• Title/Summary/Keyword: Seed generation

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Genomic Analysis of the Carrot Bacterial Blight Pathogen Xanthomonas hortorum pv. carotae in Korea

  • Mi-Hyun Lee;Sung-Jun Hong;Dong Suk Park;Hyeonheui Ham;Hyun Gi Kong
    • The Plant Pathology Journal
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    • v.39 no.4
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    • pp.409-416
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    • 2023
  • Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.

Studies on the Construction of Mutant Diversity Pool (MDP) lines, and their Genomic Characterization in Soybean

  • Dong-Gun Kim;Sang Hoon Kim;Chang-Hyu Bae;Soon-Jae Kwon
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2021.04a
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    • pp.9-9
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    • 2021
  • Mutation breeding is useful for improving agronomic characteristics of various crops. In this study, we constructed soybean Mutant Diversity Pool (MDP) from 1,695 gamma-irradiated mutants through two selection phases over M1 to M12 generations; we selected 523 mutant lines exhibiting at least 30% superior agricultural characteristics, and, second, we eliminated redundant morphological phenotypes in the M12 generation. Finally, we constructed 208 MDP lines and investigated 11 agronomic traits. We then assessed the genetic diversity and inter-relationships of these MDP lines using target region amplification polymorphism (TRAP) markers. Among the different TRAP primer combinations, polymorphism levels and PIC values averaged 59.71% and 0.15, respectively. Dendrogram and population structure analyses divided the MDP lines into four major groups. According to an analysis of AMOVA, the percentage of inter-population variation among mutants was 11.320 (20.6%), whereas mutant inter-population variation ranged from 0.231 (0.4%) to 14.324 (26.1%). Overall, the genetic similarity of each cultivar and its mutants were higher than within other mutant populations. In an analysis of the genome-wide association study (GWAS) using based on the genotyping-by-sequencing (GBS), we detected 66 SNPs located on 13 different chromosomes were found to be highly associated with four agronomic traits: days of flowering (33 SNPs), flower color (16 SNPs), node number (6 SNPs), and seed coat color (11 SNPs). These results are consistent with those previously reported for other genetic resource populations, including natural accessions and recombinant inbred line. Our observations suggest that genomic changes in mutant individuals induced by gamma rays occurred at the same loci as those of natural soybean population. This study has demonstrated that the integration of GBS and GWAS can serve as a powerful complementary approach to gamma-ray mutation for the dissection of complex traits in soybean.

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Phenotypic characterization of pre-harvest sprouting resistance mutants generated by the CRISPR/Cas9-geminiviral replicon system in rice

  • Jong Hee Kim;Jihyeon Yu;Jin Young Kim;Yong Jin Park;Sangsu Bae;Kwon Kyoo Kang;Yu Jin Jung
    • BMB Reports
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    • v.57 no.2
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    • pp.79-85
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    • 2024
  • Pre-harvest sprouting is a critical phenomenon involving germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. In this paper, we generated HDR mutant lines with one region SNP (C/T) and an insertion of 6 bp (GGT/GGTGGCGGC) in OsERF1 genes for pre-harvest sprouting (PHS) resistance using CRISPR/Cas9 and a geminiviral replicon system. The incidence of HDR was 2.6% in transformed calli. T1 seeds were harvested from 12 HDR-induced calli and named ERF1-hdr line. Molecular stability, key agronomic properties, physiological properties, and biochemical properties of target genes in the ERF1-hdr line were investigated for three years. The ERF1-hdr line showed significantly enhanced seed dormancy and pre-harvest sprouting resistance. qRT-PCR analysis suggested that enhanced ABA signaling resulted in a stronger phenotype of PHS resistance. These results indicate that efficient HDR can be achieved through SNP/InDel replacement using a single and modular configuration applicable to different rice targets and other crops. This work demonstrates the potential to replace all genes with elite alleles within one generation and greatly expands our ability to improve agriculturally important traits.

Inheritance Study of Male Sterile Transformants Containing Pollen-specific Promoter and Diphtheria Toxin A Gene (수술특이프로모터와 디프테리아 독성 유전자에 의한 웅성불임 형질전환체의 후대 유전분석)

  • Park, Young-Doo;Kim, Hyun-Uk;Park, Beom-Seok;Jin, Yong-Moon
    • Horticultural Science & Technology
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    • v.18 no.3
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    • pp.342-347
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    • 2000
  • The objectives of this study were to investigate the genetic and phenotypic features of male sterile transformants by pollen-specific expression of diphtheria toxin gene and to find out inheritance patterns of transgene to the next generation. When backcrossed (BC) progenies were tested for expression of kanamycin resistance ($Km^R$), 9 lines out of 13 lines, except 4 lines ($BC_{1}5-13,\;BC_{1}5-23,\;BC_{1}5-28,\;BC_{1}5-32$), showed the ratio of $Km^R$ to kanamycin sensitive ($Km^S$), from 1:30 to all $Km^S$. As a result, they were much lower than Mendelian segregation of a dominant gene. To determine whether male sterility is a heritable and stable trait, 5 male sterile plants ($BC_{1}5-13,\;BC_{1}5-14,\;BC_{1}5-23,\;BC_{1}5-32,\;BC_{1}5-33$ lines) which had different transgene copy numbers were backcrossed as female parents with pollens from wild type. To confirm the existence of the DTx-A gene in the genome of the progenies, PCR was conducted using specific primers of the DTx-A coding region. A PCR band of 428 bp was obtained from each generation, which is the predicted size of the DTx-A gene fragment. Trangenes were inherited to the next $BC_4T_0$ progenies and showed male sterility, however, based on the copy numbers of DTx-A gene male sterile plants did not show predicted ratio. When male sterile plants were backcrossed with fertile plants, fruit capsule sizes and seed settings were relatively reduced from those of selfing wild type plants. The fruit sizes and seed settings were reduced in proportion to the increase in the copy number of DTx-A gene.

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Iron fortification of grains by introducing a recombinant gene of ferritin with seed promoters in rice (종자 특이 프로모터와 대두 Ferritin 유전자에 의한 벼 종실의 철분강화)

  • Cho, Yong-Gu;Kim, Hyung-Keun;Choi, Jang-Sun;Jung, Yu-Jin;Kang, Kwon-Kyoo
    • Journal of Plant Biotechnology
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    • v.36 no.1
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    • pp.87-95
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    • 2009
  • The recombinant DNAs, pGBF, pGTF, and pZ4F, using soybean ferritin gene have constructed with the promoters derived from seed proteins, glutelin, globulin, and zein. The recombinant ferritin genes were transformed into rice plant by Agrobacterium-mediated transformation. Iron contents and agronomic traits have been evaluated in the transgenic progenies. The embryogenic calli survived from second selection medium were regenerated at the rates of 19.2% with pGBF, 15.0% with pGTF, and 18.4% with pZ4F in Donganbyeo and 6.7% with pGBF, 11.7% with pGTF, and 3.4% with pZ4F in Hwashinbyeo. The introduction of ferritin gene in putative transgenic rice plants was confirmed by PCR and Southern blot analysis and also the expression of ferritin gene was identified by Northern blot and Western blot analysis. The iron accumulation in transgenic rice grains of the transgenic rice plant, T1-2, with zein promoter and ferritin gene contained 171.4 ppm showing 6.4 times higher than 26.7 ppm of Hwashinbyeo seed as wild type rice, but the transgenic plants with globulin and glutelin showed a bit higher iron contents with a range from 2.1 to 3.0 times compare to wild type grain. The growth responses of transgenic plants showed the large variances in plant height and number of tillers. However, there were some transgenic plants having similar phenotype to wild type plants. In the T1 generation of transgenic plants, plant height, culm length, panicle length, and number of tillers were similar to those of wild type plants, but ripened grain ratio ranged from 53.3% to 82.2% with relatively high variation. The transgenic rice plants would be useful for developing rice varieties with high iron content in rice grains.

Inhibition of Adipocyte Differentiation by Methanol Extracts of Oenanthe javanica Seed in 3T3-L1 Preadipocytes (돌미나리씨 추출물에 의한 3T3-L1 지방전구세포의 분화 억제)

  • Ji, Hyang Hwa;Jeong, Hyun Young;Jin, Soojung;Kwon, Hyun Ju;Kim, Byung Woo
    • Journal of Life Science
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    • v.22 no.12
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    • pp.1688-1696
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    • 2012
  • Oenanthe javanica has been used as a food source and also in traditional folk medicine for its detoxifying properties and anti-microbial effects since ancient times. In this study, we evaluated the effect and mechanism of O. javanica seed methanol extract (OJSE) on adipocyte differentiation by 3T3-L1 preadipocytes. Under non-toxic conditions, OJSE treatment resulted in a dose-dependent inhibition of lipid droplet generation and triglyceride accumulation by suppressing adipocyte differentiation, which are associated with the decreased expression of key proadipogenic transcription factors including CCAAR/enhancer binding protein ${\alpha}$, ${\beta}$ ($C/EBP{\alpha}$, $C/EBP{\beta}$) and peroxisome proliferator-activated receptor ${\gamma}$ ($PPAR{\gamma}$). OJSE also significantly inhibited proliferation and differentiation of 3T3-L1 preadipocytes through G1-phase arrest, indicating that OJSE blocked mitotic clonal expansion during adipocyte differentiation. Investigation of the alteration of G1 phase arrest-related proteins indicated a dose-dependent increase in the expression of p21 and reduction in expression of cyclin E, Cdk2, E2F-1 and phospho-Rb by OSJE. Taken together, these results suggest that OJSE inhibits adipocyte differentiation by blocking the mitotic clonal expansion, which is accompanied by preadipocyte cell cycle arrest.

Subject-Balanced Intelligent Text Summarization Scheme (주제 균형 지능형 텍스트 요약 기법)

  • Yun, Yeoil;Ko, Eunjung;Kim, Namgyu
    • Journal of Intelligence and Information Systems
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    • v.25 no.2
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    • pp.141-166
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    • 2019
  • Recently, channels like social media and SNS create enormous amount of data. In all kinds of data, portions of unstructured data which represented as text data has increased geometrically. But there are some difficulties to check all text data, so it is important to access those data rapidly and grasp key points of text. Due to needs of efficient understanding, many studies about text summarization for handling and using tremendous amounts of text data have been proposed. Especially, a lot of summarization methods using machine learning and artificial intelligence algorithms have been proposed lately to generate summary objectively and effectively which called "automatic summarization". However almost text summarization methods proposed up to date construct summary focused on frequency of contents in original documents. Those summaries have a limitation for contain small-weight subjects that mentioned less in original text. If summaries include contents with only major subject, bias occurs and it causes loss of information so that it is hard to ascertain every subject documents have. To avoid those bias, it is possible to summarize in point of balance between topics document have so all subject in document can be ascertained, but still unbalance of distribution between those subjects remains. To retain balance of subjects in summary, it is necessary to consider proportion of every subject documents originally have and also allocate the portion of subjects equally so that even sentences of minor subjects can be included in summary sufficiently. In this study, we propose "subject-balanced" text summarization method that procure balance between all subjects and minimize omission of low-frequency subjects. For subject-balanced summary, we use two concept of summary evaluation metrics "completeness" and "succinctness". Completeness is the feature that summary should include contents of original documents fully and succinctness means summary has minimum duplication with contents in itself. Proposed method has 3-phases for summarization. First phase is constructing subject term dictionaries. Topic modeling is used for calculating topic-term weight which indicates degrees that each terms are related to each topic. From derived weight, it is possible to figure out highly related terms for every topic and subjects of documents can be found from various topic composed similar meaning terms. And then, few terms are selected which represent subject well. In this method, it is called "seed terms". However, those terms are too small to explain each subject enough, so sufficient similar terms with seed terms are needed for well-constructed subject dictionary. Word2Vec is used for word expansion, finds similar terms with seed terms. Word vectors are created after Word2Vec modeling, and from those vectors, similarity between all terms can be derived by using cosine-similarity. Higher cosine similarity between two terms calculated, higher relationship between two terms defined. So terms that have high similarity values with seed terms for each subjects are selected and filtering those expanded terms subject dictionary is finally constructed. Next phase is allocating subjects to every sentences which original documents have. To grasp contents of all sentences first, frequency analysis is conducted with specific terms that subject dictionaries compose. TF-IDF weight of each subjects are calculated after frequency analysis, and it is possible to figure out how much sentences are explaining about each subjects. However, TF-IDF weight has limitation that the weight can be increased infinitely, so by normalizing TF-IDF weights for every subject sentences have, all values are changed to 0 to 1 values. Then allocating subject for every sentences with maximum TF-IDF weight between all subjects, sentence group are constructed for each subjects finally. Last phase is summary generation parts. Sen2Vec is used to figure out similarity between subject-sentences, and similarity matrix can be formed. By repetitive sentences selecting, it is possible to generate summary that include contents of original documents fully and minimize duplication in summary itself. For evaluation of proposed method, 50,000 reviews of TripAdvisor are used for constructing subject dictionaries and 23,087 reviews are used for generating summary. Also comparison between proposed method summary and frequency-based summary is performed and as a result, it is verified that summary from proposed method can retain balance of all subject more which documents originally have.

The Trend and Achievements of Forest Genetics Research in Abroad (선진국(先進國)에 있어서의 임목육종연구(林木育種硏究)의 동향(動向))

  • Hyun, Sin Kyu
    • Journal of Korean Society of Forest Science
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    • v.14 no.1
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    • pp.1-20
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    • 1972
  • The trend and achievements of forest genetics research in abroad were investigated through observation tours and reference work and following facts were found to be important aspects which should be adopted in the forest genetics research program in Korea. Because of world wide recognization on the urgency of taking a measure to reserve some areas of the representative forest type on the globe before the extingtion of such forest type as the results of continuous exploitations of the natural forests to meet the timber demand all over the world, it is urgently needed to take a measure to reserve certain areas of natural stand of Pinus koraiensis, Pinus parviflora, Pinus densiflora f. erectra, Abies koreana, Quercus sp., Populus sp., etc. as gene pool to be used for the future program of forest tree improvement. And the genetic studies of those natural forest of economic tree species are also to be performed. 1. Increase of the number of selected tree for breeding purpose. Because of the fact that the number of plus tree at present is too small to carry out selection program for tree improvement, particularly for the formation of source population for recurrent selection of parent trees of the 2nd generation seed orchard it is to be strongly emphasized to increase the number of plus tree by alleviating selection criteria in order to enlarge the population size of plus trees to make the selection program more efficient. 2. Progeny testing More stress should be placed on carrying out progeny testing of selected trees with open pollinated seeds. And particular efforts are to be made for conducting studies on adult/juvenile correlation of important traits with a view to enable to predict adult performances with some traits revealed in juvenile age thus to save time for progeny testing. 3. Genotype-environment interaction Studies on genotype and environment interaction should be conducted in order to elucidate whether the plus trees selected on the good site express their superiority on the poor site or not and how the environment affect the genotype. And the justification of present classification of seed distribution area should be examined. 4. Seed orchard of broad leaf tree species. Due to the difficulty of accurate comparison of growth rate of neighbouring trees of broad leaf tree species in natural stand, it is recommended that for the improvement of broad leaf trees a seedling seed orchard is to be made by roguing the progeny test plantation planted densely with control pollinated seedlings of selected trees. 5. Breeding for insect resistant varieties. In the light of the fact that the resistant characteristics against insect such as pine gall midge (Thiecodiplosis japonensis U. et I.) and pine bark beetle (Myelophilus pinipera L.) are highly correlated with the amount and quality of resin which are known as gene controlled characteristics, breeding for insect resistance should be carried out. 6. Breeding for timber properties. With the tree species for pulp wood in particular, emphasis should be placed upon breeding for high specific gravity of timber. 7. Introduction of Cryptomeria and Japanese Cypress In the light of the fact that the major clones of Cryptomeria are originated from Yoshino source and are being planted up to considerably north and high elevation in Japan, those species should be examined on their cold resistance in Korea by planting them in further northern part of the country.

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Adaptability of the high first pod height, shattering-resistant soybean cultivar 'Saegeum' to mechanized harvesting (고착협 내탈립 기계수확 적응 장류·두부용 콩 품종 '새금')

  • Kim, Hyun Tae;Han, Won Young;Lee, Byung Won;Ko, Jong Min;Lee, Yeong Hoon;Baek, In Youl;Yun, Hong Tai;Ha, Tae Joung;Choi, Man Soo;Kang, Beom Kyu;Kim, Hyun Yeong;Seo, Jeong Hyun;Kim, Hong Sik;Shin, Sang Ouk;Oh, Jae Hyun;Kwak, Do Yeon;Seo, Min Jeong;Song, Yoon Ho;Jang, Eun Kyu;Yun, Geon Sik;Kang, Yeong Sik;Lee, Ji Yun;Shin, Jeong Ho;Choi, Kyu Hwan;Kim, Dong Kwan;Yang, Woo Sam
    • Korean Journal of Breeding Science
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    • v.51 no.4
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    • pp.496-503
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    • 2019
  • The soybean cultivar, 'Saegeum', has been developed for preparing soy-paste and tofu. The soybean cultivars 'Daepung' and 'SS98207-3SSD-168' were crossed in 2003 to obtain 'Saegeum'. Single seed descent method was used to advance the generation from F3 to F5, and the plant lines with promising traits were selected from F6 to F7 by pedigree method. The preliminary yield (PYT) and advanced yield trials (AYT) were conducted from 2009 to 2010, and the regional yield trial (RYT) was conducted in 12 regions between 2011 and 2013. The morphological characteristics of 'Saegeum' were as follows: determinate plant type, white flower, tawny pubescence color, and brown pod color. Flowering and maturity dates were August 2, XXXX and October 17, XXXX, respectively. Plant height, first pod height, number of nodes, number of branches, and number of pods were 79 cm, 18 cm, 16, 2.3, and 44, respectively. The seed characteristics of 'Saegeum' were as follows: yellow spherical shape, yellow hilum, and the 100-seed weight was 25.4 g. 'Saegeum' was resistant to bacterial pustule and SMV in the field test, and its lodging resistance was mildly strong, whereas its shattering resistance was excellent. The ability of this cultivar to be processed into tofu, soybean malt, and other fermented products was comparable with that of 'Daewonkong'. The yield of 'Saegeum' in the adaptable regions was 3.02 ton ha-1. Thus, 'Saegeum' is adaptable to mechanized harvesting because of its high first pod height, as well as lodging and shattering resistance. (Registration number: 5929)

Comparison of Germination Characteristics and Daily Seed Germinating Pattern in New Cultivars of The Third Generation of Creeping Bentgrass Grown under Alternative and Natural Room Temperature Conditions (자연실온 및 변온조건에서 제3세대 크리핑 벤트그래스 신품종의 발아특성 및 일일 발아패턴 비교)

  • Kim, Kyoung-Nam;Kwon, O-Dal;Shim, Sang-Ryul;Yoon, Jung-Seo;Park, So-Hyang
    • Asian Journal of Turfgrass Science
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    • v.25 no.1
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    • pp.1-10
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    • 2011
  • This study was conducted to investigate early germination characteristics and germination pattern of new cultivars of creeping bentgrass (CB, Agrostis pall/stris Huds.) under natural room temperature conditions and to analyze differences between alternative and natural conditions. Seven cultivars of CB were tested in the study. Daily and cumulative germination patterns were measured and analyzed on a daily basis. Significant differences were observed in germination pattern, days to the first germination, days to 50% germination, days to 85% germination, and germination rate among cultivars under different environments. The first germination in all entries was initiated between 4 and 5 days after seeding (DAS) under alternative conditions, while between 6 and 8 DAS under natural conditions, being 2 to 3 days later as compared with that of alternative conditions. As for the first germination percentage, it was generally 5 to 25% under alternative conditions. However, 'Penn A-1', 'Penncross', and 'Penn A-4' cultivars showed a vigorous germination, producing 50 to 70%. Under natural room temperature conditions, it was 5 to 10% for the most entries, except 'Penncross', 'L-93', and 'Penn A-4' cultivars which vigorously produced 20 to 50%. Days to the 50% germination in CB resulted in 4 to 10 DAS under alternative conditions, while 6 to 15 DAS under natural conditions, being 2 to 5 days later than under alternative conditions. Days to the 85% germination were 5.90 to 11.75 DAS under alternative conditions and 7.95 to 12.50 DAS under natural conditions. 'Penn A-1' and 'L-93' were the fastest cultivars under alternative and natural conditions, respectively. Regardless of the temperature conditions, the longest cultivar in germination was 'T-1', being over 11 DAS. In-depth comparative data on germination characteristics and germination patterns among CB cultivars would be usefully applied for a practical CB turf establishment in golf course construction etc.