Kazuo N. Watanabe

Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice

Common non-waxy (Wx) rice cultivars contain two different alleles at the waxy locus, designated Wxa and Wxb, which encode different levels of granule-bound starch synthases and are hence involved in the control of endosperm amylose content. The Wxa allele was predominant in non-waxy indica cultivars, whereas the Wxb allele was common to the non-waxy japonica variety. Recently, some of the molecular mechanisms underlying the differentiation of Wxa from Wxb have been characterized. One structural difference between these two alleles was shown to be due to alternative splicing caused by a single-base substitution (AGGT to AGTT) at a donor site of the first intron within the Wx gene. In the case of waxy (wx) rice, it was not possible to distinguish whether the each wx allele was derived from Wxa or Wxb alleles by phenotypic analysis. However, we succeeded in developing a derived cleaved amplified polymorphic sequence (dCAPS) marker for the detection of the one-base splicing mutation without the need for sequencing. A mismatch primer was used to generate a restriction site in the Wxa allele (AGGT) but not in the Wxb allele (AGTT). Three hundred fifty-three waxy rice strains that are widely found in Asia were then employed for analysis using this dCAPS marker. Our findings suggested that waxy rice strains have both Wxa- and Wxb-derived alleles, but that the Wxb-derived allele was predominant, and its distribution was independent of indica-japonica differentiation. The wild relatives of cultivated rice all possessed the AGGT allele. It was concluded that the waxy mutations, and the corresponding rice cultivation, originated from japonica during the evolution and domestication process of rice and was preferentially selected by most Asian peoples.

Recessive and Dominant Genes Interfere with the Vascular Transport of Potato virus A in Diploid Potatoes

Resistance to Potato virus A (PVA) was examined in a diploid cross involving Solanum tuberosum subsp. andigena as a resistance source. Hypersensitive resistance (HR) to PVA cosegregated with extreme resistance (ER) to Potato virus Y conferred by the dominant gene Ry(adg) on chromosome XI. Hence, HR to PVA was controlled by a novel, dominant resistance gene closely linked to Ry(adg), or Ry(adg) recognized both viruses but conferred a different type of resistance to each virus. The HR prevented systemic infection with PVA following mechanical inoculation but not following graft inoculation. Another, recessive gene, ra, that may be linked or even allelic with Ry(adg) fully blocked vascular transport of PVA in graft-inoculated plants. Hence, a possibility exists that the genes for the three types of resistance to potyviruses may reside at the same, resistance gene-rich chromosome region syntenic in solanaceous species and might be related. The gene ra acted against all of the three PVA strains tested and, therefore, the avirulence determinants could not be mapped. However, also, PVA strain-specific resistance was found in the progeny. It was overcome by mutations introduced into the viral genome-linked protein and the helper component proteinase and/or the coat protein.

Comparison of contemporary mating patterns in continuous and fragmented Eucalyptus globulus native forests.

While habitat fragmentation is a central issue in forest conservation studies in the face of broad‐scale anthropogenic changes to the environment, its effects on contemporary mating patterns remain controversial. This is partly because of the inherent variation in mating patterns which may exist within species and the fact that few studies have replication at the landscape level. To study the effect of forest fragmentation on contemporary mating patterns, including effective pollen dispersal, we compared four native populations of the Australian forest tree, Eucalyptus globulus. We used six microsatellite markers to genotype 1289 open‐pollinated offspring from paired fragmented and continuous populations on the island of Tasmania and in Victoria on mainland Australia. The mating patterns in the two continuous populations were similar, despite large differences in population density. In contrast, the two fragmented populations were variable and idiosyncratic in their mating patterns, particularly in their pollen dispersal kernels. The continuous populations showed relatively high outcrossing rates (86–89%) and low correlated paternity (0.03–0.06) compared with the fragmented populations (65–79% and 0.12–0.20 respectively). A greater proportion of trees contributed to reproduction in the fragmented (de/d≥ 0.5) compared with the continuous populations (de/d = 0.03–0.04). Despite significant inbreeding in the offspring of the fragmented populations, there was little evidence of loss of genetic diversity. It is argued that enhanced medium‐ and long‐distance dispersal in fragmented landscapes may act to partly buffer the remnant populations from the negative effects of inbreeding and drift.

Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.

Assessment of cytochrome P450 sequences offers a useful tool for determining genetic diversity in higher plant species

To investigate and develop new genetic tools for assessing genome-wide diversity in higher plant-species, polymorphisms of gene analogues of mammalian cytochrome P450 mono-oxygenases were studied. Data mining on Arabidopsis thaliana indicated that a small number of primer-sets derived from P450 genes could provide universal tools for the assessment of genome-wide genetic diversity in diverse plant species that do not have relevant genetic markers, or for which, there is no prior inheritance knowledge of inheritance traits. Results from PCR amplification of 51 plant species from 28 taxonomic families using P450 gene-primer sets suggested that there were at least several mammalian P450 gene mammalian-analogues in plants. Intra- and inter- specific variations were demonstrated following PCR amplifications of P450 analogue fragments, and this suggested that these would be effective genetic markers for the assessment of genetic diversity in plants. In addition, BLAST search analysis revealed that these amplified fragments possessed homologies to other genes and proteins in different plant varieties. We conclude that the sequence diversity of P450 gene-analogues in different plant species reflects the diversity of functional regions in the plant genome and is therefore an effective tool in functional genomic studies of plants.

The influence of genes regulating transmembrane transport of Na+ on the salt resistance of Aeluropus lagopoides

Plantlets of Aeluropus lagopoides (Linn.) Trin. Ex Thw. were grown at different NaCl concentrations (26, 167, 373 and 747mM) for 3, 7 and 15 days; their growth, osmotic adjustment, gas exchange, ion compartmentalisation and expression of various genes related to Na+ flux was studied. Plantlets showed optimal growth in non-saline (control; 26mM NaCl) solutions, whereas CO2/H2O gas exchange, leaf water concentration and water use efficiency decreased under all salinity treatments, accompanied by increased leaf senescence, root ash, sodium content and leaf osmolality. A decrease in malondialdehyde (MDA) content with time was correlated with Na+ accumulation in the leaf apoplast and a concomitant increase in Na+ secretion rate. A. lagopoides accumulated a higher concentration of Na+ in root than in leaf vacuoles, corresponding with higher expression of V-NHX and lower expression of PM-NHX in root than leaf tissue. It appears that V-ATPase plays a vital role during Na+ transport by producing an electromotive force, driving ion transport. Leaf calcium increased with increasing salinity, with more rapid accumulation at high salinity than at low salinity, indicating a possible involvement of Ca2+ in maintaining K+:Na+ ratio. Our results suggest that A. lagopoides successfully compartmentalised Na+ at salinities up to 373mM NaCl by upregulating the gene expression of membrane linked transport proteins (V-NHX and PM-NHX). At higher salinity (747mM NaCl), a reduction in the expression of V-NHX and PM-NHX in leaves without any change in the rate of salt secretion, is a possible cause of the toxicity of NaCl.

Potato genetics, genomics, and applications.

Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding.

Microbial Community Analyses Using a Simple, Rapid Detection Method for DNA Fingerprints with a Fluorescence Scanner

A simple detection procedure was developed for terminal restriction fragment length polymorphism and ribosomal intergenic spacer analysis for microbial community analysis. A fluorescence scanner enables generation of fingerprinting data in these methods within 3 h of obtaining PCR products of microbial communities.

Metabolic Profiling of Transgenic Potato Tubers Expressing Arabidopsis Dehydration Response Element-Binding Protein 1A (DREB1A)

Untargeted metabolome analyses play a critical role in understanding possible metabolic fluctuations of crops under varying environmental conditions. This study reports metabolic profiles of transgenic potato tubers expressing the Arabidopsis DREB1A transcription factor gene, which induces expression of genes involved in environmental stress tolerance. A combination of targeted and untargeted metabolomics demonstrated considerable metabolome differences between the transgenic lines and nontransgenic parent cultivars. In the transgenic lines, stimulation of stress responses was suggested by elevated levels of the glutathione metabolite, γ-aminobutyric acid (GABA), and by the accumulation of β-cyanoalanine, a byproduct of ethylene biosynthesis. These results suggest that the Arabidopsis DREB1A expression might directly or indirectly enhance endogenous potato stress tolerance systems. The results indicate that transgenesis events could alter the metabolic compositions in food crops, and therefore metabolomics analysis could be a most valuable tool to monitor such changes.

Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato

Global warming has become a major issue within the last decade. Traditional breeding programs for potato have focused on increasing productivity and quality and disease resistance, thus, modern cultivars have limited tolerance of abiotic stresses. The introgression of abiotic stress tolerance into modern cultivars is essential work for the future. Recently, many studies have investigated abiotic stress using transgenic techniques. This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century. Dividing studies into these three stress categories for this review was difficult. Thus, based on the study title and the transgene property, transgenic studies were classified into five categories in this review; oxidative scavengers, transcriptional factors, and above three abiotic categories. The review focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives. From a practical application perspective, further evaluation of transgenic potato with abiotic stress tolerance is required. Although potato plants, including wild species, have a large potential for abiotic stress tolerance, exploration of the factors responsible for conferring this tolerance is still developing. Molecular breeding, including genetic engineering and conventional breeding using DNA markers, is expected to develop in the future.