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Background Tetrad sterility in potato is caused by a specific cytoplasm, called TSC sto , derived from the Mexican wild tetraploid species Solanum stoloniferum . Different S. stoloniferum accessions crossed as females with S. tuberosum resulted in 12 fertile hybrids and 27 sterile hybrids exhibiting tetrad sterility. Results Whole-mitochondrial-genome sequencing was performed for two fertile hybrids and three hybrids exhibiting tetrad sterility. Two to seven contigs, with the total assembly lengths ranging from 462,716 to 535,375 bp, were assembled for each hybrid. Unlike for the reference mitochondrial genome (cv. Désirée), two different recombinant-type contigs (RC-I and RC-II) were identified. RC-I featured by the rpl5-ψrps14 gene joined to the nad6 gene, generating a novel intergenic region. Using a PCR marker (P-3), we found that this intergenic region occurred exclusively in interspecific hybrids exhibiting tetrad sterility and in their parental S. stoloniferum accessions. A part of this intergenic sequence was expressed in the pollen. From a large survey in which P-3 was applied to 129 accessions of 27 mostly Mexican wild species, RC-I was found in diploid S. verrucosum and polyploid species. From eight accessions of S. verrucosum used as females, 92 interspecific hybrids were generated, in which only those carrying RC-I exhibited tetrad sterility. Conclusions RC-I was clearly associated with tetrad sterility, and the RC-I-specific intergenic region likely contains a causal factor of tetrad sterility.

Tuber infection of Phytophthora infestans often occurs at harvest. However, it is difficult to accurately estimate the population densities of P. infestans in soil, especially Japanese soil. In the present study, P. infestans DNA was extracted from soil samples using a modified CTAB-bead method and quantified using real-time PCR to accurately, rapidly and easily estimate the P. infestans population densities in upland soils in Japan. P. infestans was well quantified in eleven types of soil samples, including nine types of upland soils in Japan, that were artificially inoculated with a zoosporangia suspension. The amounts of P. infestans DNA estimated by the real-time PCR were proportional to the inoculum densities. In the non-controlled experimental potato field, P. infestans population densities in soil corresponded to the development of symptoms and were correlated with the number of lesions on the potato foliage. These results imply that the proposed real-time PCR assay is suitable for the estimation or monitoring of P. infestans population densities in upland soils in Japan. The population densities at the ridge bottoms were larger than those at any other location in commercial potato fields. These results were similar to those of a previous report using a bioassay. Moreover, a correlation between DNA quantity and inoculum potential was observed. In conclusion, the real-time PCR assay developed in this study is suitable for indirect estimation of the inoculum potential of P. infestans .

Potato (Solanum tuberosum L.) and sweetpotato (Ipomoea batatas L.), which are nutritionally and commercially important tuberous crops, possess a perplexing heredity because of their autopolyploid genomes. To reduce cross‐breeding efforts for selecting superior cultivars from progenies with innumerable combinations of traits, DNA markers tightly linked to agronomical traits are required. To develop DNA markers, we developed a method for quantitative trait loci (QTL) mapping using whole‐genome next‐generation sequencing (NGS) in autopolyploid crops. To apply the NGS‐based bulked segregant method, QTL‐seq was modified. (1) Single parent‐specific simplex (unique for one homologous chromosome) single‐nucleotide polymorphisms (SNPs), which present a simple segregation ratio in the progenies, were exploited by filtering SNPs by SNP index (allele frequency). (2) Clusters of SNPs, which were inherited unevenly between bulked progenies with opposite phenotypes, especially those with an SNP index of 0 for the bulk that did not display the phenotypes of interest, were explored. These modifications allowed for separate tracking of alleles located on each of the multiple homologous chromosomes. By applying this method, clusters of SNPs linked to the potato cyst nematode resistance H1 gene and storage root anthocyanin (AN) content were identified in tetraploid potato and hexaploid sweetpotato, respectively, and completely linked DNA markers were developed at the site of the presented SNPs. Thus, polyploid QTL‐seq is a versatile method that is free from specialized manipulation for sequencing and construction of elaborate linkage maps and facilitates rapid development of tightly linked DNA markers in autopolyploid crops, such as potato and sweetpotato.

In 2016, in Miyakojima, Okinawa, Japan, banana plants (Musa × paradisiaca) ‘Shima-banana’ developed yellowing and wilt associated with vascular discoloration of the pseudostems. Fusarium oxysporum, identified based on morphological characters, was frequently isolated from the vascular tissue of the infected plant and reproduced the original symptoms on ‘Shima-banana’ after drench inoculation with a spore suspension. Thereby, we determined that the disease is Panama disease caused by F. oxysporum. This is the first official report of Panama disease (Panama-byo in Japanese) of banana in Japan.

Emergence of races in Fusarium oxysporum f. sp. lycopersici (Fol) is caused by loss or mutation of at least one avirulence (AVR) gene. The product of AVR1 is a small protein (Avr1) secreted by Fol in tomato xylem sap during infection. This protein triggers Fol race 1 specific resistance (I) in tomato, indicating that AVR1 is an AVR gene. Deletion of AVR1 in race 1 resulted in the emergence of race 2, and an additional mutation in AVR2 generated race 3. Previously, we reported a new biotype of race 3, KoChi-1, in which AVR1 was truncated by a transposon Hormin, which suggested a new route to evolution of races in Fol. However, to date no race 2 isolate carrying Hormin-truncated AVR1 has been reported. In this report, we describe such isolates, represented by Chiba-5, in which Hormin insertion occurred in AVR1 at a position different from that in KoChi-1. AVR1 truncation in both isolates resulted in production of defective Avr1 proteins. Chiba-5 and KoChi-1 belong to different phylogenetic clades, A1 and A2, respectively, suggesting that insertion of Hormin in AVR1 in Chiba-5 and KoChi-1 occurred as independent evolutionary events. A new path of race emergence of tomato wilt fungus is revealed by this article.

Purpose To investigate whether Parkinson’s disease (PD) can be differentiated from healthy controls and to identify neural circuit disorders in PD by applying a deep learning technique to parameter-weighted and number of streamlines (NOS)–based structural connectome matrices calculated from diffusion-weighted MRI. Methods In this prospective study, 115 PD patients and 115 healthy controls were enrolled. NOS-based and parameter-weighted connectome matrices were calculated from MRI images obtained with a 3-T MRI unit. With 5-fold cross-validation, diagnostic performance of convolutional neural network (CNN) models using those connectome matrices in differentiating patients with PD from healthy controls was evaluated. To identify the important brain connections for diagnosing PD, gradient-weighted class activation mapping (Grad-CAM) was applied to the trained CNN models. Results CNN models based on some parameter-weighted structural matrices (diffusion kurtosis imaging (DKI)–weighted, neurite orientation dispersion and density imaging (NODDI)–weighted, and g -ratio-weighted connectome matrices) showed moderate performance (areas under the receiver operating characteristic curve (AUCs) = 0.895, 0.801, and 0.836, respectively) in discriminating PD patients from healthy controls. The DKI-weighted connectome matrix performed significantly better than the conventional NOS-based matrix (AUC = 0.761) (DeLong’s test, p  < 0.0001). Alterations of neural connections between the basal ganglia and cerebellum were indicated by applying Grad-CAM to the NODDI- and g -ratio-weighted matrices. Conclusion Patients with PD can be differentiated from healthy controls by applying the deep learning technique to the parameter-weighted connectome matrices, and neural circuit disorders including those between the basal ganglia on one side and the cerebellum on the contralateral side were visualized.

A prosthetic vascular graft that induces perigraft tissue incorporation may effectively prevent serious sequelae such as seroma formation and infection. Radiation-crosslinked gelatin hydrogel (RXgel) mimics the chemical and physical properties of the in vivo extracellular matrix and may facilitate wound healing by promoting tissue organization. Fibroblasts cultured on RXgel actively migrated into the gel for up to 7 days. RXgels of three different degrees of hardness (Rx[10], soft; Rx[15], middle; Rx[20], hard) were prepared, and small disc-like samples of RXgels were implanted into rats. In vitro and in vivo results indicated that Rx[10] was too soft to coat vascular grafts. Thus, expanded polytetrafluoroethylene (ePTFE) vascular grafts coated with RXgel were developed using Rx[15] and Rx[20] gels, and ring-shaped slices of the graft were implanted into rats. Alpha-smooth muscle actin (αSMA) and type III collagen (Col-III) levels were detected by immunohistochemistry. Immunohistochemical staining for αSMA and Col-III demonstrated that RXgel-coated vascular grafts induced more granulation tissue than non-coated grafts on days 14 and 28 after implantation. RXgel-coated ePTFE vascular grafts may provide a solution for patients by reducing poor perigraft tissue incorporation.

The machine commissioning of KEKB started in December 1998 and its operation was terminated at the end of June 2010 to upgrade KEKB to SuperKEKB. In this paper, we describe the commissioning procedure of KEKB from 2002 to 2010.