start-ver=1.4 cd-journal=joma no-vol=75 cd-vols= no-issue=3 article-no= start-page=168 end-page=178 dt-received= dt-revised= dt-accepted= dt-pub-year=2025 dt-pub=2025 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon, Cucumis melo L. en-subtitle= kn-subtitle= en-abstract= kn-abstract=Melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9?mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp. melo and the East Asian subsp. agrestis were characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence. In South Asia, in addition to the Europe/US and East Asian types, recombinant types between the two types were detected and accounted for 34.8% of South Asian melon. The finding of such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types. As to Momordica popular in South Asia, seed length was intermediate between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp. agrestis of the Ic type proved to be endemic to Africa, indicating its African origin. en-copyright= kn-copyright= en-aut-name=TanakaKatsunori en-aut-sei=Tanaka en-aut-mei=Katsunori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ShigitaGentaro en-aut-sei=Shigita en-aut-mei=Gentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=DungTran Phuong en-aut-sei=Dung en-aut-mei=Tran Phuong kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=NhiPhan Thi Phuong en-aut-sei=Nhi en-aut-mei=Phan Thi Phuong kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TakahashiMami en-aut-sei=Takahashi en-aut-mei=Mami kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NishidaHidetaka en-aut-sei=Nishida en-aut-mei=Hidetaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=IshikawaRyuji en-aut-sei=Ishikawa en-aut-mei=Ryuji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KatoKenji en-aut-sei=Kato en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=University of Agriculture and Forestry, Hue University kn-affil= affil-num=5 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=6 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= affil-num=7 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= affil-num=8 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=9 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= en-keyword=chloroplast genome kn-keyword=chloroplast genome en-keyword=Cucumis melo kn-keyword=Cucumis melo en-keyword=domestication kn-keyword=domestication en-keyword=genetic diversity kn-keyword=genetic diversity en-keyword=melon kn-keyword=melon en-keyword=molecular polymorphism kn-keyword=molecular polymorphism en-keyword=seed size kn-keyword=seed size END start-ver=1.4 cd-journal=joma no-vol=135 cd-vols= no-issue=7 article-no= start-page=1329 end-page=1343 dt-received= dt-revised= dt-accepted= dt-pub-year=2025 dt-pub=20250417 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Molecular polymorphisms of the nuclear and chloroplast genomes among African melon germplasms reveal abundant and unique genetic diversity, especially in Sudan en-subtitle= kn-subtitle= en-abstract= kn-abstract=Background and Aims Africa is rich in wild species of Cucumis and is considered one of the places of origin of melon. However, our knowledge of African melon is limited, and genetic studies using melon germplasms with wide geographical coverage are required. Here, we analysed the genetic structure of African melons, with emphasis on Sudan.
Methods Ninety-seven accessions of African melon were examined along with 77 reference accessions representing Asian melon and major horticultural groups. Molecular polymorphisms in the nuclear and chloroplast genomes were investigated using 12 RAPD, 7 SSR and 3 SNP markers. Horticultural traits, including seed size, were measured for 46 accessions, mainly from Sudan.
Key Results African melons were divided into large and small seed-types based on seed length: large seed-type from Northern Africa and small seed-type from Western and Southern Africa. Both seed types are common in Sudan. Molecular genetic diversity in these geographical populations was as high as in India, the Asian centre of melon domestication. Large seed-types from Northern Africa were assigned to Pop4 by structure analysis and had Ib cytoplasm in common with Cantalupensis, Inodorus and Flexuosus. Small seed-types were highly diversified and geographically differentiated; specifically, Pop1 with Ia cytoplasm in Southern Africa and South Asia, Pop2 with Ia in East Asia, including Conomon and Makuwa, and Pop3 with Ia or Ic in Africa. Sudanese small seed-types were grouped in Pop3, while their cytoplasm type was a mixture of Ia and Ic. Sudanese Tibish had Ic cytoplasm, which was unique in Africa, common in Western Africa and Sudan, and also found in wild or feral types.
Conclusions Melon of Ic lineage, including Tibish, originated from wild melon in the ‘western Sudan region’, and independently of melon with Ia or Ib cytoplasm, which originated in Asia. This clearly indicates the polyphyletic origin of melon. en-copyright= kn-copyright= en-aut-name=ImohOdirichi Nnennaya en-aut-sei=Imoh en-aut-mei=Odirichi Nnennaya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ShigitaGentaro en-aut-sei=Shigita en-aut-mei=Gentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SugiyamaMitsuhiro en-aut-sei=Sugiyama en-aut-mei=Mitsuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=DungTran Phuong en-aut-sei=Dung en-aut-mei=Tran Phuong kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TanakaKatsunori en-aut-sei=Tanaka en-aut-mei=Katsunori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=TakahashiMami en-aut-sei=Takahashi en-aut-mei=Mami kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NishimuraKazusa en-aut-sei=Nishimura en-aut-mei=Kazusa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=NishidaHidetaka en-aut-sei=Nishida en-aut-mei=Hidetaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=GodaMashaer en-aut-sei=Goda en-aut-mei=Mashaer kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=PitratMichel en-aut-sei=Pitrat en-aut-mei=Michel kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=KatoKenji en-aut-sei=Kato en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=7 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= affil-num=8 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= affil-num=9 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= affil-num=10 en-affil=Plant Genetic Resources Conservation and Research Center, Agricultural Research Corporation kn-affil= affil-num=11 en-affil=INRAE, UR1052, G?n?tique et am?lioration des fruits et l?gumes kn-affil= affil-num=12 en-affil=Graduate School of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= en-keyword=Cucumis melo kn-keyword=Cucumis melo en-keyword=Africa kn-keyword=Africa en-keyword=chloroplast genome kn-keyword=chloroplast genome en-keyword=domestication kn-keyword=domestication en-keyword=genetic diversity kn-keyword=genetic diversity en-keyword=genetic resources kn-keyword=genetic resources en-keyword=maternal lineage kn-keyword=maternal lineage en-keyword=melon kn-keyword=melon en-keyword=phylogeny kn-keyword=phylogeny en-keyword=polyphyletic origin kn-keyword=polyphyletic origin en-keyword=seed size kn-keyword=seed size en-keyword=Tibish kn-keyword=Tibish END start-ver=1.4 cd-journal=joma no-vol=71 cd-vols= no-issue=3 article-no= start-page=1067 end-page=1083 dt-received= dt-revised= dt-accepted= dt-pub-year=2023 dt-pub=20230723 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Analysis of genetic diversity and population structure in Cambodian melon landraces using molecular markers en-subtitle= kn-subtitle= en-abstract= kn-abstract=Genetic diversity of Cambodian melons was evaluated by the analysis of 12 random amplified polymorphic DNA (RAPD) and 7 simple sequence repeat (SSR) markers using 62 accessions of melon landraces and compared with 231 accessions from other areas for genetic characterization of Cambodian melons. Among 62 accessions, 56 accessions were morphologically classified as small-seed type with seed lengths shorter than 9 mm, as in the horticultural groups Conomon and Makuwa. Gene diversity of Cambodian melons was 0.228, which was equivalent to those of the groups Conomon and Makuwa and smaller than those of Vietnamese and Central Asian landraces. A phylogenetic tree constructed from a genetic distance matrix classified 293 accessions into three major clusters. Small-seed type accessions from East and Southeast Asia formed clusters I and II, which were distantly related with cluster III consisting of large-seed type melon from other areas. All Cambodian melons belonged to cluster I (except three accessions) along with those from Thailand, Myanmar, Yunnan (China), and Vietnam (“Dua thom” in the northwest), thus indicating genetic similarity in these areas. In addition, the Cambodian melons were not differentiated among geographical populations. Conomon and Makuwa were classified into cluster II, together with melon groups from the plains of Vietnam. The presence of two groups of melons in Southeast Asia was also indicated by population structure and principal coordinate analysis. These results indicated a close genetic relationship between Cambodia and the neighboring countries, thus suggesting that Cambodian melons are not directly related to the establishment of Conomon and Makuwa. en-copyright= kn-copyright= en-aut-name=NazninPervin Mst en-aut-sei=Naznin en-aut-mei=Pervin Mst kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ImohOdirichi Nnennaya en-aut-sei=Imoh en-aut-mei=Odirichi Nnennaya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TanakaKatsunori en-aut-sei=Tanaka en-aut-mei=Katsunori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SreynechOuch en-aut-sei=Sreynech en-aut-mei=Ouch kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ShigitaGentaro en-aut-sei=Shigita en-aut-mei=Gentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SopheaYon en-aut-sei=Sophea en-aut-mei=Yon kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=SophanySakhan en-aut-sei=Sophany en-aut-mei=Sakhan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MakaraOuk en-aut-sei=Makara en-aut-mei=Ouk kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TomookaNorihiko en-aut-sei=Tomooka en-aut-mei=Norihiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=NishidaHidetaka en-aut-sei=Nishida en-aut-mei=Hidetaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=KatoKenji en-aut-sei=Kato en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=4 en-affil=Cambodian Agricultural Research and Development Institute kn-affil= affil-num=5 en-affil=Department of Life Science Systems, Technical University of Munich kn-affil= affil-num=6 en-affil=Cambodian Agricultural Research and Development Institute kn-affil= affil-num=7 en-affil=Cambodian Agricultural Research and Development Institute kn-affil= affil-num=8 en-affil=Plant Breeder, Retired Director of the Cambodian Agricultural Research and Development Institute kn-affil= affil-num=9 en-affil=Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=10 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=11 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=12 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Cambodia kn-keyword=Cambodia en-keyword=Conomon kn-keyword=Conomon en-keyword=Cucumis melo kn-keyword=Cucumis melo en-keyword=Genetic diversity kn-keyword=Genetic diversity en-keyword=Landraces kn-keyword=Landraces en-keyword=RAPD kn-keyword=RAPD en-keyword=SSR kn-keyword=SSR END start-ver=1.4 cd-journal=joma no-vol=73 cd-vols= no-issue=3 article-no= start-page=269 end-page=277 dt-received= dt-revised= dt-accepted= dt-pub-year=2023 dt-pub=2023 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection en-subtitle= kn-subtitle= en-abstract= kn-abstract=Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset (“core collection”) are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon. en-copyright= kn-copyright= en-aut-name=ShigitaGentaro en-aut-sei=Shigita en-aut-mei=Gentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=DungTran Phuong en-aut-sei=Dung en-aut-mei=Tran Phuong kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=PervinMst. Naznin en-aut-sei=Pervin en-aut-mei=Mst. Naznin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=DuongThanh-Thuy en-aut-sei=Duong en-aut-mei=Thanh-Thuy kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ImohOdirich Nnennaya en-aut-sei=Imoh en-aut-mei=Odirich Nnennaya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NishidaHidetaka en-aut-sei=Nishida en-aut-mei=Hidetaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=TanakaKatsunori en-aut-sei=Tanaka en-aut-mei=Katsunori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=SugiyamaMitsuhiro en-aut-sei=Sugiyama en-aut-mei=Mitsuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=KawazuYoichi en-aut-sei=Kawazu en-aut-mei=Yoichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=TomookaNorihiko en-aut-sei=Tomooka en-aut-mei=Norihiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=KatoKenji en-aut-sei=Kato en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=7 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=8 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=9 en-affil=Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=10 en-affil=Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=11 en-affil=Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=12 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Cucumis melo kn-keyword=Cucumis melo en-keyword=Cucurbitaceae kn-keyword=Cucurbitaceae en-keyword=genotyping-by-sequencing kn-keyword=genotyping-by-sequencing en-keyword=genetic resource kn-keyword=genetic resource en-keyword=genetic diversity kn-keyword=genetic diversity en-keyword=crop origin kn-keyword=crop origin en-keyword=core collection kn-keyword=core collection END start-ver=1.4 cd-journal=joma no-vol=13 cd-vols= no-issue= article-no= start-page=858747 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220318 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Mapping of Nematode Resistance in Hexaploid Sweetpotato Using an Next-Generation Sequencing-Based Association Study en-subtitle= kn-subtitle= en-abstract= kn-abstract=The southern root-knot nematode (SRKN; Meloidogyne incognita) is a typical parasitic nematode that affects sweetpotato [Ipomoea batatas (L.) Lam.], causing a significant decrease in crop yield and commercial value. In Japan, the SRKN is classified into 10 races: SP1-SP5, SP6-1, SP6-2, and SP7-SP9, with the dominant race differing according to the cultivation area. Soil insecticides have previously been used to reduce the soil density of SRKNs; however, this practice is both costly and labor intensive. Therefore, the development of SRKN-resistant sweetpotato lines and cultivars is necessary. However, due to the complexity of polyploid inheritance and the highly heterogeneous genomic composition of sweetpotato, genetic information and research for this species are significantly lacking compared to those for other major diploid crop species. In this study, we utilized the recently developed genome-wide association approach, which uses multiple-dose markers to assess autopolyploid species. We performed an association analysis to investigate resistance toward SRKN-SP2, which is the major race in areas with high sweetpotato production in Japan. The segregation ratio of resistant and susceptible lines in the F-1 mapping population derived from the resistant "J-Red" and susceptible "Choshu" cultivars was fitted to 1: 3, suggesting that resistance to SP2 may be regulated by two loci present in the simplex. By aligning the double digest restriction-site associated DNA sequencing reads to the published Ipomoea trifida reference sequence, 46,982 single nucleotide polymorphisms (SNPs) were identified (sequencing depth > 200). The association study yielded its highest peak on chromosome 7 (Chr07) and second highest peak on chromosome 3 (Chr03), presenting as a single-dose in both loci. Selective DNA markers were developed to screen for resistant plants using the SNPs identified on Chr03 and Chr07. Our results showed that SRKN-SP2-resistant plants were selected with a probability of approximately 70% when combining the two selective DNA markers. This study serves as a model for the identification of genomic regions that control agricultural traits and the elucidation of their effects, and is expected to greatly advance marker-assisted breeding and association studies in polyploid crop species. en-copyright= kn-copyright= en-aut-name=ObataNozomi en-aut-sei=Obata en-aut-mei=Nozomi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TabuchiHiroaki en-aut-sei=Tabuchi en-aut-mei=Hiroaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=KuriharaMiyu en-aut-sei=Kurihara en-aut-mei=Miyu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=YamamotoEiji en-aut-sei=Yamamoto en-aut-mei=Eiji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ShirasawaKenta en-aut-sei=Shirasawa en-aut-mei=Kenta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil= Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=3 en-affil=Faculty of Agriculture, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Agriculture, Meiji University kn-affil= affil-num=5 en-affil=Department of Frontier Research and Development, Kazusa DNA Research Institute kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=polyploidy kn-keyword=polyploidy en-keyword=nematode kn-keyword=nematode en-keyword=sweetpotato kn-keyword=sweetpotato en-keyword=resistant cultivar kn-keyword=resistant cultivar en-keyword=breeding kn-keyword=breeding en-keyword=association study kn-keyword=association study END start-ver=1.4 cd-journal=joma no-vol=10 cd-vols= no-issue=8 article-no= start-page=1535 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210727 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato en-subtitle= kn-subtitle= en-abstract= kn-abstract=Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato. en-copyright= kn-copyright= en-aut-name=NokiharaKanoko en-aut-sei=Nokihara en-aut-mei=Kanoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=OkadaYoshihiro en-aut-sei=Okada en-aut-mei=Yoshihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=OhataShinichiro en-aut-sei=Ohata en-aut-mei=Shinichiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=transcriptome kn-keyword=transcriptome en-keyword=RNA-seq kn-keyword=RNA-seq en-keyword=sweetpotato kn-keyword=sweetpotato en-keyword=weevil resistance kn-keyword=weevil resistance en-keyword=juvenile hormones kn-keyword=juvenile hormones en-keyword=terpenes kn-keyword=terpenes END start-ver=1.4 cd-journal=joma no-vol=70 cd-vols= no-issue=2 article-no= start-page=231 end-page=240 dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=2020 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification en-subtitle= kn-subtitle= en-abstract= kn-abstract=In this study, DNA markers were developed for discrimination of strawberry (Fragaria × ananassa L.) cultivars based on retrotransposon insertion polymorphisms. We performed a comprehensive genomic search to identify retrotransposon insertion sites and subsequently selected one retrotransposon family, designated CL3, which provided reliable discrimination among strawberry cultivars. Through analyses of 75 strawberry cultivars, we developed eight cultivar-specific markers based on CL3 retrotransposon insertion sites. Used in combination with 10 additional polymorphic markers, we differentiated 35 strawberry cultivars commonly cultivated in Japan. In addition, we demonstrated that the retrotransposon-based markers were effective for PCR detection of DNA extracted from processed food materials, whereas a SSR marker was ineffective. These results indicated that the retrotransposon-based markers are useful for cultivar discrimination for processed food products, such as jams, in which DNA may be fragmented or degraded. en-copyright= kn-copyright= en-aut-name=HirataChiharu en-aut-sei=Hirata en-aut-mei=Chiharu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=WakiTakamitsu en-aut-sei=Waki en-aut-mei=Takamitsu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShimomuraKatsumi en-aut-sei=Shimomura en-aut-mei=Katsumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=WadaTakuya en-aut-sei=Wada en-aut-mei=Takuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TanakaSeiya en-aut-sei=Tanaka en-aut-mei=Seiya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=IkegamiHidetoshi en-aut-sei=Ikegami en-aut-mei=Hidetoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=UchimuraYousuke en-aut-sei=Uchimura en-aut-mei=Yousuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=HirashimaKeita en-aut-sei=Hirashima en-aut-mei=Keita kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=NakazawaYoshiko en-aut-sei=Nakazawa en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=OkadaKaori en-aut-sei=Okada en-aut-mei=Kaori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=NamaiKiyoshi en-aut-sei=Namai en-aut-mei=Kiyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= affil-num=1 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=2 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=3 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=4 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=5 en-affil=Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University kn-affil= affil-num=6 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=7 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=8 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=9 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=10 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=11 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=12 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=13 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Fragaria × ananassa kn-keyword=Fragaria × ananassa en-keyword=high-throughput sequencing kn-keyword=high-throughput sequencing en-keyword=PCR product kn-keyword=PCR product en-keyword=processed foods kn-keyword=processed foods en-keyword=retrotransposon insertion polymorphisms kn-keyword=retrotransposon insertion polymorphisms END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200603 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases en-subtitle= kn-subtitle= en-abstract= kn-abstract=Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms. en-copyright= kn-copyright= en-aut-name=NemotoMichiko en-aut-sei=Nemoto en-aut-mei=Michiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IwakiSayako en-aut-sei=Iwaki en-aut-mei=Sayako kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MoriyaHisao en-aut-sei=Moriya en-aut-mei=Hisao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TamuraTakashi en-aut-sei=Tamura en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=InagakiKenji en-aut-sei=Inagaki en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MayamaShigeki en-aut-sei=Mayama en-aut-mei=Shigeki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ObuseKiori en-aut-sei=Obuse en-aut-mei=Kiori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=7 en-affil=Department of Biology, Tokyo Gakugei University kn-affil= affil-num=8 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Biomineralization kn-keyword=Biomineralization en-keyword=Diatom kn-keyword=Diatom en-keyword=Silica kn-keyword=Silica en-keyword=Transcriptome kn-keyword=Transcriptome en-keyword=Proteome kn-keyword=Proteome END start-ver=1.4 cd-journal=joma no-vol=26 cd-vols= no-issue=5 article-no= start-page=399 end-page=409 dt-received= dt-revised= dt-accepted= dt-pub-year=2019 dt-pub=20190803 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato en-subtitle= kn-subtitle= en-abstract= kn-abstract=The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (similar to 3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F-1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F-1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita. en-copyright= kn-copyright= en-aut-name=SasaiRumi en-aut-sei=Sasai en-aut-mei=Rumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TabuchiHiroaki en-aut-sei=Tabuchi en-aut-mei=Hiroaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShirasawaKenta en-aut-sei=Shirasawa en-aut-mei=Kenta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KishimotoKazuki en-aut-sei=Kishimoto en-aut-mei=Kazuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SatoShusei en-aut-sei=Sato en-aut-mei=Shusei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=OkadaYoshihiro en-aut-sei=Okada en-aut-mei=Yoshihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KuramotoAkihide en-aut-sei=Kuramoto en-aut-mei=Akihide kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KobayashiAkira en-aut-sei=Kobayashi en-aut-mei=Akira kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=IsobeSachiko en-aut-sei=Isobe en-aut-mei=Sachiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=3 en-affil=Kazusa DNA Research Institute kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Graduate School of Life Science, Tohoku University kn-affil= affil-num=6 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=7 en-affil=Graduate School of Agriculture, Kyoto University kn-affil= affil-num=8 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=9 en-affil=Kazusa DNA Research Institute kn-affil= affil-num=10 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=11 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=sweetpotato kn-keyword=sweetpotato en-keyword=GWAS kn-keyword=GWAS en-keyword=QTL mapping kn-keyword=QTL mapping en-keyword=polyploids kn-keyword=polyploids en-keyword=marker-assisted breeding kn-keyword=marker-assisted breeding END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140616 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform en-subtitle= kn-subtitle= en-abstract= kn-abstract=In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=YamamotoAyaka en-aut-sei=Yamamoto en-aut-mei=Ayaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShindoAkiko en-aut-sei=Shindo en-aut-mei=Akiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=Faculty of Agriculture, Okayama University affil-num=3 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=4 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University en-keyword=DNA fingerprinting kn-keyword=DNA fingerprinting en-keyword=high-throughput sequencing kn-keyword=high-throughput sequencing en-keyword=molecular marker kn-keyword=molecular marker en-keyword=retrotransposon kn-keyword=retrotransposon en-keyword=sweet potato kn-keyword=sweet potato END start-ver=1.4 cd-journal=joma no-vol=57 cd-vols= no-issue=5 article-no= start-page=245 end-page=252 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140625 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site en-subtitle= kn-subtitle= en-abstract= kn-abstract=Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5′ LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a “unique” insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=FujiiNobuyuki en-aut-sei=Fujii en-aut-mei=Nobuyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=YamaguchiKentaro en-aut-sei=Yamaguchi en-aut-mei=Kentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=IkeoKazuho en-aut-sei=Ikeo en-aut-mei=Kazuho kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=NakazawaYoshiko en-aut-sei=Nakazawa en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=WakiTakamitsu en-aut-sei=Waki en-aut-mei=Takamitsu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=HirashimaKeita en-aut-sei=Hirashima en-aut-mei=Keita kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=UchimuraYosuke en-aut-sei=Uchimura en-aut-mei=Yosuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems affil-num=3 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=4 en-affil= kn-affil=Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems affil-num=5 en-affil= kn-affil=Biotechology Division, Tochigi Prefectural Agricultural Experiment Station affil-num=6 en-affil= kn-affil=Biotechology Division, Tochigi Prefectural Agricultural Experiment Station affil-num=7 en-affil= kn-affil=Department of Research Plan and Strategy, Fukuoka Agricultural Research Center affil-num=8 en-affil= kn-affil=Department of Research Plan and Strategy, Fukuoka Agricultural Research Center affil-num=9 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University en-keyword=retrotransposon kn-keyword=retrotransposon en-keyword=primer binding site kn-keyword=primer binding site en-keyword=high-throughput sequencing kn-keyword=high-throughput sequencing en-keyword=polymorphism kn-keyword=polymorphism en-keyword=molecular markers kn-keyword=molecular markers END start-ver=1.4 cd-journal=joma no-vol=185 cd-vols= no-issue= article-no= start-page=57 end-page=62 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140920 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A rapid and enhanced DNA detection method for crop cultivar discrimination en-subtitle= kn-subtitle= en-abstract= kn-abstract=In many crops species, the development of a rapid and precise cultivar discrimination system has been required for plant breeding and patent protection of plant cultivars and agricultural products. Here, we successfully evaluated strawberry cultivars via a novel method, namely, the single tag hybridization (STH) chromatographic printed array strip (PAS) using the PCR products of eight genomic regions. In a previous study, we showed that genotyping of eight genomic regions derived from FaRE1 retrotransposon insertion site enabled to discriminate 32 strawberry cultivars precisely, however, this method required agarose/acrylamide gel electrophoresis, thus has the difficulty for practical application. In contrast, novel DNA detection method in this study has some great advantages over standard DNA detection methods, including agarose/acrylamide gel electrophoresis, because it produces signals for DNA detection with dramatically higher sensitivity in a shorter time without any preparation or staining of a gel. Moreover, this method enables the visualization of multiplex signals simultaneously in a single reaction using several independent amplification products. We expect that this novel method will become a rapid and convenient cultivar screening assay for practical purposes, and will be widely applied to various situations, including laboratory research, and on-site inspection of plant cultivars and agricultural products. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TakasakiKazuto en-aut-sei=Takasaki en-aut-mei=Kazuto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=FutoSatoshi en-aut-sei=Futo en-aut-mei=Satoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=NiwaKousuke en-aut-sei=Niwa en-aut-mei=Kousuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KawaseMitsuo en-aut-sei=Kawase en-aut-mei=Mitsuo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=AkitakeHiroto en-aut-sei=Akitake en-aut-mei=Hiroto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=FASMAC Co., Ltd. affil-num=3 en-affil= kn-affil=FASMAC Co., Ltd. affil-num=4 en-affil= kn-affil=Graduate School of Biomedical Engineering, Tohoku University affil-num=5 en-affil= kn-affil=Graduate School of Biomedical Engineering, Tohoku University affil-num=6 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=7 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University en-keyword=Cultivar discrimination kn-keyword=Cultivar discrimination en-keyword=Multiplex PCR kn-keyword=Multiplex PCR en-keyword=Strawberry kn-keyword=Strawberry en-keyword=Practical application kn-keyword=Practical application en-keyword=Retrotransposon kn-keyword=Retrotransposon END start-ver=1.4 cd-journal=joma no-vol=103 cd-vols= no-issue= article-no= start-page=21 end-page=30 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140201 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=コムギ染色体欠損系統を用いた新規活性型レトロトランスポゾン TriRe-1 の分子遺伝学的解析 kn-title=Characterization of a novel retrotransposon TriRe?1 using nullisomic-tetrasomic lines of hexaploid wheat en-subtitle= kn-subtitle= en-abstract=　レトロトランスポゾンは植物ゲノムの主要な構成要素であり，コムギゲノムにおいてはその80ｵを占める．特に LTR 型レトロトランスポゾンの割合が高く，ゲノムの拡大，配列の多様性およびゲノム構造変異等に大きく寄与し てきたと考えられている．これら配列は自身のコピー配列を複製し増幅するため，ゲノム中には数百，数千に及ぶコ ピー配列をもつ．また，ゲノム進化の過程において多数のファミリーを形成してきた．これら多数のファミリーのう ち，現在でも転移活性を示す活性型ファミリーは，品種間において高い挿入多型を示すことが知られている．このよ うな挿入多型は，連鎖解析および系統解析等各種遺伝解析に利用可能である. 本研究では，コムギにおける新規活性 型レトロトランスポゾンファミリー TriRe-1 の特徴を詳細に解析した．TriRe-1 は転移に必要なタンパク質をコー ドする内部配列をもち，また日本で育成されたコムギ近縁品種間においても高い挿入多型を示したため，現在でも転 移活性を有している，もしくはごく最近まで転移していた可能性が高いと考えられた．一方で，コムギ染色体欠損系 統（ナリソミックテトラソミック系統）を用い，TriRe-1 の挿入箇所を比較解析した．その結果，大部分の挿入箇所 は複数の同祖染色体に存在すると考えられたが，Ｂゲノムにおいて最も多くの特異的な挿入箇所が同定された．よっ て，Ｂゲノム祖先種において活発に増幅してきた可能性が示唆された．今回の結果により，新規活性型レトロトラン スポゾン TriRe-1 の品種間挿入多型を利用した DNA マーカー，また，各ゲノム（Ａ，Ｂ，Ｄゲノム）特異的な挿 入箇所を利用したゲノム識別性に優れた DNA マーカーの開発の可能性が期待される． kn-abstract=　Retrotransposons constitute the large fraction (〜80%) of the wheat genome where numerous and diverse retrotransposon families exist, where especially the long terminal repeat (LTR) retrotransposon family is known to be predominant. Thus, they have been considered to contribute to the genome expansion, sequence diversification and the genome structure alternation in the wheat genome. In addition, the insertion polymorphism of the LTR retrotransposon family among the cultivars has been known to be quite useful for the genetic analysis such as the linkage mapping and the phylogenetic studies. Here, we report the characteristics of a novel active LTR retrotransposon family TriRe?1, which belongs to the Ty1?copia group in the hexaploid wheat (Triticum aestivum L.) genome. This retroelement appears to encode all proteins required for the transposition and showed high insertion polymorphism among the hexaploid wheat cultivars, suggesting its potential of transpositional activity with at least recent transposition during wheat evolution. We studied the chromosomal localization of the TriRe?1 insertion site based on the genome-wide comparative analysis using the nullisomic-tetrasomic lines of the cultivar Chinese Spring. The results showed that although the majority of the TriRe?1 insertion sites exist across the homoeologous chromosomes of A, B or D genomes, a higher number of insertions in the B genome was detected compared to A or D genome, suggesting a specific amplification in the history of B genome progenitors. In conclusion, a novel LTR retrotransposon TriRe?1 should be valuable for the development of molecular markers based on insertion polymorphism among the cultivars, and also the genome-specific TriRe?1 insertion site can be utilized to study evolutional history of wheat genomes. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name=門田有希 kn-aut-sei=門田 kn-aut-mei=有希 aut-affil-num=1 ORCID= en-aut-name=TakaiTakeru en-aut-sei=Takai en-aut-mei=Takeru kn-aut-name=高井健 kn-aut-sei=高井 kn-aut-mei=健 aut-affil-num=2 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name=田原誠 kn-aut-sei=田原 kn-aut-mei=誠 aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 affil-num=3 en-affil= kn-affil=岡山大学 en-keyword=Retrotransposon kn-keyword=Retrotransposon en-keyword=Wheat kn-keyword=Wheat en-keyword=Molecular markers kn-keyword=Molecular markers en-keyword=Nullisomic-tetrasomic lines kn-keyword=Nullisomic-tetrasomic lines END