This page has only limited features, please log in for full access.

Prof. Dr. Nakao Kubo
Affiliation 1: Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo 606-8522, Kyoto, Japan

Basic Info


Research Keywords & Expertise

0 Classification
0 Tea
0 plant mitochondria
0 Vegetable
0 Linkage analysis

Fingerprints

Classification
plant mitochondria
Vegetable
Flowering lotus
Tea

Honors and Awards

The user has no records in this section


Career Timeline

The user has no records in this section.


Short Biography

The user biography is not available.
Following
Followers
Co Authors
The list of users this user is following is empty.
Following: 0 users

Feed

Research article
Published: 17 June 2021 in Genetic Resources and Crop Evolution
Reads 0
Downloads 0

To assess the current genetic status of a useful coastal plant Glehnia littoralis F. Schmidt ex Miq. in Japan, the genetic diversity within and among natural populations was investigated. A total of 601 individuals from 32 local populations were genotyped using inter-primer binding site (iPBS) markers. In addition, most likelihood inference of the outcrossing rate was determined based on genotyping of maternal families from two populations using newly developed microsatellite markers. A total of 34 polymorphic bands were detected with seven iPBS primers. All populations showed genetic variation, with Shannon’s I ranging from 0.577 to 0.107. Analysis of molecular variance (AMOVA), neighbor-joining analysis, and Bayesian cluster analysis revealed that the populations were differentiated into a group on the Sea of Japan coast and another on the Pacific Ocean coast. Furthermore, populations in geographic proximity were genetically more similar to each other. These results suggested that long-distance gene flow among local populations is limited. Nonetheless, a high within-population component of genetic diversity after AMOVA (77.4%) and high population’s Q values (an average of 0.781) indicated that the level of genetic differentiation among populations is moderate. Outcrossing rate estimates based on eight microsatellite loci were 0.88 to 0.80 for two different populations, showing the mostly panmictic nature of the species. Substantial level of genetic variation within and among populations implicates that genetic improvement on desirable traits is possible via artificial selection. On the other hand, the present study showed that maintenance of population size is critical to avoid fitness decline in natural populations via inbreeding depression and fixation of deleterious alleles by genetic drift.

ACS Style

Yasuhiro Tamura; Nakao Kubo; Takanori Ohsako. Genetic diversity among Japanese local populations of an edible and medicinal coastal plant Glehnia littoralis F. Schmidt ex Miq. Genetic Resources and Crop Evolution 2021, 1 -13.

AMA Style

Yasuhiro Tamura, Nakao Kubo, Takanori Ohsako. Genetic diversity among Japanese local populations of an edible and medicinal coastal plant Glehnia littoralis F. Schmidt ex Miq. Genetic Resources and Crop Evolution. 2021; ():1-13.

Chicago/Turabian Style

Yasuhiro Tamura; Nakao Kubo; Takanori Ohsako. 2021. "Genetic diversity among Japanese local populations of an edible and medicinal coastal plant Glehnia littoralis F. Schmidt ex Miq." Genetic Resources and Crop Evolution , no. : 1-13.

Journal article
Published: 30 December 2020 in International Journal of Molecular Sciences
Reads 0
Downloads 0

Floral organs have evolved from leaves for reproduction, and the morphological analyses help to understand the plant diversity and evolution. Habenaria radiata (syn. Pecteilis radiata) is a terrestrial orchid living in wetlands in Japan, Russia, South Korea, and China. The habitats of this plant in Japan have been reduced because of environmental destruction and overexploitation, and thus it is on the Red List of Japan as a Near Threatened species. One of the three petals of the H. radiata flower is called a lip or labellum, which resembles a flying white bird, egret, or white heron, with its proposed function being to attract pollinators. To understand the diversity of H. radiata plants in different areas, we examined the lip morphology and phylogeny of populations from eight habitats in the Kinki area, Japan. The complex shapes of the lips were quantified and presented as a radar chart, enabling characterization of the morphological difference among populations. Phylogenetic analysis with microsatellite markers that we generated showed the variation of genetic diversity among populations, suggesting the different degrees of inbreeding, outbreeding, and vegetative propagation. Our approach offers a basic method to characterize the morphological and genetic diversity in natural populations.

ACS Style

Tsutomu Tachibana; Yuki Nishikawa; Nakao Kubo; Seiji Takeda. Morphological and Genetic Diversities of Habenaria radiata (Orchidaceae) in the Kinki Area, Japan. International Journal of Molecular Sciences 2020, 22, 311 .

AMA Style

Tsutomu Tachibana, Yuki Nishikawa, Nakao Kubo, Seiji Takeda. Morphological and Genetic Diversities of Habenaria radiata (Orchidaceae) in the Kinki Area, Japan. International Journal of Molecular Sciences. 2020; 22 (1):311.

Chicago/Turabian Style

Tsutomu Tachibana; Yuki Nishikawa; Nakao Kubo; Seiji Takeda. 2020. "Morphological and Genetic Diversities of Habenaria radiata (Orchidaceae) in the Kinki Area, Japan." International Journal of Molecular Sciences 22, no. 1: 311.

Brief report
Published: 22 October 2020 in Horticulturae
Reads 0
Downloads 0

Squash (Cucurbita moschata) displays wide morphological and genetic variations; however, limited information is available regarding the genetic loci of squash that control its agronomic traits. To obtain basic genetic information for C. moschata, an F2 population was prepared derived from a cross between the Vietnamese cultivar ‘Bí Hồ Lô TN 6 (TN 6)’ and the Japanese cultivar ‘Shishigatani’, and flowering and fruit traits were examined. Overall, the traits showed a continuous distribution in the F2 population, suggesting that they were quantitative traits. A linkage map was constructed based on simple sequence repeat and restriction site-associated DNA (RAD) markers to detect quantitative trait loci (QTLs). Twelve QTLs for flowering and fruit traits, as well as one phenotypic trait locus, were successfully localized on the map. The present QTLs explained the phenotypic variations at a moderate to relatively high level (16.0%–47.3%). RAD markers linked to the QTLs were converted to codominant cleaved amplified polymorphic sequence (CAPS) and derived CAPS markers for the easy detection of alleles. The information reported here provides useful information for understanding the genetics of Cucurbita and other cucurbit species, and for the selection of individuals with ideal traits during the breeding of Cucurbita vegetables.

ACS Style

Takuma Hashimoto; Nakao Kubo; Kanako Nishimura; Atsushi Nagano; Azusa Sasaki; Yasushi Nakamura; Yutaka Mimura. Quantitative Trait Locus Analysis in Squash (Cucurbita moschata) Based on Simple Sequence Repeat Markers and Restriction Site-Associated DNA Sequencing Analysis. Horticulturae 2020, 6, 71 .

AMA Style

Takuma Hashimoto, Nakao Kubo, Kanako Nishimura, Atsushi Nagano, Azusa Sasaki, Yasushi Nakamura, Yutaka Mimura. Quantitative Trait Locus Analysis in Squash (Cucurbita moschata) Based on Simple Sequence Repeat Markers and Restriction Site-Associated DNA Sequencing Analysis. Horticulturae. 2020; 6 (4):71.

Chicago/Turabian Style

Takuma Hashimoto; Nakao Kubo; Kanako Nishimura; Atsushi Nagano; Azusa Sasaki; Yasushi Nakamura; Yutaka Mimura. 2020. "Quantitative Trait Locus Analysis in Squash (Cucurbita moschata) Based on Simple Sequence Repeat Markers and Restriction Site-Associated DNA Sequencing Analysis." Horticulturae 6, no. 4: 71.

Journal article
Published: 01 January 2019 in The Horticulture Journal
Reads 0
Downloads 0

In Japan, many turnip (Brassica rapa) cultivars are known as heirloom vegetables, especially in Shiga Prefecture, which is close to the old capital of Japan, Kyoto. Of these, ‘Omikabu’, an heirloom white turnip cultivar in Shiga Prefecture is referred to as the ancestor of the white turnip cultivars, ‘Shogoinkabu’, ‘Tennojikabu’, and ‘Yoriikabu’. Many “red turnip” cultivars that are red or purple-skinned varieties (and sometimes with colored flesh and petioles), also grow in Shiga Prefecture, and are mainly processed into pickled vegetables. However, their origins have not yet been fully verified. In this study, construction of neighbor-joining phylograms and population structure analyses were performed based on eight simple sequence repeat markers for white and red turnips, plus two non-turnip B. rapa vegetables (Chinese cabbage and mizuna). For the white turnip-related lines, a claim that ‘Shogoinkabu’, ‘Tennojikabu’, and ‘Yoriikabu’ are derived from ‘Omikabu’ could not be supported in this study because ‘Omikabu’ lines were separated from the above three cultivars in the phylogram. In contrast, an ‘Omikabu’ line, ‘Omikabura RU’, formed a cluster with ‘Jonansensuji mizuna’, suggesting a genetic relationship (a crossing in the past) between them. For red turnips, close placements of ‘Kisobenikabu’-‘Shinshukabu’, ‘Hinona’-‘Kitanoshokabu’, and ‘Biwakobenikabu’-‘Yurugikabu’ were found in the phylogram, each of which was in good agreement with the proposed cultivar’s origin. The data in this study provide useful information for understanding the genetic relationships among Japanese heirloom turnip cultivars.

ACS Style

Nakao Kubo; Hayato Ueoka; Shigeru Satoh. Genetic Relationships of Heirloom Turnip (Brassica rapa) Cultivars in Shiga Prefecture and Other Regions of Japan. The Horticulture Journal 2019, 88, 471 -480.

AMA Style

Nakao Kubo, Hayato Ueoka, Shigeru Satoh. Genetic Relationships of Heirloom Turnip (Brassica rapa) Cultivars in Shiga Prefecture and Other Regions of Japan. The Horticulture Journal. 2019; 88 (4):471-480.

Chicago/Turabian Style

Nakao Kubo; Hayato Ueoka; Shigeru Satoh. 2019. "Genetic Relationships of Heirloom Turnip (Brassica rapa) Cultivars in Shiga Prefecture and Other Regions of Japan." The Horticulture Journal 88, no. 4: 471-480.

Journal article
Published: 01 January 2019 in Breeding Science
Reads 0
Downloads 0

Carrot (Daucus carota) is cultivated in temperate regions for its taproot. Eastern and Western types have been differentiated. In Japan, the former type is categorized into Kintoki, Takinogawa oonaga, and Toso, with a few local cultivars. However, their genetic relationships are unclear because of the paucity of reports. We classified the Japanese Eastern and selected Western types based on simple sequence repeat (SSR) markers. Field traits, including root weight, length, diameter, and skin color, were also examined. Our field tests showed clear differences between the Kintoki and Western-type cultivars, confirming their differentiation. A phylogram based on nine SSRs classified 24 cultivars into groups I and II. Group I included all Eastern-type carrots examined (Kintoki and Toso groups, plus two local and two foreign cultivars), with the exception of an Indian cultivar ('Pusa rudhira red'). Among them, red carrots including Kintoki were clustered into two subgroups. Western-type, Eastern-Western hybrid, and 'Pusa rudhira red' were included in group II. A population structure analysis revealed the split between the Eastern and the other types. This study elucidates the genetic characteristics of the Eastern type of carrot, which will be valuable information for carrot breeding, especially when using the Eastern type as a source.

ACS Style

Nakao Kubo; Risa Yamashita; Michiyo Tani; Koji Ozaki; Toshiro Fujiwara; Yutaka Mimura. Classification of "Kintoki ninjin" and other groups of carrot (Daucus carota) based on simple sequence repeat markers. Breeding Science 2019, 69, 688 -695.

AMA Style

Nakao Kubo, Risa Yamashita, Michiyo Tani, Koji Ozaki, Toshiro Fujiwara, Yutaka Mimura. Classification of "Kintoki ninjin" and other groups of carrot (Daucus carota) based on simple sequence repeat markers. Breeding Science. 2019; 69 (4):688-695.

Chicago/Turabian Style

Nakao Kubo; Risa Yamashita; Michiyo Tani; Koji Ozaki; Toshiro Fujiwara; Yutaka Mimura. 2019. "Classification of "Kintoki ninjin" and other groups of carrot (Daucus carota) based on simple sequence repeat markers." Breeding Science 69, no. 4: 688-695.

Journal article
Published: 01 January 2019 in Breeding Science
Reads 0
Downloads 0

Brassica rapa or B. napus vegetables for eating as young inflorescences and stalks are called “nabana”. Japanese nabana includes “flower-bud type” and “stem-and-leaf type”. Chinese and European types are also known (cai-xin, zicaitai, and broccoletto). We classified nabana belonging to B. rapa and other B. rapa vegetables. In a simple sequence repeat-based phylogram, 49 ingroup samples were classified into four groups (I–IV). Flower-bud and stem-and-leaf types were separated into groups I and III, respectively, with a slight overlap in group II. Cai-xin and non-heading Chinese cabbages were included in group IV. Broccoletto was placed in group III, close to turnips. Zicaitai cultivars were included in group II. We tested for clubroot resistance (CR) and its marker genotypes in nabana because of their agronomical importance. Ten cultivars were resistant to group 4 pathogen but not to group 2. Most of the CR cultivars had heterozygous resistance alleles in the CRb and Crr1 loci, consistent with inoculation tests. Our results suggest that Japanese nabana lines and foreign types were differentiated according to their consumption parts and cultivar origins, respectively. This study elucidates the relationships and CR properties of nabana and provides valuable information for the breeding of nabana cultivars.

ACS Style

Nakao Kubo; Kumiko Onnazaka; Shinji Mizuno; Gento Tsuji. Classification of “nabana” (Brassica rapa) cultivars and landraces based on simple sequence repeat markers. Breeding Science 2019, 69, 179 -185.

AMA Style

Nakao Kubo, Kumiko Onnazaka, Shinji Mizuno, Gento Tsuji. Classification of “nabana” (Brassica rapa) cultivars and landraces based on simple sequence repeat markers. Breeding Science. 2019; 69 (1):179-185.

Chicago/Turabian Style

Nakao Kubo; Kumiko Onnazaka; Shinji Mizuno; Gento Tsuji. 2019. "Classification of “nabana” (Brassica rapa) cultivars and landraces based on simple sequence repeat markers." Breeding Science 69, no. 1: 179-185.

Research article
Published: 16 November 2018 in Genetic Resources and Crop Evolution
Reads 0
Downloads 0

The tea plant (Camellia sinensis (L.) Kuntze) of Japan is now thought to have originated in China. Actual cultivation of tea plants presumably started in Kyoto, and then spread to other regions of Japan. Tea gardens used to be composed of heterogenic, seed-derived populations—landraces—selected for climatic preferences and cultivation methods. Cultivars were bred from landraces in the modern era. A number of landraces remain in Kyoto Prefecture. However, little is known about their genetic characteristics compared with other landraces. We investigated the relationships of tea landraces and cultivars from Kyoto Prefecture and other regions. A neighbor-joining phylogram was constructed from 113 lines including 68 landraces, 44 cultivars, and one wild relative, based on simple sequence repeat markers. The lines could be classified into four groups (I–IV). In group I, most of the Kyoto landraces were close to other Japanese landraces, supporting the idea of the spread of tea plants from Kyoto to other regions in the country. The remaining lines were included into groups III and IV, apart from group II, which contained Shizuoka lines. Similar results were observed by restriction site-associated DNA sequencing analysis using 44 cultivars. Our data provide valuable information for the classification of tea lines, especially for the relationships of Kyoto lines among Japanese tea varieties.

ACS Style

Nakao Kubo; Yutaka Mimura; Tomohiro Matsuda; Atsushi J. Nagano; Nobuhiro Hirai; Shigekazu Higashimoto; Hiromi Yoshida; Norihiro Uemura; Takao Fujii. Classification of tea (Camellia sinensis) landraces and cultivars in Kyoto, Japan and other regions, based on simple sequence repeat markers and restriction site-associated DNA sequencing analysis. Genetic Resources and Crop Evolution 2018, 66, 441 -451.

AMA Style

Nakao Kubo, Yutaka Mimura, Tomohiro Matsuda, Atsushi J. Nagano, Nobuhiro Hirai, Shigekazu Higashimoto, Hiromi Yoshida, Norihiro Uemura, Takao Fujii. Classification of tea (Camellia sinensis) landraces and cultivars in Kyoto, Japan and other regions, based on simple sequence repeat markers and restriction site-associated DNA sequencing analysis. Genetic Resources and Crop Evolution. 2018; 66 (2):441-451.

Chicago/Turabian Style

Nakao Kubo; Yutaka Mimura; Tomohiro Matsuda; Atsushi J. Nagano; Nobuhiro Hirai; Shigekazu Higashimoto; Hiromi Yoshida; Norihiro Uemura; Takao Fujii. 2018. "Classification of tea (Camellia sinensis) landraces and cultivars in Kyoto, Japan and other regions, based on simple sequence repeat markers and restriction site-associated DNA sequencing analysis." Genetic Resources and Crop Evolution 66, no. 2: 441-451.

Journal article
Published: 11 September 2018 in Plants
Reads 0
Downloads 0

Symplocarpus nipponicus, a member of the Araceae family, is an endangered plant in several prefectures in Japan. For the conservation of this wild species, we investigated the morphology, life cycle, and genetic diversity of three wild populations. By fixed-point observation over several years, we found that it takes at least four years for the plant to set the inflorescences consisting of spadices and spathes, and another two years for it to set mature seeds. To examine the genetic diversity in the wild population, we developed 11 novel microsatellite markers and investigated the genetic variation in three populations in Kyoto Prefecture: Ayabe, Hanase, and Momoi. The Ayabe population carried less genetic variation than the other two areas, suggesting the isolation of the habitat and thus a higher risk of extinction. Our results provide basic knowledge of the ecological aspects of S. nipponicus, as well as molecular techniques for the assessment of its genetic diversity, and thus are useful for the conservation of this endangered species.

ACS Style

Seiji Takeda; Yusuke Onishi; Yoshio Fukui; Takanori Ohsako; Nakao Kubo. Life Cycle and Genetic Diversity of Symplocarpus nipponicus (Araceae), an Endangered Species in Japan. Plants 2018, 7, 73 .

AMA Style

Seiji Takeda, Yusuke Onishi, Yoshio Fukui, Takanori Ohsako, Nakao Kubo. Life Cycle and Genetic Diversity of Symplocarpus nipponicus (Araceae), an Endangered Species in Japan. Plants. 2018; 7 (3):73.

Chicago/Turabian Style

Seiji Takeda; Yusuke Onishi; Yoshio Fukui; Takanori Ohsako; Nakao Kubo. 2018. "Life Cycle and Genetic Diversity of Symplocarpus nipponicus (Araceae), an Endangered Species in Japan." Plants 7, no. 3: 73.

Journal article
Published: 31 May 2018 in Annual Report of The Kansai Plant Protection Society
Reads 0
Downloads 0

We investigated the effect of various plants on the population density of Plasmodiophora brassicae, which causes clubroot disease in crucifers. The amount of P. brassicae in soil samples was measured using quantitative real-time PCR (qPCR). The impact of the plants used in this study was generally small under both greenhouse and field conditions. P. brassicae does not cause clubroot disease in leaf radish (ha-daikon), but is known to be able to proliferate in the root hairs of the plant. The qPCR could also detect an increased density of P. brassicae in soil where leaf radishes were grown.

ACS Style

Kurumi Sunada; Ui Ono; Shigemitsu Kimura; Nakao Kubo; Gento Tsuji. Assessment of various plants to reduce the population density of Plasmodiophora brassicae in soil. Annual Report of The Kansai Plant Protection Society 2018, 60, 81 -84.

AMA Style

Kurumi Sunada, Ui Ono, Shigemitsu Kimura, Nakao Kubo, Gento Tsuji. Assessment of various plants to reduce the population density of Plasmodiophora brassicae in soil. Annual Report of The Kansai Plant Protection Society. 2018; 60 ():81-84.

Chicago/Turabian Style

Kurumi Sunada; Ui Ono; Shigemitsu Kimura; Nakao Kubo; Gento Tsuji. 2018. "Assessment of various plants to reduce the population density of Plasmodiophora brassicae in soil." Annual Report of The Kansai Plant Protection Society 60, no. : 81-84.

Journal article
Published: 01 February 2018 in Agriculture and Natural Resources
Reads 0
Downloads 0

Nelumbo nucifera is a symbolic flower of Buddhism and widely used for decoration in Asia. In most cases its buds are used as cut-flowers, which usually do not open and the outer petals turn black, leading to loss of visual quality and thus decreasing their economic value in markets. In Thailand, two major cultivars, Sattabongkot and Saddhabutra, are used and exported to foreign countries. To investigate the difference between these two cultivars, their molecular phylogeny and postharvest morphology were examined. Using 25 simple sequence repeat (SSR) markers, the cultivar Saddhabutra was very close to the cultivar Satabuto. These results showed a high bootstrap (BS) value of 96%. In contrast, lotus cultivars in Thailand including Sattabongkot and Saddhabutra, showed a BS value of 90%. Saddhabutra and Satabuto are classified in the same group with high similarity, whereas Sattabongkot shows relatively lower similarity. Petal blackening started earlier in Saddhabutra than Sattabongkot, indicating a vase-life difference among cultivars, with Sattabongkot and Saddhabutra having a vase life of 72 and 54 hr, respectively. The epidermal cells of normal petals of Sattabongkot and Saddhabutra showed freshness and a round shape with turgid cells. The petal blackening was accompanied with a reduction of the area and perimeter in both cultivars. Sattabongkot had fewer stomata than Saddhabutra. The study provided a molecular classification of the Thailand lotus cultivars and provides a useful technique for the quantification of the postharvest quality of lotus cultivars.

ACS Style

Nurainee Salaemae; Seiji Takeda; Nakao Kubo; Samak Kaewsuksaeng. Molecular phylogeny and postharvest morphology of petals in two major Nelumbo nucifera cultivars in Thailand. Agriculture and Natural Resources 2018, 52, 45 -52.

AMA Style

Nurainee Salaemae, Seiji Takeda, Nakao Kubo, Samak Kaewsuksaeng. Molecular phylogeny and postharvest morphology of petals in two major Nelumbo nucifera cultivars in Thailand. Agriculture and Natural Resources. 2018; 52 (1):45-52.

Chicago/Turabian Style

Nurainee Salaemae; Seiji Takeda; Nakao Kubo; Samak Kaewsuksaeng. 2018. "Molecular phylogeny and postharvest morphology of petals in two major Nelumbo nucifera cultivars in Thailand." Agriculture and Natural Resources 52, no. 1: 45-52.

Article
Published: 11 March 2017 in European Journal of Plant Pathology
Reads 0
Downloads 0

Clubroot disease caused by Plasmodiophora brassicae is one of the most serious diseases in cruciferous crops. To classify isolates, we developed simple sequence repeat (SSR) markers for P. brassicae. Twenty-four Japanese isolates were used in this study: 12 isolates of an unknown pathotype from the Kyoto Prefecture, as well as 12 isolates of known pathotypes, including three single-spore lines. From the 12 isolates from Kyoto Prefecture, 11 were classified into either pathotype 2 (three isolates) or 4 (eight isolates). We designed 23 SSR markers based on the P. brassicae genome, of which 11 markers from intergenic regions showed polymorphisms in the 24 isolates. Many haploid isolates belonging to pathotypes 2 and 4 were monomorphic, and typical alleles were detected in some isolates not belonging to pathotype 4. Two bands were detected for eight SSR loci in five isolates, indicating that different genotypes were mixed in these isolates. We constructed a phylogram based on the 11 polymorphic SSRs. Pathotypes 2 and 4 formed a cluster, from which pathotypes 3 and 1 were successively placed. These results strongly suggest a close genetic relationship between isolates in pathotypes 2 and 4, consistent with our finding that isolates in these two pathotypes were found at one collection site. In combination with pathotype classification and other marker systems, the SSR markers can be used for more detailed analyses to improve the control of clubroot disease.

ACS Style

Nakao Kubo; Kumiko Onnazaka; Ui Ono; Gento Tsuji. Development of simple sequence repeat markers for the classification of the clubroot pathogen Plasmodiophora brassicae. European Journal of Plant Pathology 2017, 149, 733 -738.

AMA Style

Nakao Kubo, Kumiko Onnazaka, Ui Ono, Gento Tsuji. Development of simple sequence repeat markers for the classification of the clubroot pathogen Plasmodiophora brassicae. European Journal of Plant Pathology. 2017; 149 (3):733-738.

Chicago/Turabian Style

Nakao Kubo; Kumiko Onnazaka; Ui Ono; Gento Tsuji. 2017. "Development of simple sequence repeat markers for the classification of the clubroot pathogen Plasmodiophora brassicae." European Journal of Plant Pathology 149, no. 3: 733-738.

Journal article
Published: 03 March 2017 in Journal of Plant Research
Reads 0
Downloads 0

Brassica rapa show a wide range of morphological variations. In particular, the leaf morphologies of the Japanese traditional leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey) are distinctly different, even though they are closely related cultivars that are easy to cross. In addition to the differences in the gross morphology of leaves, some cultivars of Mibuna (Kyo-nishiki) have many trichomes on its leaves, whereas Mizuna (Kyo-mizore) does not. To identify the genes responsible for the different number of trichomes, we performed a quantitative trait loci (QTL) analysis of Mizuna and Mibuna. To construct linkage maps for these cultivars, we used RNA-seq data to develop cleaved amplified polymorphic sequence (CAPS) markers. We also performed a restriction site-associated DNA sequencing (RAD-seq) analysis to detect single-nucleotide polymorphisms (SNPs). Two QTL analyses were performed in different years, and both analyses indicated that the largest effect was found on LG A9. Expression analyses showed that a gene homologous to GLABRA1 (GL1), a transcription factor implicated in trichome development in Arabidopsis thaliana, and the sequences 3'-flanking (downstream) of BrGL1, differed considerably between Mizuna (Kyo-mizore) and Mibuna (Kyo-nishiki). These results indicate that BrGL1 on LG A9 is one of the candidate genes responsible for the difference in trichome number between Mizuna and Mibuna. Detecting genes that are responsible for morphological variations allows us to better understand the breeding history of Mizuna and Mibuna.

ACS Style

Yaichi Kawakatsu; Hokuto Nakayama; Kaori Kaminoyama; Kaori Igarashi; Masaki Yasugi; Hiroshi Kudoh; Atsushi J. Nagano; Kentaro Yano; Nakao Kubo; Seisuke Kimura. A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis. Journal of Plant Research 2017, 130, 539 -550.

AMA Style

Yaichi Kawakatsu, Hokuto Nakayama, Kaori Kaminoyama, Kaori Igarashi, Masaki Yasugi, Hiroshi Kudoh, Atsushi J. Nagano, Kentaro Yano, Nakao Kubo, Seisuke Kimura. A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis. Journal of Plant Research. 2017; 130 (3):539-550.

Chicago/Turabian Style

Yaichi Kawakatsu; Hokuto Nakayama; Kaori Kaminoyama; Kaori Igarashi; Masaki Yasugi; Hiroshi Kudoh; Atsushi J. Nagano; Kentaro Yano; Nakao Kubo; Seisuke Kimura. 2017. "A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis." Journal of Plant Research 130, no. 3: 539-550.

Article
Published: 27 December 2016 in Environmental Biology of Fishes
Reads 0
Downloads 0

Simple sequence repeat (SSR) markers were developed for the brown alga Sargassum horneri (also known as “akamoku”) from an SSR-enriched genomic library. Of 22 SSR markers developed, 10 primer pairs produced clearly distinguishable DNA bands, indicating polymorphisms in S. horneri populations collected around Wakasa Bay, Kyoto, Japan. Ten primer pairs among the newly developed SSRs were also applicable to any of five other Sargassum species tested. To assess the utility of SSR markers for the classification of S. horneri, we genotyped 86 akamoku individuals from six populations (Naryu, Obase, Oshima, Satohami, Tai, and Taiza). We detected 148 alleles using 11 markers (10 new and 1 previously published). The allele number per locus ranged from 4 to 32 (average, 13.5). Based on the genotyping data for the 11 SSR markers, three of the six akamoku populations were separated on a phylogram. These results indicate that the SSR markers developed in this study are informative and useful for genetic analyses in Sargassum species.

ACS Style

Nakao Kubo; Akio Douke; Tomokazu Nishigaki; Gento Tsuji. Development and characterization of simple sequence repeat markers for genetic analyses of Sargassum horneri (Sargassaceae, Phaeophyta) populations in Kyoto, Japan. Environmental Biology of Fishes 2016, 29, 1729 -1733.

AMA Style

Nakao Kubo, Akio Douke, Tomokazu Nishigaki, Gento Tsuji. Development and characterization of simple sequence repeat markers for genetic analyses of Sargassum horneri (Sargassaceae, Phaeophyta) populations in Kyoto, Japan. Environmental Biology of Fishes. 2016; 29 (3):1729-1733.

Chicago/Turabian Style

Nakao Kubo; Akio Douke; Tomokazu Nishigaki; Gento Tsuji. 2016. "Development and characterization of simple sequence repeat markers for genetic analyses of Sargassum horneri (Sargassaceae, Phaeophyta) populations in Kyoto, Japan." Environmental Biology of Fishes 29, no. 3: 1729-1733.

Journal article
Published: 01 January 2015 in The Journal of Horticultural Science and Biotechnology
Reads 0
Downloads 0
ACS Style

T. Inoue; Nakao Kubo; T. Kondo; M. Hirai. Detection of quantitative trait loci for heading traits inBrassica rapausing different heading types of Chinese cabbage. The Journal of Horticultural Science and Biotechnology 2015, 90, 311 -317.

AMA Style

T. Inoue, Nakao Kubo, T. Kondo, M. Hirai. Detection of quantitative trait loci for heading traits inBrassica rapausing different heading types of Chinese cabbage. The Journal of Horticultural Science and Biotechnology. 2015; 90 (3):311-317.

Chicago/Turabian Style

T. Inoue; Nakao Kubo; T. Kondo; M. Hirai. 2015. "Detection of quantitative trait loci for heading traits inBrassica rapausing different heading types of Chinese cabbage." The Journal of Horticultural Science and Biotechnology 90, no. 3: 311-317.

Journal article
Published: 01 January 2015 in Breeding Research
Reads 0
Downloads 0
ACS Style

Nakao Kubo; Akio Kaneko; Kazuki Yamamoto. Classification of flowering lotus cultivars in Japan, including “Ogura-ike group cultivars”, based on SSR markers. Breeding Research 2015, 17, 45 -54.

AMA Style

Nakao Kubo, Akio Kaneko, Kazuki Yamamoto. Classification of flowering lotus cultivars in Japan, including “Ogura-ike group cultivars”, based on SSR markers. Breeding Research. 2015; 17 (2):45-54.

Chicago/Turabian Style

Nakao Kubo; Akio Kaneko; Kazuki Yamamoto. 2015. "Classification of flowering lotus cultivars in Japan, including “Ogura-ike group cultivars”, based on SSR markers." Breeding Research 17, no. 2: 45-54.

Journal article
Published: 01 January 2013 in Breeding Science
Reads 0
Downloads 0

The radish displays great morphological variation but the genetic factors underlying this variability are mostly unknown. To identify quantitative trait loci (QTLs) controlling radish morphological traits, we cultivated 94 F4 and F5 recombinant inbred lines derived from a cross between the rat-tail radish and the Japanese radish cultivar ‘Harufuku’ inbred lines. Eight morphological traits (ovule and seed numbers per silique, plant shape, pubescence and root formation) were measured for investigation. We constructed a map composed of 322 markers with a total length of 673.6 cM. The linkage groups were assigned to the radish chromosomes using disomic rape-radish chromosome-addition lines. On the map, eight and 10 QTLs were identified in 2008 and 2009, respectively. The chromosome-linkage group correspondence, the sequence-specific markers and the QTLs detected here will provide useful information for further genetic studies and for selection during radish breeding programs.

ACS Style

Tomoko Hashida; Ryoichi Nakatsuji; Holger Budahn; Otto Schrader; Herbert Peterka; Tatsuhito Fujimura; Nakao Kubo; Masashi Hirai. Construction of a chromosome-assigned, sequence-tagged linkage map for the radish, Raphanus sativus L. and QTL analysis of morphological traits. Breeding Science 2013, 63, 218 -226.

AMA Style

Tomoko Hashida, Ryoichi Nakatsuji, Holger Budahn, Otto Schrader, Herbert Peterka, Tatsuhito Fujimura, Nakao Kubo, Masashi Hirai. Construction of a chromosome-assigned, sequence-tagged linkage map for the radish, Raphanus sativus L. and QTL analysis of morphological traits. Breeding Science. 2013; 63 (2):218-226.

Chicago/Turabian Style

Tomoko Hashida; Ryoichi Nakatsuji; Holger Budahn; Otto Schrader; Herbert Peterka; Tatsuhito Fujimura; Nakao Kubo; Masashi Hirai. 2013. "Construction of a chromosome-assigned, sequence-tagged linkage map for the radish, Raphanus sativus L. and QTL analysis of morphological traits." Breeding Science 63, no. 2: 218-226.

Article
Published: 27 March 2012 in Euphytica
Reads 0
Downloads 0

Plant architecture plays an important role in the yield, product quality, and cultivation practices of many crops. Branching pattern is one of the most important components in the plant architecture of melon (Cucumis melo L.). ‘Melon Chukanbohon Nou 4 Go’ (Nou-4) has a short-lateral-branching trait derived from a weedy melon, LB-1. This trait is reported to be controlled by a single recessive or incompletely dominant major gene called short lateral branching (slb). To find molecular markers for marker-assisted selection of this gene, we first constructed a linkage map using 94 F2 plants derived from a cross between Nou-4 and ‘Earl’s Favourite (Harukei-3)’, a cultivar with normal branching. We then conducted quantitative trait locus (QTL) analysis and identified two loci for short lateral branching. A major QTL in linkage group (LG) XI, at which the Nou-4 allele is associated with short lateral branching, explained 50.9 % of the phenotypic variance, with a LOD score of 12.5. We suggest that this QTL corresponds to slb because of the magnitude of its effect. Another minor QTL in LG III, at which the Harukei-3 allele is associated with short lateral branching, explained 9.9 % of the phenotypic variance, with a LOD score of 4.2. Using an independent population, we demonstrated that an SSR marker linked to the QTL in LG XI (slb) could be used to select for short lateral branching. This is the first report of mapping a gene regulating the plant architecture of melon.

ACS Style

Nobuko Fukino; Takeshi Ohara; Masaaki Sugiyama; Nakao Kubo; Masashi Hirai; Yasuhiko Sakata; Sen Matsumoto. Mapping of a gene that confers short lateral branching (slb) in melon (Cucumis melo L.). Euphytica 2012, 187, 133 -143.

AMA Style

Nobuko Fukino, Takeshi Ohara, Masaaki Sugiyama, Nakao Kubo, Masashi Hirai, Yasuhiko Sakata, Sen Matsumoto. Mapping of a gene that confers short lateral branching (slb) in melon (Cucumis melo L.). Euphytica. 2012; 187 (1):133-143.

Chicago/Turabian Style

Nobuko Fukino; Takeshi Ohara; Masaaki Sugiyama; Nakao Kubo; Masashi Hirai; Yasuhiko Sakata; Sen Matsumoto. 2012. "Mapping of a gene that confers short lateral branching (slb) in melon (Cucumis melo L.)." Euphytica 187, no. 1: 133-143.

Journal article
Published: 04 March 2012 in Conservation Genetics
Reads 0
Downloads 0

Viola grayi, a coastal violet, is found on sandy seashores in limited regions in Japan, but not on rocky sea cliffs or in inland areas. This stemmed violet is classified in the subsection Rostratae. Because of recent human activity on sandy seashores, this species is now recorded as endangered. The present status of this species was surveyed and its genetic diversity was analyzed using 17 newly developed simple sequence repeat markers. The results are compared with those for two commonly found inland violet species in the same subsection, V. grypoceras and V. kusanoana. The coastal violet populations showed markedly lower genetic diversity than those of the common species, V. grypoceras, whereas V. kusanoana showed intermediate genetic diversity. About a half of the total genetic variation of V. grayi is found among populations in analysis of molecular variance. In contrast, only less than 25% of the total variation is found among populations for the two common violets. These three species showed a remarkably high inbreeding coefficient, which indicates high inbreeding under natural mating conditions, although these species have both chasmogamous and cleistogamous flowers. In a population-based dendrogram, V. grayi was clustered in a single and concise group, whereas V. grypoceras and V. kusanoana were found in somewhat discrete positions. In the Bayesian analysis of genetic structure of the coastal violet, delta K was the highest at K = 7, and the seven clusters almost correspond to seven populations studied here. Implications of the conservation of this endangered coastal violet are presented.

ACS Style

Masashi Hirai; Nakao Kubo; Takanori Ohsako; Tomoko Utsumi. Genetic diversity of the endangered coastal violet Viola grayi Franchet et Savatier (Violaceae) and its genetic relationship to the species in subsection Rostratae. Conservation Genetics 2012, 13, 837 -848.

AMA Style

Masashi Hirai, Nakao Kubo, Takanori Ohsako, Tomoko Utsumi. Genetic diversity of the endangered coastal violet Viola grayi Franchet et Savatier (Violaceae) and its genetic relationship to the species in subsection Rostratae. Conservation Genetics. 2012; 13 (3):837-848.

Chicago/Turabian Style

Masashi Hirai; Nakao Kubo; Takanori Ohsako; Tomoko Utsumi. 2012. "Genetic diversity of the endangered coastal violet Viola grayi Franchet et Savatier (Violaceae) and its genetic relationship to the species in subsection Rostratae." Conservation Genetics 13, no. 3: 837-848.

Journal article
Published: 01 January 2012 in Breeding Science
Reads 0
Downloads 0

Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar ‘California Wonder’ and a Malaysian small-fruited cultivar ‘LS2341 (JP187992)’, which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.

ACS Style

Yutaka Mimura; Takahiro Inoue; Yasuhiro Minamiyama; Nakao Kubo. An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. Breeding Science 2012, 62, 93 -98.

AMA Style

Yutaka Mimura, Takahiro Inoue, Yasuhiro Minamiyama, Nakao Kubo. An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. Breeding Science. 2012; 62 (1):93-98.

Chicago/Turabian Style

Yutaka Mimura; Takahiro Inoue; Yasuhiro Minamiyama; Nakao Kubo. 2012. "An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps." Breeding Science 62, no. 1: 93-98.

Journal article
Published: 01 January 2011 in Breeding Science
Reads 0
Downloads 0

Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed clear polymorphisms between two radish lines; a rat-tail radish and a Japanese cultivar, ‘Harufuku’. As a test case for evaluation of the present SSRs, we conducted two studies. First, we selected 16 SSRs to calculate polymorphism information contents (PICs) using 16 radish cultivars and four other Brassicaceae species. These markers detected 3–15 alleles (average = 9.6). PIC values ranged from 0.54 to 0.92 (average = 0.78). Second, part of the present SSRs were tested for mapping using our previously-examined mapping population. The map spanned 672.7 cM with nine linkage groups (LGs). The 21 radish SSR markers were distributed throughout the LGs. The SSR markers developed here would be informative and useful for genetic analysis in radish and its related species.

ACS Style

Ryoichi Nakatsuji; Tomoko Hashida; Naoko Matsumoto; Masato Tsuro; Nakao Kubo; Masashi Hirai. Development of genomic and EST-SSR markers in radish (Raphanus sativus L.). Breeding Science 2011, 61, 413 -419.

AMA Style

Ryoichi Nakatsuji, Tomoko Hashida, Naoko Matsumoto, Masato Tsuro, Nakao Kubo, Masashi Hirai. Development of genomic and EST-SSR markers in radish (Raphanus sativus L.). Breeding Science. 2011; 61 (4):413-419.

Chicago/Turabian Style

Ryoichi Nakatsuji; Tomoko Hashida; Naoko Matsumoto; Masato Tsuro; Nakao Kubo; Masashi Hirai. 2011. "Development of genomic and EST-SSR markers in radish (Raphanus sativus L.)." Breeding Science 61, no. 4: 413-419.