• Title/Summary/Keyword: temperate japonica

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Disentangling Evolutionary Pattern and Haplotype Distribution of Starch Synthase III-1 (SSIIIb) in Korean Rice Collection

  • Bhagwat Nawade ;Yong-Jin Park
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.214-214
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    • 2022
  • Soluble starch synthases (SSs) elongate α-glucans from ADP-Glc to the glucan nonreducing ends and play a critical role in synthesizing resistant starch in the rice. A total of 10 SSs isoforms were reported in rice, including granules-bound starch synthase I (GBSSI), GBSSII, starch synthase I (SSI), SSIIa (SSII-3), SSIIb (SSII-2), SSIIc (SSII-1), SSIIIa (SSIII-2), SSIIIb (SSIII-1), SSIVa (SSIV-1), and SSIVb (SSIV-2). SSIII proteins are involved in forming the B chain and elongating cluster filling chains in amylopectin metabolism. The functions of SSIIIb (SSIII-1) are less clear as compared to SSs. Here, we sought to shed light on the genetic diversity profiling of the SSIII-1 gene in 374 rice accessions composed of 54 wild-type accessions and 320 bred cultivars (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture). In total, 17 haplotypes were identified in the SSIII-1 coding region of 320 bred cultivars, while 44 haplotypes were detected from 54 wild-type accessions. The genetic diversity indices revealed the most negative Tajima's D value in the temperate-japonica, followed by the wild type, while Tajima's D values in other ecotypes were positive, indicating balancing selection. Nucleotide diversity in the SSIII-1 region was highest in the wild group (0.0047) while lowest in temperate-japonica. Lower nucleotide diversity in the temperate-japonica is evidenced by the negative Tajima's D and suggested purifying selection. The fixation index (FST) revealed a very high level of gene flow (low FST) between the tropical-japonica and admixture groups (FST=-0.21) followed by admixture and wild groups (-0.04), indica and admixture groups (0.02), while low gene flow with higher FST estimates between the temperate-japonica and aus groups (0.72), tropical-japonica and aromatic groups (0.71), and temperate-japonica and admixture groups (0.52). Taken together, our study offers insights into haplotype diversity and evolutionary fingerprints of SSIII-1. It provides genomic information to increase the resistant starch content of cooked rice.

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Yield Potential of Improved Tropical Japonica Rice under Temperate Environment in Korea

  • Lee, Kyu-Seong;Ko, Jae-Kwon;Kim, Jong-Seok;Lee, Jae-Kil;Shin, Hyun-Tak;Cho, Soo-Yeon
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.44 no.3
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    • pp.214-220
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    • 1999
  • Rice production in Korea has markedly increased during the last two decades due to newly developed high yielding varieties and improved production technology. This experiment was conducted to determine the potential of tropical japonica germplasm in enhancing the yield of temperate japonica. The yield performance of two tropical japonicas (IR 65597-29-3-2 and IR66154-52-1-2) and one temperate japonica (Dongjinbyeo) was compared at different plant densities and nitrogen levels under Korean environmental conditions. Although tropical japonicas showed low tillering habit and large panicles, they had similar leaf area index and dry weight at heading stage to Dongjinbyeo of the high tillering type indicating that there was not much difference between tropical and temperate japonica in terms of biomass production. The highest milled rice yield of 6.15 t/ha was obtained from Dongjinbyeo at a high nitrogen level with less planting density (220 kg N/ha and 30 $\times$ 15 cm). However, those of the two tropical japonicas were 5.36 t/ha at the condition of 165 kg N/ha and 30 x 10 cm planting density and 5.06 t/ha at the condition of 165kgN/ha and 15 x 15 cm planting density, respectively. Ripened grain of tropical japonicas ranged from 65 to 87%, while that Dongjinbyeo ranged from 82 to 97% under Korean conditions.

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Study of Vegetation Structure about Shrine Forest in Jirisan National Park with Regard to Global Warming (지구온난화를 고려한 지리산 국립공원 내 사찰림의 식생구조 연구)

  • Lee, Sung-Je;Ahn, Young-Hee
    • Journal of Environmental Science International
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    • v.23 no.11
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    • pp.1863-1879
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    • 2014
  • This study aims at classifying and interpreting on the shrine forest vegetation located in Jirisan national park affiliated to an ecotone in southern part of Korea, foreseeing a vegetation change based on composition species and dominant species on canopy, and proposing the direction of vegetation management. The shrine forests were classified into the 7 community units as Chamaecyparis obtusa-Cryptomeria japonica afforestation, Pinus densiflora community, Pinus rigida afforestation, Quercus variabilis-Quercus serrata community, Zelkova serrata-Kerria japonica for. japonica community, Phyllostachys bambusoides forest, Camellia japonica community. This research is also expatiated on the analogous results of ordination analysis with phytosociological analysis. The constituents of deciduous broad-leaved forest in the warm temperate zone were appeared in the most vegetations. It emerged less that the constituents of evergreen broad-leaved forest in the warm-temperate zone and deciduous broad-leaved forest in the cold-temperature zone. The life form analyses were made use with the two ways: appearance species in total communities and each community. The species diversity of shrine forests is declined because the high dominances of Sasa borealis and Pseudosasa japonica emerged in the shrub and herb layers. These shrine forests will be succession to Q. variabilis-Q. serrata community as the representative vegetation of deciduous broad-leaved forest in the warm-temperate zone, owing to the temperature rise by global warming, and an evergreen broad-leaved forest will be able to be also formed if a temperate rise will be continued. The one of the artificial management of shrine forests is to consider the introduction of the constituents of evergreen broad-leaved forest in the warm-temperate zone.

Genetic Analysis of Traits Associated with Panicle and Flag Leaf in Tropical Japonica Rice

  • Chang, Jae-Ki;Oh, Byeong-Geun;Kim, Ho-Yeong;Lim, Sang-Jong;Kim, Soon-Chul;Sohn, Jae-Keun
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.43 no.3
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    • pp.135-140
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    • 1998
  • Diallel analysis was conducted with FI's derived from crossing in all combinations without reciprocals among six rice varieties; three tropical japonica and three temperate japonica varieties, with different traits associated with panicle and flag leaf. Epistasis was observed in the number of primary branches (PB) per panicle and of spikelets per panicle, while flag leaf length, flag leaf color, PB length and neck node thickness were explained with the additive-dominance model. The estimated genetic mode of flag leaf length and PB length was a positive complete dominance model with high heritability, and that of flag leaf color and neck node thickness was an incomplete dominance model. In particular, tropical japonica varieties with low-tillering and heavy-panicle appear to have higher number of dominant genes for flag leaf length and PB length than temperate japonica varieties.

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The Vegetation and Ecological Characteristics of Warm Temperate Forest in Dalma Mountain, Haenam (해남 달마산 상록활엽수림 식생과 생태적 특성)

  • Cho, Ji-Woong;Lee, Kye-Han
    • Journal of Environmental Science International
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    • v.31 no.2
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    • pp.181-193
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    • 2022
  • The study was conducted to provide basic data for stable forest management according to climate change by identifying the ecological characteristics of Mt. Dalma warm temperate forest. 30 survey plots were established for vegetation structure analysis, and communities which classified by applying TWINSPAN analysis and DCA analysis techniques. Four plant communities were subdivided into Quercus acuta-Eurya japonica community, Quercus acuta community, Quercus salicina-Camellia japonica community, and Quercus acuta-Camellia japonica community. The tree layers were dominated by Quercus acuta and Quercus salicina, and the subtree layers were dominated by Camellia japonica and Eurya japonica, and the Sasa borealis. The species diversity index were in the range of 0.849 to 0.969, and the degree of Evenness index were 0.514 to 0.569, and the similarity index were 59.57 to 75.47%. The species composition in the community indicated that the deciduous broad-leaved and coniferous trees have already been eliminated in competition with evergreen broad-leaved trees. Tree species with good cold resistance such as Quercus acuta and Quercus salicina were dominant species under current climatic conditions, but the dominant species might be changed to more shade-tolerance evergreen broad-leaved through the succession.

Allometric equations, stem density and biomass expansion factors for Cryptomeria japonica in Mount Halla, Jeju Island, Korea

  • Jung, Sung Cheol;Lumbres, Roscinto Ian C.;Won, Hyun Kyu;Seo, Yeon Ok
    • Journal of Ecology and Environment
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    • v.37 no.4
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    • pp.177-184
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    • 2014
  • This study was conducted to develop allometric equations and to determine the stem density and biomass expansion factor (BEF) for the estimation of the aboveground and belowground biomass of Cryptomeria japonica in Jeju Island, Korea. A total of 18 trees were harvested from the 40-year-old C. japonica stands in Hannam experimental forest, Jeju Island. The mean biomass of the C. japonica was $50.4Mg\;ha^{-1}$ in stem wood, $23.1Mg\;ha^{-1}$ in root, $9.6Mg\;ha^{-1}$ in branch, $4.6Mg\;ha^{-1}$ in needle and $4.3Mg\;ha^{-1}$ in stem bark. The diameter at breast height (DBH) was selected as independent variable for the development of allometric equations. To evaluate the performance of these equations, coefficient of determination ($R^2$) and root mean square error (RMSE) were used and results of the evaluation showed that $R^2$ ranged from 71% (root biomass equation) to 96% (aboveground biomass equation) and the RMSE ranged from 0.10 (aboveground biomass equation) to 0.33 (root biomass equation). The mean stem density of C. japonica was $0.37g\;cm^{-3}$ and the mean aboveground BEF was $1.28g\;g^{-1}$. Furthermore, the ratio of the root biomass to aboveground biomass was 0.32.

Genetic Diversity and Population Structure Analyses of SSIV-2 Gene in Rice

  • Thant Zin Maung;Yong-Jin Park
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.212-212
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    • 2022
  • Soluble starch synthase (SS) IV-2 is one of the starch synthase gene family members and responsible for starch chain elongation interacting with other rice eating and cooking quality controlling genes (e.g., AGPlar and PUL). SSIV-2 is mainly expressed in leaves, especially at grain-filling stage and its alleles can significantly affect rice quality. Here, we investigated the genetic diversity and population structure analyses of SSIV-2 gene by using 374 rice accessions. This rice set was grouped into 320 cultivated bred (subsequently classified into temperate japonica, indica, tropical japonica, aus, aromatic and admixture) and 54 wild rice. Haplotyping of cultivated rice accessions provided a total of 7 haplotypes, and only three haplotypes are functional indicating four substituted SNPs in two exons of chromosome 5: T/A and G/T in exon 4, and C/G and G/A in exon 13. Including the wild, a highest diverse group (0.0041), nucleotide diversity analysis showed temperate japonica (0.0001) had a lowest diversity value indicating the origin information of this gene evolution. Higher and positive Tajima5s D value of indica (1.9755) indicate a selective signature under balancing selection while temperate japonica (-0.9018) was in lowest Tajima's D value due to a recent selective sweep by positive selection. We found the most diverse genetic components of the wild in PCA but shared in some portion with other cultivated groups. Fixation index (FST-values) and phylogenetic analysis indicate a closer relationship of the wild with indica (FST=0.256) than to its association to both of temperate japonica (FST=0.589). Structure analysis shows a clear separation of cultivated subpopulations at every K value, but genetic components were admixed within the wild illustrating the same genetic background with japonica and indica in some proportion.

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Genetic Diversity and Characterization of DPE1 Gene in Rice Germplasm

  • Aueangporn Somsri;Yong-Jin Park
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.220-220
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    • 2022
  • Disproportionating Enzyme 1 (DPE1) is an a-1,4-D-glucanotransferase that cleavages the a-1,4-glucosidic bonds and transfers glucosyl groups. In rice endosperm, it participates in starch synthesis by transferring maltooligosyl groups from amylose and amylopectin to amylopectin. Here, we investigated the haplotype variations and evolutionary indices (e.g., genetic diversity and population structure) for the DPE1 gene in 374 rice accessions representing seven subgroups (wild, indica, temperate japonica, tropical japonica, aus, aromatic, and admixture). Variant calling analysis of DPE1 coding regions leads to the identification of six functional haplotypes representing/occupying 8 nonsynonymous SNPs. Nucleotide diversity analysis revealed the highest pi-value in wild group (0.0556) compared to other cultivated groups, of which temperate japonica showed the most reduction of genetic diversity value (0.003). A significant positive Tajima's D value (1.6330) of admixture highlights sudden population contraction under balancing selection, while temperate japonica with the lowest Tajima's D value (-1.3523) showed a selection signature of DPE1 domestication which might be the cause of excess of rare alleles. Moreover, these two subpopulations exhibits a greater differentiation (FST=0.0148), indicating a higher genetic diversity. Our findings on functional DPE1 haplotypes will be useful in future breeding programs, and the evolutionary indices can also be applicable in functional studies of the DPE1 gene.

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Functional Haplotypes and Evolutionary Analyses of SBE1 in Collected Rice Germplasm

  • Thant Zin Maung;Yong-Jin Park
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.216-216
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    • 2022
  • The starch-branching enzymes (BEs) are responsible for synthesizing the amylopectin, which plays an important role in determining the structural and physical properties of starch granules. BE has two differently functioning isoforms (BEI and BEIIa/b) based on their difference in the chain-length pattern by the degree of polymerization (DP), which mainly contributes to the amylopectin chain length distribution in starch biosynthesis. In this study, we investigated functional haplotypes and evolutionary analyses of SBE1 in 374 rice accessions (320 Korean bred and 54 wild). The analyses were performed based on the classified subpopulations. Haplotype analysis generates a total of 8 haplotypes, of which only four haplotypes were functional carrying four functional SNPs in four different exons of SBE1 on chromosome 6. Nucleotide diversity analysis showed a highest pi-value in aromatic group (0.0029), while the lowest diversity value was in temperate japonica (0.0002), indicating the signal of this gene evolution origin. Different directional selections could be estimated by negative Tajima's D value of temperate japonica (-1.1285) and positive Tajima's D value of tropical japonica (0.9456), where the selective sweeps were undergone by both positive purifying and balancing selections. Phylogenetic analysis indicates a closer relationship of the wild with most of the cultivated subgroups indicating a common ancestor for SBE1 gene. FST-values indicate distant genetic relationships of temperate japonica from all other classified groups. PCA and population structure analysis show an admixed structure of wild and cultivated subpopulations in some proportions.

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Effects of Artificial Shading on Flowering and Growth of Maesa japonica Seedlings (차광 처리가 빌레나무(Maesa japonica)의 개화 및 생장에 미치는 영향)

  • Park, Min Ji;Seo, Yeon Ok;Choi, Hyung Soon;Choi, Byoung Ki;Im, Eun Young;Yang, Ju Eun;Lee, Chae bin
    • Korean Journal of Plant Resources
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    • v.34 no.5
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    • pp.462-469
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    • 2021
  • Maesa japonica (Thunb.) Moritzi & Zoll. is a rare evergreen shrub that occurs in west Gotjawal, Jeju island, Korea. This study was conducted to investigate effects of an artificial shading on flowering and growth characteristics of M. japonica seedlings. The level of shading had been set to be 35%, 55% and 75% using shading net. The stage of flowering and flowering ratio, seedling height, the number of leaves and stems, leaf area were measured. Flowering timings were delayed by shading. The number of flowering seedlings per plot and inflorescences per seedling were the most in 55% shading level. Tendency of decreased seedling height with increased shading level was shown. The number of leaves and stems were the fewest values in 75% shading level. The increased biomass with decreased shading level was statistically significant. Aboveground and underground biomass were 2.1 and 1.7 times higher in shading 35% than in shading 75%, respectively. Meanwhile, all seedlings in non-shading plots were dead in winter. Such might be speculated as results of the light stress. As a result, we conclude that M. japonica vitally demands the shading for growth and the optimal shading levels for growth and flowering are 35% and 55%, respectively.