Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

<p>Abstract</p> <p>Background</p> <p>To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.</p> <p>Results</p> <p>The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7× the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity</p> <p>Conclusions</p> <p>Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.</p

Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing

Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions–deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7% of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi (http://www.nodai-genome.org/oryza_sativa_en.html)

Resection of the Gastric Tube Reconstructed through the Retrosternal Route without Sternotomy

With advances of combined modality therapy, prognoses in esophageal cancer have been improving. After resection of esophageal cancer, the development of gastric tube cancer is a risk. While such cancer in an early stage can be cured endoscopically, total gastric tube resection is indicated in advanced stages. A 68-year-old man underwent subtotal esophagectomy reconstructed with a gastric tube through the retrosternal route. Gastric cancer was found one and a half years postoperatively. The gastric tube was resected without sternotomy. This is the first report of a patient undergoing resection of the gastric tube reconstructed through the retrosternal route without sternotomy

Toward a Model for Marking up Non-SI Units and Measurements

This paper presents a markup model for encoding non-SI units and measurements. Historical texts contain many examples of compound measurements, composed of sets of units and numerical components. Instead of using the element, which requires a single set of @unit and @quantity, we propose a newly defined set of tags for encoding idiosyncratic measurement semantics, namely (model.encodingDescPart), (model.global and contained by ), (model.measureLike), and a relevant attribute @factor (which shows factors of numerical values given in a referenced element). All of these elements and attributes will be included in the TEI P5 Guidelines, and they are especially useful when encoding units that are not based on the decimal system. Though this paper offers example encodings based on a Japanese historical source, the Engi-Shiki, this model is also applicable to the markup of units used for measurement within various cultural spheres other than Japan

Spatially resolved measurement of helium atom emission line spectrum in scrape-off layer of Heliotron J by near-infrared Stokes spectropolarimetry

1視線の観測のみで核融合プラズマ中のヘリウム近赤外輝線の発光分布を推定. 京都大学プレスリリース. 2022-09-26.For plasma spectroscopy, Stokes spectropolarimetry is used as a method to spatially invert the viewing-chord-integrated spectrum on the basis of the correspondence between the given magnetic field profile along the viewing chord and the Zeeman effect appearing on the spectrum. Its application to fusion-related toroidal plasmas is, however, limited owing to the low spatial resolution as a result of the difficulty in distinguishing between the Zeeman and Doppler effects. To resolve this issue, we increased the relative magnitude of the Zeeman effect by observing a near-infrared emission line on the basis of the greater wavelength dependence of the Zeeman effect than of the Doppler effect. By utilizing the increased Zeeman effect, we are able to invert the measured spectrum with a high spatial resolution by Monte Carlo particle transport simulation and by reproducing the measured spectra with the semiempirical adjustment of the recycling condition at the first walls. The inversion result revealed that when the momentum exchange collisions of atoms are negligible, the velocity distribution of core-fueling atoms is mainly determined by the initial distribution at the time of recycling. The inversion result was compared with that obtained using a two-point emission model used in previous studies. The latter approximately reflects the parameters of atoms near the emissivity peak

Cortical Factor Feedback Model for Cellular Locomotion and Cytofission

Eukaryotic cells can move spontaneously without being guided by external cues. For such spontaneous movements, a variety of different modes have been observed, including the amoeboid-like locomotion with protrusion of multiple pseudopods, the keratocyte-like locomotion with a widely spread lamellipodium, cell division with two daughter cells crawling in opposite directions, and fragmentations of a cell to multiple pieces. Mutagenesis studies have revealed that cells exhibit these modes depending on which genes are deficient, suggesting that seemingly different modes are the manifestation of a common mechanism to regulate cell motion. In this paper, we propose a hypothesis that the positive feedback mechanism working through the inhomogeneous distribution of regulatory proteins underlies this variety of cell locomotion and cytofission. In this hypothesis, a set of regulatory proteins, which we call cortical factors, suppress actin polymerization. These suppressing factors are diluted at the extending front and accumulated at the retracting rear of cell, which establishes a cellular polarity and enhances the cell motility, leading to the further accumulation of cortical factors at the rear. Stochastic simulation of cell movement shows that the positive feedback mechanism of cortical factors stabilizes or destabilizes modes of movement and determines the cell migration pattern. The model predicts that the pattern is selected by changing the rate of formation of the actin-filament network or the threshold to initiate the network formation