Loss of seed shattering was one of the key phenotypic changes selected for in the domestication of many crop species. Asian cultivated rice, Oryza sativa L., was domesticated from its wild ancestor, O. rufipogon, and three seed-shattering loci, qSH1, sh4 and qSH3, have been reported to be involved in the loss of seed shattering in cultivated rice. Here, we analysed the seed-shattering behaviour of wild rice using introgression lines carrying the cultivated alleles from O. sativa Nipponbare in the genetic background of wild rice, O. rufipogon W630. We first carried out fine mapping of the qSH3 region and found that the qSH3 locus is localized in an 850-kb region on chromosome 3. We then analysed the effects of the Nipponbare alleles at sh4 and qSH3 on seed-shattering behaviour in wild rice, as a mutation at qSH1 was not commonly found in rice cultivars. Seed-shattering behaviour did not change in the two types of introgression line independently carrying the Nipponbare-homozygous alleles at sh4 or qSH3 in the genetic background of wild rice. However, the introgression lines having the Nipponbare-homozygous alleles at both sh4 and qSH3 showed a reduction in the degree of seed shattering. Histological and scanning electron microscopy analyses revealed that abscission layer formation was inhibited around the vascular bundles in these lines. Since the qSH3 region, as well as sh4, has been shown to be under artificial selection, the interaction of mutations at these two loci may have played a role in the initial loss of seed shattering during rice domestication.

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Reactive oxygen species (ROS) generated during energy production processes are a major cause of oxidative DNA damage. A DNA glycosylase encoded by the Ogg1 gene removes oxidized guanine bases and is widely conserved. However, the biological role of the gene in individual organisms has not yet been characterized in Drosophila, which is a suitable model to study the influence of oxidative damage on senescence. Here, we performed a genetic analysis to confirm that Ogg1 plays an essential role in the removal of 8-oxo-guanines from nuclei. We first confirmed by quantitative real-time PCR that Ogg1 mRNA expression was reduced by 30–55% in Ogg1 mutants and in flies expressing inducible Ogg1 dsRNA compared to control flies. We then showed that additional accumulation of 8-oxo-guanines occurred in the nuclei of epithelial midgut cells after paraquat feeding in flies with downregulated Ogg1 expression. We confirmed that a transposon possessing the UAS sequence was integrated in the 5′-UTR of the Ogg1 alleles and that it is oriented in the same transcriptional direction as the gene. Using the Gal4/UAS system, which enables us to induce ectopic expression in Drosophila, we induced overexpression of Ogg1 by 40-fold. We observed a lower amount of 8-oxo-guanine in the midgut epithelial cells of adults overexpressing Ogg1. These genetic data strongly suggest that the Drosophila Ogg1 ortholog CG1795 plays an essential role in the suppression of 8-oxo-guanines, consistent with its role in other organisms. Although adult flies with reduced Ogg1 expression failed to show elevated sensitivity to paraquat, those with Ogg1 overexpression showed resistance to oxidative stress by paraquat feeding and had a significantly longer lifespan in normal feeding conditions. These observations are consistent with the hypothesis that oxidative DNA damage by ROS accumulation is a major contributor to senescence.

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The Indian subcontinent and Southeast Asia are hotspots of murine biodiversity, but no species from the Arakan Mountain system that demarcates the border between the two areas has been subjected to molecular phylogenetic analyses. We examined the mitochondrial cytochrome b gene sequences in six murine species (the Rattus rattus species complex, R. norvegicus, R. nitidus, Berylmys manipulus, Niviventer sp. and Mus musculus) from Manipur, which is located at the western foot of the mountain range. The sequences of B. manipulus and Niviventer sp. examined here were distinct from available congeneric sequences in the databases, with sequence divergences of 10–15%. Substantial degrees of intrapopulation divergence were detected in R. nitidus and the R. rattus species complex from Manipur, implying ancient habitation of the species in this region, while the recent introduction by modern and prehistoric human activities was suggested for R. norvegicus and M. musculus, respectively. In the nuclear gene Mc1r, also analyzed here, the R. rattus species complex from Manipur was shown to possess allelic sequences related to those from the Indian subcontinent in addition to those from East Asia. These results not only fill gaps in the phylogenetic knowledge of each taxon examined but also provide valuable insight to better understand the biogeographic importance of the Arakan Mountain system in generating the species and genetic diversity of murine rodents.

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The long-tailed goral, Naemorhedus caudatus, is an internationally endangered species. This species is distributed throughout Northeastern Asia including Northeastern China, the Russian Far East and the Korean peninsula. The population size of long-tailed gorals is currently decreasing in South Korea, and thus effective conservation of the animal is urgently needed. Although the evolution and phylogeny of this animal have been studied, population genetic studies are needed to design effective conservation and management strategies. To evaluate the present status of genetic diversity and genetic structure of long-tailed gorals in South Korea, we investigated genetic variability among 68 goral individuals from different regions, including 11 captive zoo animals, at 12 microsatellite loci. The level of genetic diversity was moderate in wild goral populations, but lower in the captive group. The goral population from the lower northeast region of South Korea was distinct from the upper northeast population, probably due to the natural climatic and geographic conditions. The genetic characteristics of the captive group were more similar to those of the upper northeast population than the lower northeast, confirming that the zoo animals originated in the Seorak Mountain range. Direct translocations between the upper and lower northeast populations are not currently recommended considering the natural population structure and the moderate levels of genetic diversity in the two populations. This study highlights the importance of genetic information in designing effective conservation strategies and translocations of endangered animals, including the Korean goral.

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Unsupervised data mining capable of extracting a wide range of information from big sequence data without prior knowledge or particular models is highly desirable in an era of big data accumulation for research on genes, genomes and genetic systems. By handling oligonucleotide compositions in genomic sequences as high-dimensional data, we have previously modified the conventional SOM (self-organizing map) for genome informatics and established BLSOM for oligonucleotide composition, which can analyze more than ten million sequences simultaneously and is thus suitable for big data analyses. Oligonucleotides often represent motif sequences responsible for sequence-specific binding of proteins such as transcription factors. The distribution of such functionally important oligonucleotides is probably biased in genomic sequences, and may differ among genomic regions. When constructing BLSOMs to analyze pentanucleotide composition in 50-kb sequences derived from the human genome in this study, we found that BLSOMs did not classify human sequences according to chromosome but revealed several specific zones, which are enriched for a class of CG-containing pentanucleotides; these zones are composed primarily of sequences derived from pericentric regions. The biological significance of enrichment of these pentanucleotides in pericentric regions is discussed in connection with cell type- and stage-dependent formation of the condensed heterochromatin in the chromocenter, which is formed through association of pericentric regions of multiple chromosomes.

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Several types of hemoglobin D (Hb D) are distinguishable by DNA analysis, and the aim of this study was to identify the types of Hb D variant and β-globin gene haplotypes linked to Hb D in Mazandaran Province, northern Iran. Fifty five individuals were identified as Hb D carriers, and PCR-RFLP analysis revealed that all 55 had the Hb D-Los Angeles type. To identify haplotypes associated with the β^D allele, family linkage analysis, using the PCR-RFLP method for seven polymorphisms in the β-globin gene cluster, was carried out on families of 23 of these 55 individuals. We observed three different haplotypes in association with Hb D-Los Angeles. In most cases (91.4%) β^D alleles were linked to haplotype I [+ – – – – + +]. Haplotype II [– + + – + + +] and an atypical haplotype [– + + – – + –] were each in association with the β^D allele in only one case (4.3%). This is the first report worldwide of the [– + + – – + –] haplotype in association with Hb D-Los Angeles. We conclude that more than 90% of the evaluated Hb D-Los Angeles alleles in Mazandaran have the same origin, and the two rare haplotypes may represent different genetic origins and/or other molecular events, such as gene conversion or recombination, in the region.

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The first sentence in the acknowledgment on p. 234 should be changed to “This study was supported in part by the Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University and the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korean government (MEST) (No. 2009-0080227).”

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