diversity in plant genetic resources is vital for the improvement of plant species. A sorghum diversity research set (SDRS) was developed by using SSR markers. A total of 320 sorghum accessions were selected based on geographic distribution from more than 3,500 germplasm accessions comprising Asia (East, Southeast, South and Southwest Asia) and Africa, conserved at NIAS Genebank, Japan. We selected 38 simple sequence repeats (SSR) markers which generated 146 alleles, covering ten chromosomes of sorghum from a three different published SSR linkage map of sorghum. The average percentage of polymorphic loci (P) and gene diversity (He) observed in this study were 82.8 and 0.217 respectively. Analysis showed a positive correlation with geographic pattern of differentiation. Based on SSR assessment, 107 sorghum accessions were selected as diversity research set. There was no significant difference in pattern of genetic spectrum between SDRS and base population. Similarly no greater change was observed for variability parameters (Dice, %P, He) and almost all of the SSR alleles were retained in selected sorghum accessions except for the loss of a single allele at locus Xtxp287. SDRS was sown during sorghum sowing season in two replications. Data were recorded on 26 important morphological traits according to the standard sorghum descriptors at Genebank. Analysis of variance showed a highly significant difference among all accessions for all of the traits. Morpho-agronomic traits could not effectively classify the accessions according to geographic origin by using cluster analysis.

The effect of environmental temperature on distribution of unit chains of rice amylopectin

The effects of environmental temperature during the early development of seeds on the structural characteristics of the endosperm starch were investigated using near-isogenic lines of rice plants (Taichung 65, waxy), grown under temperature controlled conditions. High performance gel permeation chromatography (HPLC) demonstrated that Pseudomonas isoamylase-debranched amylopectins of rice plants grown at lower temperature (25 °C) contain increased amounts of short chains and decreased amounts of long chains as compared with amylopectins obtained from rice plants grown at higher temperature (30°C). By high performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) of isoamylase-debranched amylopectins it was detected that the amount of unit chains with degree of polymerization (DP) 6 and 11-13, in the amylopectin of rice plants grown at lower temperature (25°C) had significantly increased and the amount of unit chains with DP 8, 22-24 and 29 had significantly decreased, as compared with the amylopectin of rice plants grown at higher temperature (30°C ). It was confirmed that the environmental temperature between 5 and 10 d after pollination strongly influenced the structure characteristics of the endosperm starch of rice plants.

Genetic differentiation and geographical distribution of barley germplasm based on RAPD markers

Random amplified polymorphic DNA (RAPD) analysis was used to characterize barley germplasm genetic diversity. For the analysis 303 morphologically distinctive accessions were selected from the VIR germplasm collection, St. Petersburg, Russia and the MAFF Genebank, Tsukuba, Japan to represent the principal regions of barley cultivation. A total of 93 polymorphic bands scored from RAPD patterns were used to generate a genetic distance matrix, which was used in both cluster and principal coordinate analysis. Both analysis clearly separated barley cultivars and local populations into three distinctive groups, which evidently reflect different directions in evolution and geographical distribution of barley. The hierarchy of accessions clustering in the first group indicates the westward distribution of barley from West Asia to Europe and New World across Ethiopia and then Mediterranean region. The principal breeding trends based on spike morphology are also observed in this group. The second group is associated with eastward distribution of the crop and represents a unified genetic group, which consists of East Asian and Central Asian accessions. The third distinctive group identified is connected with the evolution and dissemination of hulless forms in Central Asia and the Caucasus region. The conformity of identified genetic groups and clusters with the global centers of crops diversity (gene centers) determined by Vavilov (1926) and modern ecogeographical classification of barley is discussed.

Genetic diversity of Central Asian and north Caucasian Aegilops species as revealed by RAPD markers

RAPD analysis of 112 accessions of Aegilops tauschii Coss. (genome DD), Ae. cylindrica Host (CCDD), Ae. crassa Boiss. (DDMM), Ae. biuncialis Vis. (UUMM) and Ae. triuncialis L. (UUCC) collected in the Central Asia and north Caucasia was conducted. Aegilops accessions were divided into two major groups, corresponding to the D genome species and the U genome species. These groups were also separated into sub-groups according to species, except for the Ae. tauschii-cylindrica complex of accessions from Central Asia. Aegilops tauschii from north Caucasia was divided into two varietal groups, tauschii and meyeri. The Central Asian accessions of Aegilops species were more diverse than the accessions from north Caucasia. Aegilops tauschii and Ae. cylindrica accessions from north Caucasia were genetically uniform. Associations between altitudal variation of Aegilops species and variability of RAPD markers were not found.

Diversity in phenotypic profiles in landrace populations of Vietnamese rice: a case study of agronomic characters for conserving crop genetic diversity on farm

Phenotypic variation of agronomic characters in aromatic rice (Oryza sativa L.) was analyzed in order to elucidate the genetic diversity of the populations of rice landraces. Thirteen populations in Namdinh province, in the Red River Delta of Vietnam, were studied in both of farmers fields and an experimental field. Only small differences were found in agronomic characters among the populations, including populations containing different varieties. Variations among the populations in the frequency distributions of several characters suggested different degrees of diversity among the populations even among populations with the same variety name. The phenotypic profiles of farmers fields were different from those in an experimental field suggesting the environmental differences between them. One variety cultivated in the Myloc district had different phenotypic characters from the other varieties in the Haihau district more clearly in the experimental field. Since the small phenotypic variation in each of farm might be due to the genetic drift and selection by the farmers, on farm conservation of the landraces of rice is considered to be under a force to decrease phenotypic diversity. The present study suggests that the targeting several farms with different phenotypic profiles contribute to the conservation of regional genetic diversity of the landraces of rice.

RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.)

Abstract Complementary recessive genes hwd1 and hwd2 controlling hybrid breakdown (weakness of F2 and later generations) were mapped in rice using RFLP markers. These genes produce a plant that is shorter and has fewer tillers than normal plants when the two loci have only one or no dominant allele at both loci. A cultivar with two dominant alleles at the hwd1 locus and a cultivar with two dominant alleles at the hwd2 locus were crossed with a double recessive tester line. Linkage analysis was carried out for each gene independently in two F2 populations derived from these crosses. hwd1 was mapped on the distal region of rice genetic linkage map for chromosome 10, flanked by RFLP markers C701 and R2309 at a distance of 0.9 centiMorgans (cM) and 0.6 cM, respectively. hwd2 was mapped in the central region of rice genetic linkage map for chromosome 7, tightly linked with 4 RFLP markers without detectable recombination. The usefulness of RFLP mapping and map information for the genes controlling reproductive barriers are discussed in the context of breeding using diverse rice germplasm, especially gene introduction by marker-aided selection.

Intraspecific differentiation and geographical distribution of Wx alleles for low amylose content in endosperm of foxtail millet, Setaria italica (L.) Beauv.

To clarify the genetic mechanism which controls the variation in amylose content among nonwaxy landraces of foxtail millet, the inheritance of different starch types in endosperm was examined by I2-KI staining. The level of starch granule bound protein in foxtail millet endosperm was also analyzed using SDS-PAGE. The segregation for starch types in F2 and F3 seeds determined by I2-KI staining showed that there are three different alleles at the waxy (wx) locus. A major protein bound to starch granules was detected in nonwaxy endosperm but it was absent in most of the waxy endosperm, suggesting that the protein is the Wx gene product which is responsible for the synthesis of amylose in endosperm. The level of Wx protein proportionally corresponded to the amylose content among nonwaxy landraces. This implies that two different Wx alleles regulate quantitative levels of Wx protein. Landraces with the allele for low amylose content are from Taiwan, the Philippines, Indonesia and Thailand.