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Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections

  • Tingyan Dong;Yongsi Wang;Chunxia Qi;Wentao Fan;Junting Xie;Haitao Chen;Hao Zhou;Xiaodong Han
    • Journal of Microbiology and Biotechnology
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    • v.34 no.8
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    • pp.1617-1626
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    • 2024
  • Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.

Effect of Exogenous Application of Sodium Nitroprusside on Alleviation of Low Temperature Stress in Kimchi Cabbage (Brassica rapa ssp. pekinensis) (Sodium Nitroprusside 처리가 배추의 저온 스트레스 경감에 미치는 영향)

  • Jinhyoung Lee;Seunghwan Wi;Hyejin Lee;Sanggyu Lee;Minseo Kang;Taeyang Kim;Seonghoe Jang;Heeju Lee
    • Journal of Bio-Environment Control
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    • v.32 no.4
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    • pp.377-383
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    • 2023
  • The effects of exogenous sodium nitroprusside (SNP, nitric oxide donor) on the growth, yield, photosynthetic characteristics, and antioxidant enzyme activity of kimchi cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt) was studied under the low temperature conditions. Kimchi cabbages were treated with SNP of three concentrations (7.5, 15, 30 mg·L-1) for three times at four-day intervals and exposed to low temperature (16/7℃) stress for seven days. SNP treatment induced increases of net photosynthetic rate (Pn), stomatal conductance (Gs), intracellular CO2 concentration (Ci) and transpiration rate (Tr) under the stress condition with the highest level after the third treatment. The contents of malondialdehyde (MDA) and H2O2 were significantly lower in the treatment of SNP compared to the non-treated control. The activity of ascorbate peroxidase (APX), catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD), increased in treated plants by up to 38, 187, 24 and 175%, respectively compared to the non-treated control. SNP-treated and untreated plants had similar growth characteristics. Compared to the control group, SNP-treatment increased fresh weight and leaf area by 5%. Overall, our findings suggest that the application of sodium nitroprusside to the leaves contributes to reducing physiological damage and enhancing the activities of antioxidant enzymes, thereby improving low temperature stress tolerance in kimchi cabbage.

Comparison of Basal Physicochemical Changes of Reused Rockwool Substrate in Hydroponic Tomato Cultivation (수경재배 토마토 재사용 암면 배지의 기초 물리화학성 변화 비교)

  • Jae Seong Lee;Jong Hwa Shin
    • Journal of Bio-Environment Control
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    • v.33 no.2
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    • pp.114-119
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    • 2024
  • Rockwool substrate has superior physicochemical characteristics and is often used in crop cultivation. However, rockwool substrate has the disadvantages of high purchase cost and difficulty in disposal. Reuse of substrate can compensate for these disadvantages. Substrate must be disinfected and rehydrated during reuse, and various physicochemical changes during this process must also be considered. This study was to compare the physical properties of two types of rockwool substrates (reused and unused) and to evaluate the reuse potential of rockwool substrate by analyzing the chemical properties of the reused rockwool substrate during the rehydration process. The experiment on substrate physicochemical properties comparison was conducted from March to August 2023 using used rockwool substrates in tomato cultivation and unused rockwool substrates. Drainage time, drainage volume, and substrate weight were measured using load cells installed at the top and bottom of the irrigation monitoring system. The reused rockwool substrate weight and density were higher than those of the unused rockwool substrate, while the average drainage time after irrigation was 1.5 times longer for the reused rockwool than for the unused rockwool. The salinity concentration in different parts of the reused rockwool substrate was found to be lower in the reused rockwool substrate compared to the unused rockwool substrate. The electrical conductivity of the drainage was at its peak at the beginning of the drainage and decreased exponentially as the drainage volume increased. Change in electrical conductivity of the drainage over the irrigation time showed an exponential decay pattern. Through the experiments, the potential reusability of the rock wool substrate was assessed by conducting a comparative analysis of its physicochemical properties.

Comparing Molecular Weight Dependent Absorption Rates of Collagen in Oral Mucosal and Epidermis/dermis Tissue Models

  • Ji Yoon Hong;Areum Cha;Gi Jung Kim;Yelim Jang;Jung-Yoon Lee;Emmanouil Apostolidis;Tae Yang Kim;Young-In Kwon
    • Journal of Food Hygiene and Safety
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    • v.39 no.4
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    • pp.299-303
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    • 2024
  • Collagen, as an indicator of skin health, has been developed and used for various purposes. The development of an optimized collagen product suitable for use has become an important research field as the consumption of collagen increases. In particular, various efforts are being made to increase its absorption rate. In this study, the transdermal and oral epithelial cell permeabilities of various molecular weight collagen products sold in Korea were compared using a Franz diffusion cell system. The collagen absorption rate of oral mucosal tissue compared to skin epidermis/dermis tissue was significantly higher than that of collagen at M.W. 500 and 1,000 (approximately 10 times and 2 times higher, respectively). Additionally, collagen with a molecular weight of 500 Da increased the absorption rates by 2-3 times compared with products with a molecular weight of 1,000. Collagen with a molecular weight of 500 Da showed the highest Cmax and AUCt values, and all parameters in the oral mucosal cell test group were higher than those in the skin epidermis/dermis cells. Our findings suggest an increased absorption rate through oral mucosal cells rather than skin absorption, confirming that low molecular weight collagen is a major factor increasing the absorption rate.

Preoperative MRI Features Associated With Axillary Nodal Burden and Disease-Free Survival in Patients With Early-Stage Breast Cancer

  • Junjie Zhang;Zhi Yin;Jianxin Zhang;Ruirui Song;Yanfen Cui;Xiaotang Yang
    • Korean Journal of Radiology
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    • v.25 no.9
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    • pp.788-797
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    • 2024
  • Objective: To investigate the potential association among preoperative breast MRI features, axillary nodal burden (ANB), and disease-free survival (DFS) in patients with early-stage breast cancer. Materials and Methods: We retrospectively reviewed 297 patients with early-stage breast cancer (cT1-2N0M0) who underwent preoperative MRI between December 2016 and December 2018. Based on the number of positive axillary lymph nodes (LNs) determined by postoperative pathology, the patients were divided into high nodal burden (HNB; ≥3 positive LNs) and non-HNB (<3 positive LNs) groups. Univariable and multivariable logistic regression analyses were performed to identify independent risk factors associated with ANB. Predictive efficacy was evaluated using the receiver operating characteristic (ROC) curve and area under the curve (AUC). Univariable and multivariable Cox proportional hazards regression analyses were performed to determine preoperative features associated with DFS. Results: We included 47 and 250 patients in the HNB and non-HNB groups, respectively. Multivariable logistic regression analysis revealed that multifocality/multicentricity (adjusted odds ratio [OR] = 3.905, 95% confidence interval [CI]: 1.685-9.051, P = 0.001) and peritumoral edema (adjusted OR = 3.734, 95% CI: 1.644-8.479, P = 0.002) were independent risk factors for HNB. Combined peritumoral edema and ultifocality/multicentricity achieved an AUC of 0.760 (95% CI: 0.707-0.807) for predicting HNB, with a sensitivity and specificity of 83.0% and 63.2%, respectively. During the median follow-up period of 45 months (range, 5-61 months), 26 cases (8.75%) of breast cancer recurrence were observed. Multivariable Cox proportional hazards regression analysis indicated that younger age (adjusted hazard ratio [HR] = 3.166, 95% CI: 1.200-8.352, P = 0.021), larger tumor size (adjusted HR = 4.370, 95% CI: 1.671-11.428, P = 0.002), and multifocality/multicentricity (adjusted HR = 5.059, 95% CI: 2.166-11.818, P < 0.001) were independently associated with DFS. Conclusion: Preoperative breast MRI features may be associated with ANB and DFS in patients with early-stage breast cancer.

Analysis of Microbial Communities of Salted Cabbage and Kimchi according to Cultivation Areas (재배지역에 따른 절임배추 및 김치의 미생물 군집 분석)

  • Chang Eun Kim;Soo Hyun Kim;Min Seo Jung;Seung Lim Lee
    • Microbiology and Biotechnology Letters
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    • v.52 no.3
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    • pp.304-313
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    • 2024
  • In this study, the microbial distribution and diversity of kimchi manufactured in the same method as salted cabbage manufactured from Pyeongchang, Andong, and Haenam cabbage according to the storage period were compared. Among Pyeongchang, Andong, and Haenam salted cabbages, the Haenam salted cabbage microbial community showed the highest diversity on the 1st day of storage. As the storage period of salted cabbage increased, the alpha diversity value increased, the proportion of cyanobacteria decreased, and bacteria derived from sea salt and water increased. Principal coordinates analysis(PCoA) and unweighted pair group method with arithmetic mean(UPGMA) trees showed that Andong salted cabbage on the 5th day of storage had a microbial community close to salted cabbage on the 10th day of storage. At the species level, Sinocapsa zengkensis was 78.65%, 90.64%, and 63.44%, respectively, in Pyeongchang, Andong, and Haenam salted cabbages on the 1st day of storage. Marinomonas primoryensis was showed in Pyeongchang, Andong, and Haenam salted cabbage on the 5th day of storage at 24.39%, 26.60%, and 21.75%, respectively, and at 42.17%, 31.43%, and 45.21%, respectively, on the 10th day of storage. Kimchi made from Pyeongchang, Andong, and Haenam salted cabbages showed Janthinobacterium lividum at 30.47%, 29.60%, and 25.97%, respectively. In addition, Leuconostoc spp. involved in fermentation were showed from the 5th day of storage, but Andong salted cabbage on the 10th day of storage was not showed. These results show to be due to differences in soil, climate, and cultivation methods of cabbage.

MICROSTRUCTURE AND ELECTROCHEMICAL BEHAVIORS OF EQUIATOMIC TiMoVCrZr AND Ti-RICH TiMoVCrZr HIGH-ENTROPY ALLOYS FOR METALLIC BIOMATERIALS

  • HOCHEOL SONG;SEONGI LEE;KWANGMIN LEE
    • Archives of Metallurgy and Materials
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    • v.65 no.4
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    • pp.1317-1322
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    • 2020
  • The present study investigated various thermodynamic parameters, microstructures and electrochemical behaviors of TiMoVCrZr and Ti-rich TiMoVCrZr high-entropy alloys (HEAs) prepared by vacuum arc remelting. The microstructures of the alloys were analyzed using X-ray diffraction (XRD) analysis, field emission scanning electron microscopy (FE-SEM), and potentiodynamic polarization tests. The determined thermodynamic values of the Ω-parameter and the atomic size difference (δ) for the HEAs were determined to be in the range of Ω ≥ 1.1, and δ ≤ 6.6% with valance electron configuration (VEC) ≤ 5.0, suggesting the HEAs were effective at forming solid solutions. XRD patterns of the equiatomic Ti20Mo20V20Cr20Zr20 HEA revealed four phases consisting of the body centered cubic1 (BCC1), BCC2, hexagonal close-packed (HCP), and intermetallic compound Cr2Zr phases. Three phases were observed in the XRD patterns of Ti-rich Ti40Mo15V15Cr15Zr15 (BCC, HCP, and Cr2Zr) and a single BCC phase was observed in Ti-rich Ti60Mo10V10Cr10Zr10 HEAs. The backscattered-electron (BSE) images on the equiatomic Ti20Mo20V20Cr20Zr20 HEA revealed BCC and HCP phases with Cr2Zr precipitates, suggesting precipitation from the HCP solid solution during the cooling. The micro-segregation of Ti-rich Ti60Mo10V10C10Zr10 HEAs appeared to decrease remarkably. The alloying elements in the HEAs were locally present and no phase changes occurred even after additional HIP treatment. The lowest current density obtained in the polarization potential test of Ti-rich Ti40Mo15V15Cr15Zr15 HEA was 7.12×10-4 mA/cm2 was obtained. The studied TiMoVCrZr HEAs showed improved corrosion characteristics as compared to currently available joint replacement material such as ASTM F75 alloy.

Evaluation Study of Performance for Solar Energy Blocking of Smart Windows based on Phase Retardation Film (Phase Retardation 필름 기반 스마트윈도우의 태양열차단 성능 평가 시험 연구)

  • Il-Gu Kim;Ho-Chang Yang;Young-Min Park;Yo-Han Suh;Seung Hyun Lee;Young Kyu Hong
    • Journal of the Microelectronics and Packaging Society
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    • v.31 no.3
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    • pp.67-71
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    • 2024
  • A smart window based on a retarder can transmit or block polarized lights by overlapping two smart windows. In the study, tests were conducted to evaluate the performance of blocking solar heat using smart windows with a size of 300×300 mm2. Solar heat gain coefficient (SHGC) values were derived through simulation using transmission and reflectance data of the smart windows. As a result of the simulation, it showed that SGHC is effective in blocking solar heat by obtaining values of 0.722 and 0.615 in transmission and blocking mode of smart windows, respectively. The test boxes were fabricated in order to verify the effect of suppressing temperature rise when applying smart windows, the inside temperature in test boxes, which are installed bare glass (reference) and two smart windows with transmission and blocking mode, were measured at 10 minutes-interval for 7 days. As of 1 p.m., the inside temperature of the test boxes with the smart windows applied showed lower temperature compared to the reference. In particular, on the day when the temperature of reference box was the highest at 66.1℃, the temperature of the test box with the smart window applied showed 61.0℃, which was lowered by 5.1℃.

The Behaviors of Phosphorus-32 and Ptoassium-42 under the Control of Thermoperiod and Potassium Level (가리(加里)와 온도주기성(溫度週期性)이 고구마 생육(生育) 및 인(燐)-32, 가리(加里)-42 동태(動態)에 미치는 영향(影響))

  • Kim, Y.C.
    • Korean Journal of Soil Science and Fertilizer
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    • v.1 no.1
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    • pp.89-115
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    • 1968
  • 1. The experiment was carried out for investigating the interaction between potassium nutrition and thermoperiod (as an environment regulating factor) in relation to behaviors of several nutrients including phosphorus-32 and Potassium-42 in IPOMOEA BATAS. 2. To obtain same condition to trace the behaviors of phosphorus and potassum-42 they were simultaneously incorporated to roots. The determination of each CPM by counting twice with adequate interval and calculating true CPM of each isotope according to different half-life, was carried out with satisfactory. 3. Some specific symptoms i.e, chlorosis and withering of growing point under the condition of lower potassium level were found and was accelerated by the low night temperature. 4. A manganese shortage in growing point of the lower potassium level was found by activiation analysis and very low distribution ratio of phosphorus-32 and potassium-42 in the growing point of the lower potassium level was manifested, though the contents of nitrogen, phosphorus, potassium, sodium and magnesium were not in great difference. 5. In addition to the low water content with appearence of "hard", shorterning internode and lower ratio of roots to shoot as well as the symptoms of potassium deficiency such as brown spot in leaf blade and necrosis of leaf margin were appeared at later stage of experiment at the lower potassium level. 6. Very stimulating vegetative growth, e.g, large plant length, leaf expansion, increasing node number and fresh weight as well as high ratio of roots to shoot, high water content was resulted in the condition of higher potassium level. 7. A specific interaction between higher potassium level and thermoperiod was found, that is, the largest tuber production and the largest ratio of roots to shoot were resulted in the combined condition of higher potassium level and constant temperature while the largest plant length, fresh weight etc. i.e. the most stimulative vegetative growth was resulted in the combined condition of higher potassium level and low night temperature. 8. Comparatively low water content in the former condition of stimulative tuber production was resulted(especially at the tuber thickening stage), while high water content in the latter condition of stimulative vegetation was resulted though the higher potassium level made generally high water contents. 9. The nitrogen contents of soluble and insoluble did not make distinct difference between the lower and higher potassium level. 10. Though the phosphorus contents were not distinctly different by the potassium level, the lower potassium level made the percentage of phosphorus increased at tuber forming stage accumulating more phosphorus in roots, while the higher potassium level decreased percentage of phosphorus at that stage. 11. The higher potassium level made distinctly high potassium contents than the lower potassium level and increased contents at the tuber forming stage through both conditions. 12. The sodium contents were low in the condition of higher potassium level than the lower potassium level and decreased at tuber forming stage in both conditions, on the contary of potassium. 13. Except the noticeable deficeney of manganese in the growing point of the lower potassium level, mangense and magnesium contents in other organs did not make distinct difference according to the potassium level. 14. Generally more uptake and large absorption rate of phosphorus-32 and potassium-42 were resulted at the higher potassium level, and the most uptake, and the largest absorption rate of phosphorus and potassium-42 (especially potassium-42 at tuber forming stage) were resulted in the condition of higher potassium level and constant temperature which made the highest tuber production. 15. The higher potassium level stimulated the translocation of phoshorus-32 and potassium-42 from roots to shoots while the lower potassium level suppressed or blocked the translocation. 16. Therefore, very large distribution rate of $p^{32}$, $K^{42}$ in shoot, especially, in growing point, compared with roots was resulted in the higher potassium level. 17. The lower potassium level suppressed the translocation of phosporus-32 from roots to shoot more than that of potassium-42. 18. The uptake of potassium-42 and translocation in IPOMOEA BATATAS were more vivid than phosphorus-32. 19. A specific interaction between potassium nutrition and thermoperiod which resulted the largest tuber production etc. was discussed in relation to behaviors of minerals and potasium-42 etc. 20. Also, the specific effect of the lower and higher potassium level on the growth pattern of IPOMOEA BATATAS were discussed in relation to behaviors of minerals and isotopes. 21. An emphasize on the significance of the higher potassium level as well as the interaction with the regulating factor and problem of potassium level (gradient) for crops product ion were discussed from the point of dynamical and variable function of potassium.

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Studies on the Inheritance of Agronomic Characteristics in Upland Cotton Varieties (Gossypium hirsutum L.) in Korea (육지면품종의 유용형질의 유전에 관한 연구)

  • Bang-Myung Kae
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.21 no.2
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    • pp.281-313
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    • 1976
  • To obtain fundamental informations on cotton breeding efficiences for Korea, individual genetic relationships and interrelationships between the agronomic characteristics of Upland cotton were investigated. These experiments were couducted at the Mokpo Branch Station $(34^{\circ}48'N, $ $126^{\circ}23'E$ and altitude of 10m above sea level) from 1969 through 1972. Heterosis, combining ability, dominance and recessive gene action, genetic variance, and phenotypic and genotypic correlation were investigated by $F_1'S$ from an 11-parent partial diallel cross and the segregating $F_2$ and $F_3$ populations of the cross Paymaster times Heujueusseo Trice. The following points resulted from this study, 1. Heteroses for number of bolls per plant and lint yield were significant at 27, 84% and 37.26%, respectively. No other character had significant heteroses. 2. The GCA estimates for all studied characteristics were higher than the SCA estimates. Varieties with high GCA effects were Suwon 1 for earliness, Paymaster and Arijona for high lint percent, and Arijona for long fiber, etc, 3. SCA estimates for lint yield varied widely in crosses with Mokpo 4, Mokpo 6 and Heujueusseo Trice. Those crosses with the highest SCA effects were combinations with large characteristics differences, Example of these crosses are Mokpo 4 times Acala 1517W, Mokpo 4 times D. P. L. and Heujueusseo Trice aud Paymaster. 4. Early-maturing varieties were completely dominant to late-maturing varieties in some combinations while other crosses gave intermediate phenotypes. These results suggest additive genetic action by multi-genes. Heujueusseo Trice, Mokpo 6, and Suwon 1 showed highest degree of dominance for earliness. 5. There were no significant trends for inheritance of weight of boll and 100 seeds weight. 6. Long staple was partially to completely dominant to short staple. Though there were single gene ratios the rate of dominance decreased in the $F_2$ and $F_3$ populations in the cross between the long staple variety Paymaster and the short staple variety Heujueusseo Trice. Diallel cross $F_1$ hybrids showed complicated allelic gene action for staple length. Various dominance degree were shown by varieties. 7. Number of bolls per plant indicated strong over-dominance and small non-allelic additive gene action. 8. Lint Yield was characterized by over-dominance and by multiple non-allelic-gene action. High-yielding varieties were dominant to low-yielding ones. However, the low-yielding variety Heujueusseo Trice showed over-dominance, indicating different reactions according to the varieties and combinations. 9. Broad sense heritability for days to flowering was 34-39% while narrow sense heritability was 11%. Large variations of individual plants caused by Korean climatic conditions cause this situation. Heritability estimates for weight of boll was 30% for broad sense and 22% for narrow sense. 10. Heritability estimates for staple length and lint percent were very high suggesting strong selection effects. 11. Narrow sense heritability estimates for number of bolls per plant was 30% in the diallel cross $F_1$ hybrids and 36% in the $F_2$ population of the special cross. Broad sense heritability was estimated at 67% suggesting that. 12. Heritability estimates for lint yield was low due to high over-dominance in the diallel cross $F_1$ hybrids. Heritability estimates for yield was low in the $F_1$ hybrids but high in the $F_2$ and $F_3$ populations. 13. Phenotypic and genotypic correlations between lint percent and days to flowering and between staple length and days to flowering were high in the $F_1, $ $F_2$ and $F_3$ populations. Late-maturing varieties and individuals had long staple and high lint percent in general. As the correlation between days to flowering and lint yield was extremely low, the two traits were considered independent of each other. Days to flowering and number of bolls per plant were negatively correlated in the $F_3$ population, indicating early-maturing individual plants with many bolls may be readily selected. 14. Phenotypic and genotypic correlations between lint percent and staple length were high in $F_1, $ $F_2$ and $F_3$ populations. Accordingly, long staple varieties were high in lint percent. It was recognized that lint yield and lint percent were positively correlated in the diallel cross $F_1$ hybrids, and lint percent and staple length were positively correlated in the $F_2$ population, indicating that lint percent and staple length affect lint yield. 15. Lint yield was significantly and positively phenotypically correlated with number of bolls per plant in $F_1, $ $F_2$ and $F_3$ populations. A high genotypic correlation was also noted indicating a close genetic relationship. The selection efficiencies for a high-yielding variety can be increased when individual plants with many bolls are selected in later generations. The selection efficiencies for good fiber quality can be enhanced when individuals with long staple and high lint percent are selected in early generations.

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