Five Gram-reaction-negative, aerobic, motile with one to three polar flagella, rod-shaped bacterial strains, MAFF 212408T, MAFF 212409, MAFF 212410, MAFF 301498 and MAFF 730085, were isolated from diseased Welsh onion (Allium fistulosum L.) in Japan. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas with the highest similarity to Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas antarctica CMS 35T (99.79 %) and Pseudomonas poae DSM 14936T (99.72%). The genomic DNA G+C content was 59.5 mol% and the major fatty acids (>5 %) were summed feature 3, C16 : 0, summed feature 8 and C12 : 0 2-OH. Multilocus sequence analysis using the rpoD, gyrB and rpoB gene sequences and phylogenomic analysis based on the 90 core genes demonstrated that the strains are members of the P. fluorescens subgroup, but are distant from all closely related species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analysis confirmed low genomic relatedness to their closest relatives [below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation]. The strains were characterized by using API 20NE and Biolog GEN III tests, and inoculation tests in Welsh onion, showing that they are phenotypically differentiated from their closest relatives. Based on the genetic and phenotypic evidence, the strains should be classified as representing a novel species, for which the name Pseudomonas kitaguniensis sp. nov. is proposed. The type strain is MAFF 212408T (=ICMP 23530T).

Phytopathogenic bacteria, MAFF 212426, MAFF 212427T, MAFF 212428 and MAFF 212429, were isolated from head rot lesions of broccoli (Brassica oleracea L. var. italica Plenck) in Hokkaido, Japan, and subjected to polyphasic taxonomic characterization. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella, rod-shaped and formed pale yellow colonies. Results of 16S rRNA gene sequence analysis showed that they belong to the genus Pseudomonas with the highest similarity to ‘Pseudomonas qingdaonensis’ JJ3T (99.86 %), Pseudomonas laurentiana GSL-010T (99.22 %), Pseudomonas huaxiensis WCHPs060044T (99.01 %), Pseudomonas japonica NBRC 103040T (98.87 %) and Pseudomonas alkylphenolica KL28T (98.73 %). The genomic DNA G+C content was 63.4 mol% and the major fatty acids (>5 % of the total fatty acids) were summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c) and C17 : 0 cyclo. Multilocus sequence analysis using the partial rpoD, gyrB and rpoB gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas putida group, but form a monophyletic, robust clade separated from their closest relatives. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values corroborated their novel species status, with 88.39 % (ANI) and 35.8 % (dDDH) as the highest scores with ‘P. qingdaonensis’ JJ3T. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity on broccoli, and whole-cell MALDI-TOF mass spectrometry profiles. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, for which the name Pseudomonas brassicae sp. nov. is proposed. The type strain is MAFF 212427T (=ICMP 23635T).

In yellow soybean, seed coat pigmentation is inhibited by post-transcriptional gene silencing (PTGS) of chalcone synthase (CHS) genes. A CHS cluster named GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is suggested to cause PTGS in yellow-hilum cultivars. Cold-induced seed coat discoloration (CD), a commercially serious deterioration of seed appearance, is caused by an inhibition of this PTGS upon exposure to low temperatures. In the highly CD-tolerant cultivar Toyoharuka, the GmIRCHS structure differs from that of other cultivars. The aim of this study was to determine whether the variation of GmIRCHS structure among cultivars is related to variations in CD tolerance. Using two sets of recombinant inbred lines between Toyoharuka and CD-susceptible cultivars, we compared the GmIRCHS genotype and CD tolerance phenotype during low temperature treatment. The GmIRCHS genotype was related to the phenotype of CD tolerance. A QTL analysis around GmIRCHS showed that GmIRCHS itself or a region located very close to it was responsible for CD tolerance. The variation in GmIRCHS can serve as a useful DNA marker for marker-assisted selection for breeding CD tolerance. In addition, QTL analysis of the whole genome revealed a minor QTL that also affected CD tolerance.

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