Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing

Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world’s most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between ‘Purple Sweet Lord’ (PSL) and ‘90IDN-47’ cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (~90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato.     

Geographical differentiation of Asian taro, Colacasia esculenta (L.) Schott, detected by RAPD and isozyme analyses

Geographical differentiation and phylogenetic relationships of Asian taros, Colocasia esculenta (L.) Schott, and related species were analyzed by random amplified polymorphic DNA (RAPD) and isozymes of 13 enzyme systems with special interest in the accessions from the Yunnan area of China, which supposedly has served the secondary center of taro diversification and dispersal into the temperate Far East Asia. The RAPD analysis was found to be better suited for detecting genetic differences within taros and among its related species. However, both RAPD and isozyme analyses estimated quite similar genetic relationships within taros and between related species. Genetic differentiation was evident in the taro accessions of Nepal, Yunnan and other Asian areas; but, phylogenetic relationships between the differentiated taro groups were not clearly determined. When taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro populations was transferred possibly causing random differentiation among locally adapted taro populations. Some of the Yunnan and Japanese accessions were found to be direct descendants of the common triploid population. Further analysis on taros from the eastern China and Korea is necessary to clarify the Yunnan's role in taro diversification and dispersal. The significant local differentiation in Asian taros was clearly demonstrated by RAPD and isozyme analyses in this study, and the results of this study will serve as a base to establish evolutionary and genetic relationships among Asian taros. This revised version was published online in August 2006 with corrections to the Cover Date.     

Optimal sampling strategies for evaluating fruit softening after harvest in apple breeding

Environmental variance components associated with year, tree, and harvest date were estimated for fruit softening after harvest in apple (Malus × domestica Borkh.) to determine their relative importance and design optimum sampling strategies to discriminate genotypes in apple breeding. Fruit were stored after harvest under 20± 2 ^∘C and 80± 5%RH. Softening was evaluated by adapting the change in firmness during storage to a linear regression and defining the regression coefficient as the softening rate. Environmental variances associated with genotype × year interaction, among trees, year × tree interaction, and among harvest dates were all very small, namely, 2.7, 0.1, 5.2, and 5.7%, respectively, to the total variance obtained from the analysis of variance for the softening rate. The variance associated with genotype, at 57.3%, was very large. On the basis of the number of fruit necessary for firmness measurements, two times harvest is an efficient strategy to determine a genotype mean for the softening.     

Facing the Challenge of Social Forestry in Japan: The Case of Reviving Harmonious Coexistence Between Forest and People in Okayama Prefecture

Social forestry as a development strategy has evolved since the 1970s, especially in the tropics, to address forest degradation and promote local community development amidst the burgeoning population in these areas. As a practice, however, social forestry has been in place since ancient times in many parts of the world, including Japanese forest communities. Forest-people relationships in Japan drastically changed through massive afforestation programs after the energy source change and with the industrialization of the forest sector in 1950s. The majority of the planted forests are underutilized today and forest communities are marginalized due to the decline of forestry operations, depopulation, and changes in people’s values. Some communities address this concern by inviting potential urban migrants who may be interested in settling in rural areas. Using the case of the Nishiawakura Village in Okayama Prefecture, this paper explores the recent challenges confronting social forestry in Japan. It is found that underutilization of forest resources can be a cause of serious environmental degradation and marginalization of forest communities, and that Nishiawakura’s journey to renew forest management in partnership with migrants is a process of revisiting and creating the forest-people relationship. This study advances two related arguments, namely (1) the interaction of the local people and the migrants brings new perspectives to forest management, and (2) in a community facing depopulation and underutilization of forest resources, social forestry can be an effective approach to rediscover traditional forest management in a new form and revitalize forests and local communities.     

Characterization of a Phytophthora mating hormone

Water molds of the genus Phytophthora include many plant pathogens responsible for epidemics such as potato blight and sudden oak death, causing global economic damages. Sexual reproduction is of biological importance in Phytophthora and has been believed to be stimulated by unknown endogenous factors named a hormones. We describe here the chemical characterization of a Phytophthora mating hormone, a1, which was obtained from approximately 2 tons of culture fluid of one mating type of a species and which induced sexual spores on the counter-mating type at a nanogram level.     

Formation of a one-dimensional array of oxygen in a microporous metal-organic solid

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O2 locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O-O stretching Raman band and magnetic susceptibilities are characteristic of the confined O2 molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).     

Mitogenic influence of human R-spondin1 on the intestinal epithelium

Several described growth factors influence the proliferation and regeneration of the intestinal epithelium. Using a transgenic mouse model, we identified a human gene, R-spondin1, with potent and specific proliferative effects on intestinal crypt cells. Human R-spondin1 (hRSpo1) is a thrombospondin domain-containing protein expressed in enteroendocrine cells as well as in epithelial cells in various tissues. Upon injection into mice, the protein induced rapid onset of crypt cell proliferation involving beta-catenin stabilization, possibly by a process that is distinct from the canonical Wnt-mediated signaling pathway. The protein also displayed efficacy in a model of chemotherapy-induced intestinal mucositis and may have therapeutic application in gastrointestinal diseases.