start-ver=1.4 cd-journal=joma no-vol=73 cd-vols= no-issue=5 article-no= start-page=435 end-page=444 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=Genomic traces of Japanese malting barley breeding in two modern high-quality cultivars, ‘Sukai Golden’ and ‘Sachiho Golden’ en-subtitle= kn-subtitle= en-abstract= kn-abstract=Two modern high-quality Japanese malting barley cultivars, ‘Sukai Golden’ and ‘Sachiho Golden’, were subjected to RNA-sequencing of transcripts extracted from 20-day-old immature seeds. Despite their close relation, 2,419 Sukai Golden-specific and 3,058 Sachiho Golden-specific SNPs were detected in comparison to the genome sequences of two reference cultivars: ‘Morex’ and ‘Haruna Nijo’. Two single nucleotide polymorphism (SNP) clusters respectively showing the incorporation of (1) the barley yellow mosaic virus (BaYMV) resistance gene rym5 from six-row non-malting Chinese landrace Mokusekko 3 on the long arm of 3H, and (2) the anthocyanin-less ant2 gene from a two-row Dutch cultivar on the long arm of 2H were detected specifically in ‘Sukai Golden’. Using 221 recombinant inbred lines of a cross between ‘Ishukushirazu’ and ‘Nishinochikara’, another BaYMV resistance rym3 gene derived from six-row non-malting Japanese cultivar ‘Haganemugi’ was mapped to a 0.4-cM interval on the proximal region of 5H. Haplotype analysis of progenitor accessions of the two modern malting cultivars revealed that rym3 of ‘Haganemugi’ was independently introduced into ‘Sukai Golden’ and ‘Sachiho Golden’. Residual chromosome 5H segments of ‘Haganemugi’ surrounding rym3 were larger in ‘Sukai Golden’. Available results suggest possibilities for malting quality improvement by minimizing residual segments surrounding rym3. en-copyright= kn-copyright= en-aut-name=TaketaShin en-aut-sei=Taketa en-aut-mei=Shin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KimJune-Sik en-aut-sei=Kim en-aut-mei=June-Sik kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TakahashiHidekazu en-aut-sei=Takahashi en-aut-mei=Hidekazu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=YajimaShunsuke en-aut-sei=Yajima en-aut-mei=Shunsuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KoshiishiYuichi en-aut-sei=Koshiishi en-aut-mei=Yuichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SotomeToshinori en-aut-sei=Sotome en-aut-mei=Toshinori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KatoTsuneo en-aut-sei=Kato en-aut-mei=Tsuneo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Faculty of Food and Agricultural Sciences, Fukushima University kn-affil= affil-num=4 en-affil=NODAI Genome Research Center, Tokyo University of Agriculture kn-affil= affil-num=5 en-affil=NODAI Genome Research Center, Tokyo University of Agriculture kn-affil= affil-num=6 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=7 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=8 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= en-keyword=genetic diversity kn-keyword=genetic diversity en-keyword=Hordeum vulgare kn-keyword=Hordeum vulgare en-keyword=RNA-sequencing kn-keyword=RNA-sequencing en-keyword=seed transcriptome kn-keyword=seed transcriptome en-keyword=single nucleotide polymorphism kn-keyword=single nucleotide polymorphism en-keyword=virus disease resistance genes kn-keyword=virus disease resistance genes 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=73 cd-vols= no-issue=2 article-no= start-page=219 end-page=229 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=Melon diversity on the Silk Road by molecular phylogenetic analysis in Kazakhstan melons en-subtitle= kn-subtitle= en-abstract= kn-abstract=To uncover population structure, phylogenetic relationship, and diversity in melons along the famous Silk Road, a seed size measurement and a phylogenetic analysis using five chloroplast genome markers, 17 RAPD markers and 11 SSR markers were conducted for 87 Kazakh melon accessions with reference accessions. Kazakh melon accessions had large seed with exception of two accessions of weedy melon, Group Agrestis, and consisted of three cytoplasm types, of which Ib-1/-2 and Ib-3 were dominant in Kazakhstan and nearby areas such as northwestern China, Central Asia and Russia. Molecular phylogeny showed that two unique genetic groups, STIa-2 with Ib-1/-2 cytoplasm and STIa-1 with Ib-3 cytoplasm, and one admixed group, STIAD combined with STIa and STIb, were prevalent across all Kazakh melon groups. STIAD melons that phylogenetically overlapped with STIa-1 and STIa-2 melons were frequent in the eastern Silk Road region, including Kazakhstan. Evidently, a small population contributed to melon development and variation in the eastern Silk Road. Conscious preservation of fruit traits specific to Kazakh melon groups is thought to play a role in the conservation of Kazakh melon genetic variation during melon production, where hybrid progenies were generated through open pollination. 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=SugiyamaMitsuhiro en-aut-sei=Sugiyama en-aut-mei=Mitsuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 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=3 ORCID= en-aut-name=MurakamiRyoma en-aut-sei=Murakami en-aut-mei=Ryoma kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 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=5 ORCID= en-aut-name=AierkenYasheng en-aut-sei=Aierken en-aut-mei=Yasheng kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=ArtemyevaAnna M en-aut-sei=Artemyeva en-aut-mei=Anna M kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MamypbelovZharas en-aut-sei=Mamypbelov en-aut-mei=Zharas kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 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=9 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=10 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=11 ORCID= affil-num=1 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=2 en-affil=Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Faculty of Agriculture and Life Science, Hirosaki University kn-affil= affil-num=5 en-affil=Faculty of Agronomy, University of Agriculture and Forestry, Hue University kn-affil= affil-num=6 en-affil=Center for Hami Melon, Xinjiang Academy of Agricultural Sciences kn-affil= affil-num=7 en-affil=All-Russian Institute of Plant Genetic Resources on the name of N.I.Vavilov (VIR) kn-affil= affil-num=8 en-affil=Kazakhstan Research Institute of Potato and Vegetable Growing LLC kn-affil= affil-num=9 en-affil=Faculty of Agriculture and Life Science, Hirosaki University 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=Central Asia kn-keyword=Central Asia en-keyword=Cucumis melo kn-keyword=Cucumis melo en-keyword=diversity kn-keyword=diversity en-keyword=genetic resources kn-keyword=genetic resources en-keyword=on-farm conservation kn-keyword=on-farm conservation END start-ver=1.4 cd-journal=joma no-vol=71 cd-vols= no-issue=4 article-no= start-page=405 end-page=416 dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20211001 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Targeted genome modifications in cereal crops en-subtitle= kn-subtitle= en-abstract= kn-abstract=The recent advent of customizable endonucleases has led to remarkable advances in genetic engineering, as these molecular scissors allow for the targeted introduction of mutations or even precisely predefined genetic modifications into virtually any genomic target site of choice. Thanks to its unprecedented precision, efficiency, and functional versatility, this technology, commonly referred to as genome editing, has become an effective force not only in basic research devoted to the elucidation of gene function, but also for knowledgebased improvement of crop traits. Among the different platforms currently available for site-directed genome modifications, RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) endonucleases have proven to be the most powerful. This review provides an application-oriented overview of the development of customizable endonucleases, current approaches to cereal crop breeding, and future opportunities in this field. en-copyright= kn-copyright= en-aut-name=HisanoHiroshi en-aut-sei=Hisano en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=AbeFumitaka en-aut-sei=Abe en-aut-mei=Fumitaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HoffieRobert E. en-aut-sei=Hoffie en-aut-mei=Robert E. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KumlehnJochen en-aut-sei=Kumlehn en-aut-mei=Jochen kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Crop Science, National Agriculture and Food Research Organization kn-affil= affil-num=3 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) kn-affil= affil-num=4 en-affil=Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) kn-affil= en-keyword=barley kn-keyword=barley en-keyword= CRISPR kn-keyword= CRISPR en-keyword= maize kn-keyword= maize en-keyword=rice kn-keyword=rice en-keyword=TALEN kn-keyword=TALEN en-keyword=wheat kn-keyword=wheat en-keyword=zinc-finger nucleases kn-keyword=zinc-finger nucleases END start-ver=1.4 cd-journal=joma no-vol=71 cd-vols= no-issue=2 article-no= start-page=155 end-page=166 dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210217 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Transcriptomic analysis of developing seeds in a wheat (Triticum aestivum L.) mutant RSD32 with reduced seed dormancy en-subtitle= kn-subtitle= en-abstract= kn-abstract=Seed dormancy, a major factor regulating pre-harvest sprouting, can severely hinder wheat cultivation. Reduced Seed Dormancy 32 (RSD32), a wheat (Triticum aestivum L.) mutant with reduced seed dormancy, is derived from the pre-harvest sprouting tolerant cultivar, 'Norin61'. RSD32 is regulated by a single recessive gene and mutant phenotype expressed in a seed-specific manner. Gene expressions in embryos of 'Norin61' and RSD32 were compared using RNA sequencing (RNA-seq) analysis at different developmental stages of 20, 30, and 40 days after pollination (DAP). Numbers of up-regulated genes in RSD32 are equivalent in all developmental stages. However, down-regulated genes in RSD32 are more numerous on DAP20 and DAP30 than on DAP40. In central components affecting the circadian clock, homologues to the morning-expressed genes are expressed at lower levels in RSD32. However, higher expressions of homologues acting as evening-expressed genes are observed in RSD32. Homologues of Ca2+ signaling pathway related genes are specifically expressed on DAP20 in 'Norin61'. Lower expression is shown in RSD32. These results suggest that RSD32 mutation expresses on DAP20 and earlier seed developmental stages and suggest that circadian clock regulation and Ca2+ signaling pathway are involved in the regulation of wheat seed dormancy. en-copyright= kn-copyright= en-aut-name=RikiishiKazuhide en-aut-sei=Rikiishi en-aut-mei=Kazuhide kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SugimotoManabu en-aut-sei=Sugimoto en-aut-mei=Manabu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MaekawaMasahiko en-aut-sei=Maekawa en-aut-mei=Masahiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=mutant kn-keyword=mutant en-keyword=seed development kn-keyword=seed development en-keyword=seed dormancy kn-keyword=seed dormancy en-keyword=transcriptome kn-keyword=transcriptome en-keyword=wheat kn-keyword=wheat 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=69 cd-vols= no-issue=4 article-no= start-page=633 end-page=639 dt-received= dt-revised= dt-accepted= dt-pub-year= dt-pub= dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections en-subtitle= kn-subtitle= en-abstract= kn-abstract=Direct seeding saves time and labour in the cultivation of rice. However, seedling establishment is often unstable, and yields are lower than in transplanting. Anaerobic germination (AG) is a key trait for improvement of direct seeding of rice. We established a simple and reliable method of evaluating AG in rice breeding. We germinated seeds in distilled water or deoxygenated water and measured coleoptile length several days later; compared the results of each method with survival rate in flooded soil; and used the anoxic water method for QTL analysis and for testing cultivars. Coleoptile elongation in anoxic water and survival rate in flooded soil were significantly correlated (r = 0.879, P < 0.01). A significant QTL, likely to be a major gene (AG1), was found in chromosome segment substitution lines and in a backcrossed F2 population derived from tolerant and sensitive lines. Diverse rice genetic resources were classified into tolerant or sensitive accession groups reflecting their ecotypes. Our study revealed that anoxic water evaluation method saves space and time in a stable environment compared with flooded soil evaluation. It is applicable to QTL analysis and isolation of genes underlying anaerobic germination. en-copyright= kn-copyright= en-aut-name=KuyaNoriyuki en-aut-sei=Kuya en-aut-mei=Noriyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SunJian en-aut-sei=Sun en-aut-mei=Jian kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=IijimaKen en-aut-sei=Iijima en-aut-mei=Ken kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=VenuprasadRamaiah en-aut-sei=Venuprasad en-aut-mei=Ramaiah kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=YamamotoToshio en-aut-sei=Yamamoto en-aut-mei=Toshio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil=Institute of Crop Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=2 en-affil=Institute of Crop Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=3 en-affil=Institute of Crop Science, National Agriculture and Food Research Organization (NARO) kn-affil= affil-num=4 en-affil=Africa Rice Center (AfricaRice) kn-affil= affil-num=5 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=QTL kn-keyword=QTL en-keyword=anaerobic germination kn-keyword=anaerobic germination en-keyword=anoxic water kn-keyword=anoxic water en-keyword=direct seeding kn-keyword=direct seeding en-keyword=genetic resources kn-keyword=genetic resources en-keyword=phenotyping method kn-keyword=phenotyping method en-keyword=rice kn-keyword=rice END