Landrace of japonica rice,Akamai exhibits enhanced root growth and efficient leaf phosphorus remobilization in response to limited phosphorus availability

Aims

Phosphorus (P) acquisition through extensive root growth and P allocation to different plant organs through efficient remobilization are important for acclimation of crop plants to P-limited environments. This study elucidated changes in rice root growth and leaf P-remobilization and their influence on grain yield under P deficiency.

Methods

Two pot experiments were conducted with (P100) and without (P0) inorganic P supply using two Japanese rice cultivars: Akamai (Yamagata) and Koshihikari. Multiple harvests were made until the panicle initiation stage. Root and shoot growth response, P acquisition, and temporal leaf P-remobilization efficiency were measured. A separate experiment ascertained the final yield and grain P status.

Results

The Akamai rice cultivar showed enhanced root growth and more acquired soil P. The Akamai root dry weight was 66% greater than that of Koshihikari under P0. Confronting P deficiency, Akamai remobilized some P from its lower mature leaves to upper younger leaves starting from early growth. The remobilized P fraction increased to 72% at panicle initiation under P0. Under P0, Akamai exhibited two-fold higher leaf P-remobilization efficiency than under P100.

Conclusions

Enhanced root growth that facilitates acquisition of more soil P through better soil exploration coupled with efficient leaf P remobilization from the early growth stage improves adaptation of Akamai rice cultivar to P-limited environments. Nevertheless, P-starvation responses did not facilitate higher grain yields in P-limited conditions.

     

Genome‐wide association mapping for phenotypic plasticity in rice

Phenotypic plasticity of plants in response to environmental changes is important for adapting to changing climate. Less attention has been paid to exploring the advantages of phenotypic plasticity in resource‐rich environments to enhance the productivity of agricultural crops. Here, we examined genetic variation for phenotypic plasticity in indica rice (Oryza sativa L.) across two diverse panels: (1) a Phenomics of Rice Adaptation and Yield (PRAY) population comprising 301 accessions; and (2) a Multi‐parent Advanced Generation Inter‐Cross (MAGIC) indica population comprising 151 accessions. Altered planting density was used as a proxy for elevated atmospheric CO₂ response. Low planting density significantly increased panicle weight per plant compared with normal density, and the magnitude of the increase ranged from 1.10 to 2.78 times among accessions for the PRAY population and from 1.05 to 2.45 times for the MAGIC population. Genome‐wide‐association studies validate three E nvironmental R esponsiveness (ER) candidate alleles (qER1–3) that were associated with relative response of panicle weight to low density. Two of these alleles were tested in 13 genotypes to clarify their biomass responses during vegetative growth under elevated CO₂ in Japan. Our study provides evidence for polymorphisms that control rice phenotypic plasticity in environments that are rich in resources such as light and CO₂.     

The teleomorph of Leptographium yunnanense, discovered in crosses among isolates from Thailand, China, and Japan

A teleomorph was discovered in crosses among isolates of Leptographium yunnanense isolated from Pinus spp. originating in Thailand, China, and Japan. The ascocarps are black, globose to subglobose, and lacking necks. Ascospores are hyaline, 1-celled, surrounded by hyaline sheaths, and appear cucullate in side view, quadrangular in face view, and triangular in end view. Three species were known to have teleomorphs morphologically similar to the present fungus. However, their anamorphs were distinguishable from L. yunnanense. Thus, this teleomorph is described as Grosmannia yunnanensis. Contribution No. 214, Laboratory of Plant Parasitic Mycology, Graduate School of Life & Environmental Sciences, University of Tsukuba.     

NMR‐based characterization of a refolding intermediate of β2‐microglobulin labeled using a wheat germ cell‐free system

In patients with dialysis‐related amyloidosis, β2‐microglobulin (β2‐m) is a major structural component of amyloid fibrils. It has been suggested that the partial unfolding of β2‐m is a prerequisite to the formation of amyloid fibrils, and that the folding intermediate trapped by the non‐native trans‐Pro32 isomer leads to the formation of amyloid fibrils. Although clarifying the structure of this refolding intermediate by high resolution NMR spectroscopy is important, this has been made difficult by the limited lifetime of the intermediate. Here, we studied the structure of the refolding intermediate using a combination of amino acid selective labeling with wheat germ cell‐free protein synthesis and NMR techniques. The HSQC spectra of β2‐ms labeled selectively at either phenylalanine, leucine, or valine enabled us to monitor the structures of the refolding intermediate. The results suggested that the refolding intermediate has an overall fold and cores similar to the native structure, but contains disordered structures around Pro32. The fluctuation of the β‐sheet regions especially the last half of the βB strand and the first half of the βE strand, both suggested to be important for amyloidogenicity, may transform β2‐m into an amyloidogenic structure.     

Constant association of ophiostomatoid fungi with the bark beetle <Emphasis Type="Italic">Ips subelongatus</Emphasis> invading Japanese larch logs

Ceratocystiopsis, Ceratocystis, Grosmannia, and Ophiostoma species were isolated from Ips subelongatus and beetle-infested Japanese larch logs collected at several areas in central and northern Honshu Island, Japan, to determine constant associates of I. subelongatus. Ceratocystiopsis minuta, two species of Ceratocystis, three species of Grosmannia, and four species of Ophiostoma were isolated. Of the fungi isolated in the present study, G. laricis, O. brunneociliatum, and O. piceae were constant associates of the beetles. Ceratocystis fujiensis, Ceratocystiopsis minuta, and Ophiostoma sp. F were occasionally isolated with high frequencies of occurrence but were not consistent associates. Ceratocystis fujiensis was most often isolated as the leading fungal invasion in the sapwood of Japanese larch logs invaded by I. subelongatus, confirming that the fungus acts as a primary invader of sapwood in beetle-attacked logs. Contribution No. 221, Laboratory of Plant Parasitic Mycology, Graduate School of Life and Environmental Sciences, University of Tsukuba     

Characterization of teleost Mdga1 using a gene‐trap approach in medaka (Oryzias latipes)

MAM domain containing glycosilphosphatidilinositol anchor 1 (MDGA1) is an IgCAM protein present in many vertebrate species including humans. In mammals, MDGA1 is expressed by a subset of neurons in the developing brain and thought to function in neural cell migration. We identified a fish ortholog of mdga1 by a gene‐trap screen utilizing the Frog Prince transposon in medaka (Japanese killifish, Oryzias latipes). The gene‐trap vector was inserted into an intronic region of mdga1 to form a chimeric protein with green fluorescent protein, allowing us to monitor mdga1 expression in vivo. Expression of medaka mdga1 was seen in various types of embryonic brain neurons, and specifically in neurons migrating toward their target sites, supporting the proposed function of MDGA1. We also isolated the closely related mdga2 gene, whose expression partially overlapped with that of mdga1. Despite the fact that the gene‐trap event eliminated most of the functional domains of the Mdga1 protein, homozygous embryos developed normally without any morphological abnormality, suggesting a functional redundancy of Mdga1 with other related proteins. High sequential homology of MDGA proteins between medaka and other vertebrate species suggests an essential role of the MDGA gene family in brain development among the vertebrate phylum. genesis 47:505–513, 2009. © 2009 Wiley‐Liss, Inc.     

An inexpensive high-throughput method to extract high yields of good quality DNA from fungi

We developed an efficient method for high-throughput extraction of high-quality DNA from various fungi. In this method, fungal mycelia were cultured and harvested on the surfaces of membranes on media plates. We degraded cell walls using a lytic enzyme (Yatalase). Purification was performed on 96-well glass fibre filter plates. DNA was successfully extracted from various fungi provided (102 genus 132 species) at high yields and quality, and proved suitable for storage, polymerase chain reaction amplification and restriction enzyme digestion. The method described is rapid, inexpensive and automation friendly. This enables the simultaneous extraction of large numbers of samples, significantly improving the potential throughput in genomics, particularly in diagnostic and population studies.     

Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.     

Partial agonistic effect of 9-hydroxycorynantheidine on mu-opioid receptor in the guinea-pig ileum

Mitragynine is an indole alkaloid isolated from the Thai medicinal plant Mitragyna speciosa that is reported to have opioid agonistic properties. The 9-demethyl analogue of mitragynine, 9-hydroxycorynantheidine, is synthesized from mitragynine. 9-Hydroxycorynantheidine inhibited electrically stimulated guinea-pig ileum contraction, but its maximum inhibition was weaker than that of mitragynine and its effect was antagonized by naloxone, suggesting that 9-hydroxycorynantheidine possesses partial agonist properties on opioid receptors. Receptor binding assays revealed that 9-hydroxycorynantheidine has high affinity for mu-opioid receptors. In an assay of the guinea-pig ileum, naloxone shifted the concentration-response curves for [D-Ala(2), N-MePhe(4), Gly-ol(5)]-enkephalin (DAMGO), (5alpha,7alpha,8beta)-(+)-N-Methyl-N-[7-(1-pyrrolidinyl)-1-oxaspiro[4.5]dec-8-yl]-benzeneacetamide (U69593) and 9-hydroxycorynantheidine to the right in a competitive manner. The pA(2) values of naloxone against 9-hydroxycorynantheidine and DAMGO were very similar, but not that against U69593. As indicated by the two assay systems, the opioid effect of 9-hydroxycorynantheidine is selective for the mu-opioid receptor. 9-Hydroxycorynantheidine shifted the concentration-response curve for DAMGO slightly to the right. Pretreatment with the mu-opioid selective and irreversible antagonist beta-funaltorexamine hydrochloride (beta-FNA) shifted the concentration-response curve for DAMGO to the right without affecting the maximum response. On the other hand, beta-FNA did not affect the curve for 9-hydroxycorynantheidine, but decreased the maximum response because of the lack of spare receptors. These studies suggest that 9-hydroxycorynantheidine has partial agonist properties on mu-opioid receptors in the guinea-pig ileum.     

Unintentional introductions of microscopic organisms associated with forest insects

International trade and travel are devastating native flora and fauna in many countries through the intentional and/or unintentional introduction of exotic organisms. Pathway control appears to be particularly effective for microscopic organisms such as mites, nematodes, and fungi that are difficult to see with the naked eye. However, taxonomic and ecological information on such organisms is scarce, sometimes causing time lags or failure in eradication programs. Several groups of mites, nematodes, and fungi commonly share a habitat with insects or use them as dispersal agents (phoresy). Some exotic mites and nematodes are introduced simultaneously with exotic insects, sometimes in wood materials. In Japan, mites, nematodes, and fungi have been collected from lucanid beetles introduced as pets from Southeast Asia. While no lethal nematode species have been collected from lucanid beetles, one hemolymph-sucking mite species, inhabiting the sub-elytral space of its native host, is able to easily switch to the Japanese beetle, Dorcus rectus, killing the insect. Yeasts have also been reported on exotic beetles and laboulbeniomycetes have been found on mites associated with the beetles, although their interactions are unknown. Despite the lack of information available about other mites, nematodes, and fungi associated with intentionally and unintentionally introduced forest insects, our analysis of insect species listed by the International Union for Conservation of Nature suggests that unintentional introductions of the microscopic organisms are quite common as a consequence of the existence of symbiotic relationships such as phoresy and parasitism.