• Title/Summary/Keyword: $R^2$ Selection

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Signatures of positive selection underlying beef production traits in Korean cattle breeds

  • Edea, Zewdu;Jung, Kyoung Sub;Shin, Sung-Sub;Yoo, Song-Won;Choi, Jae Won;Kim, Kwan-Suk
    • Journal of Animal Science and Technology
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    • v.62 no.3
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    • pp.293-305
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    • 2020
  • The difference in the breeding programs and population history may have diversely shaped the genomes of Korean native cattle breeds. In the absence of phenotypic data, comparisons of breeds that have been subjected to different selective pressures can aid to identify genomic regions and genes controlling qualitative and complex traits. In this study to decipher genetic variation and identify evidence of divergent selection, 3 Korean cattle breeds were genotyped using the recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array. The three Korean cattle breeds clustered according to their coat color phenotypes and breeding programs. The Heugu breed reliably showed smaller effective population size at all generations considered. Across the autosomal chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the two pairwise comparisons. The most important signals of selection were detected on bovine chromosomes 14 (24.39-25.13 Mb) and 18 (13.34-15.07 Mb), containing genes related to body size, and coat color (XKR4, LYN, PLAG1, SDR16C5, TMEM68, CDH15, MC1R, and GALNS). Some of the candidate genes are also associated with meat quality traits (ACSF3, EIF2B1, BANP, APCDD1, and GALM) and harbor quantitative trait locus (QTL) for beef production traits. Further functional analysis revealed that the candidate genes (DBI, ACSF3, HINT2, GBA2, AGPAT5, SCAP, ELP6, APOB, and RBL1) were involved in gene ontology (GO) terms relevant to meat quality including fatty acid oxidation, biosynthesis, and lipid storage. Candidate genes previously known to affect beef production and quality traits could be used in the beef cattle selection strategies.

Analysis of the axle load of an agricultural tractor during plow tillage and harrowing

  • Hong, Soon-Jung;Park, Seung-Je;Kim, Wan-Soo;Kim, Yong-Joo;Park, Seong-un
    • Korean Journal of Agricultural Science
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    • v.43 no.4
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    • pp.665-669
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    • 2016
  • Analysis of the load on the tractor during field operations is critical for the optimal design of the tractor. The purpose of this study was to do a load analysis of an agricultural tractor during plowing and harrowing. First, a load measurement system was developed and installed in a 71 kW agricultural tractor. Strain-gauges with a telemetry system were installed in the shaft located between the axles and the wheels, and used to measure the torque of the four driving axles. Second, field experiments were conducted for two types of field operations (plowing, harrowing), each at two gear levels (M2, M3). Third, load analysis was conducted according to field operation and gear level. At M2 gear selection for plowing, the maximum, minimum, and average (S. D.) torque values were 13,141 Nm; 4,381 Nm; and 6,971 Nm (${\pm}397.8Nm$, respectively). For harrowing, at M2 gear selection, torque values were, 14,504 Nm; 1,963 Nm; and 6,774 Nm (${\pm}459.4Nm$, respectively). At M3 gear selection for plowing, the maximum, minimum, and average (S. D.) torque values were,17,098 Nm; 6,275 Nm; and 8,509 Nm (${\pm}462.4Nm$, respectively). For harrowing at M3 gear selection, maximum, minimum, and average (S. D.) torque values were, 20,266 Nm; 2,745 Nm; and 9,968 Nm (${\pm}493.2$). The working speed of the tractor increased by approximately 143% when shifted from M2 (7.2 km/h) to M3 (10.3 km/h); while during plow tillage and harrowing, the load of the tractor increased approximately 1.2 times and 1.5 times, respectively.

Multi-objective Genetic Algorithm for Variable Selection in Linear Regression Model and Application (선형회귀모델의 변수선택을 위한 다중목적 유전 알고리즘과 응용)

  • Kim, Dong-Il;Park, Cheong-Sool;Baek, Jun-Geol;Kim, Sung-Shick
    • Journal of the Korea Society for Simulation
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    • v.18 no.4
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    • pp.137-148
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    • 2009
  • The purpose of this study is to implement variable selection algorithm which helps construct a reliable linear regression model. If we use all candidate variables to construct a linear regression model, the significance of the model will be decreased and it will cause 'Curse of Dimensionality'. And if the number of data is less than the number of variables (dimension), we cannot construct the regression model. Due to these problems, we consider the variable selection problem as a combinatorial optimization problem, and apply GA (Genetic Algorithm) to the problem. Typical measures of estimating statistical significance are $R^2$, F-value of regression model, t-value of regression coefficients, and standard error of estimates. We design GA to solve multi-objective functions, because statistical significance of model is not to be estimated by a single measure. We perform experiments using simulation data, designed to consider various kinds of situations. As a result, it shows better performance than LARS (Least Angle Regression) which is an algorithm to solve variable selection problems. We modify algorithm to solve portfolio selection problem which construct portfolio by selecting stocks. We conclude that the algorithm is able to solve real problems.

Effects of a Porcine MC4R Polymorphism(892G>A) on Carcass Traits in Commercial Pigs (돼지 MC4R 유전자 892G>A 다형성이 비육돈의 도체형질에 미치는 영향)

  • Han, S.H.;Lee, S.S.;Ko, M.S.;Seong, P.N.;Park, B.Y.;Cho, I.C.
    • Journal of Animal Science and Technology
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    • v.49 no.5
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    • pp.569-576
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    • 2007
  • receptor(MC4R) gene and carcass traits was examined in randomly selected commercial pigs. A porcine MC4R gene was genotyped for Asp298Asn(nt. 892G>A) by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). A total of three genotypes, A/A, A/G, and G/G, were found with 28.8, 22.8, and 48.4% frequencies, respectively. In the whole population, pigs containing 892A/- showed significantly higher marbling score than those of homozygotes G/G(P<0.05). Two homozygotes, A/A and G/G showed lower in meat color score but higher in water holding capacity than those of heterozygotes A/G(P<0.01). However, the carcass weight of the barrows containing wild type -/G was significantly higher(i.e. more than 2.5kg) than those of homozygotes A/A(P<0.05). The effects of each genotype on carcass traits in the gilts were similar to those of the whole population, but not in barrows, suggesting an unknown sex-related effect on carcass traits. This study suggested that the genotype MC4R A/- could improve the meat quality in the commercial pig production. However, since the genetic polymorphism of MC4R gene differentially affected the carcass traits in sex-related manner, therefore, both parameters, the sex and genotype, should be considered for marker-assisted selection in commercial pig production.

Development of a Constituent Prediction Model of Domestic Rice Using Near Infrared Reflectance Analyzer(I) -Constituent Prediction Model of Brown and Milled Rice- (근적외선분석계를 이용한 국내산 쌀의 성분예측모델 개발(I) -현미와 백미의 성분예측모델-)

  • 한충수;동하원강
    • Journal of Biosystems Engineering
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    • v.21 no.2
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    • pp.198-207
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    • 1996
  • To measure the moisture content, protein and viscosity of brown and milled rice with Near Infrared Reflectance(NIR) analyzer, the comparison and analysis of the data from the chemical analysis and NIR analyzer were conducted. The purpose of this study is to find out the fundamental data required for the prediction of rice qualify and taste rank, and to develop a measuring method of constituents and physical characteristics of domestic rice with NIR analyzer. The important results can be summarized as follows. 1. The $r^2$ and SEC of moisture calibration from brown rice powder were 0.87 and 0.09 respectively, those of milled rice powder were 0.95 and 0.08 respectively. 2. The $r^2$ and SEC of protein calibration from brown rice powder were 0.83 and 0.20 respectively, those of milled rice powder were 0.86 and 0.20 respectively. 3. The $r^2$ and SEC of viscosity calibration from brown rice powder were 0.36 and 15.50 respectively, those of milled rice powder were 0.55 and 12.98 respectively. Further study is required to develop better prediction model for viscosity. It is necessary the continuous study including wavelength selection, because $r^2$ is small for practical use. 4. The regression equation for one rice variety was nearly coincident with other. Therefore, it is required that the prediction model should be developed for the all rice samples.

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High-efficiency development of herbicide-resistant transgenic lilies via an Agrobacterium-mediated transformation system (고효율의 아그로박테리움 형질전환법을 이용한 제초제저항성 나리 식물체 개발)

  • Jong Bo Kim
    • Journal of Plant Biotechnology
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    • v.50
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    • pp.56-62
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    • 2023
  • Transgenic lilies have been obtained using Agrobacterium tumefaciens (AGL1) with the plant scale explants, followed by DL-phosphinothricin (PPT) selection. In this study, scales of lily plants cv. "red flame" were transformed with the pCAMBIA3301 vector containing the gus gene as a reporter and the blpR gene as a selectable marker, as well as a gene of interest showing herbicide tolerance, both driven by the CaMV 35S promoter. Using a 20-minute infection time and a 5-day cultivation period, factors that optimized and demonstrated a high transformation efficiency were achieved. With these conditions, approximately 22-27% efficiency was observed for Agrobacterium-mediated transformation in lilies. After transformation with Agrobacterium, scales of lilies were transferred to MS medium without selective agents for 2 weeks. They were then placed on selection MS medium containing 5 mg/L PPT for a month of further selection and then cultured for another 4-8 weeks with a 4-week subculture regime on the same selection medium. PPT-resistant scales with shoots were successfully rooted and regenerated into plantlets after transferring into hormone-free MS medium. Also, most survived putatively transformed plantlets indicated the presence of the blpR gene by PCR analysis and showed a blue color indicating expression of the gus gene. In conclusion, when 100 scales of lily cv. "red flame" are transformed with Agrobacterium, approximately 22-27 transgenic plantlets can be produced following an optimized protocol. Therefore, this protocol can contribute to the lily breeding program in the future.

SHADE PERCEPTION ABILITY AMONG DIFFERENT DENTAL PERSONNEL (치과 종사자간의 색조 식별 능력)

  • Kim Ja-Yeong;Lee Im-Gi;Yoon Tae-Ho;Ahn Seung-Geun;Park Charn-Woon
    • The Journal of Korean Academy of Prosthodontics
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    • v.44 no.4
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    • pp.455-465
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    • 2006
  • Statement of problem: Many factors influence shade determination in clinical practice and shade matching is highly affected by the viewing conditions. Purpose : This study investigated the differences in shade perception among distinct groups of dental personnel (10 prosthodontists, 10 general practitioners, 10 last-year dental students and 10 dental technicians) Material and method: Four groups of dental personnel were investigated. They were tested to eliminate color blindness. To compare shade selection ability, they were asked to match four test tabs of shades A3, B2, C2 and D4 (VITAPAN$^{(R)}$ Classical shade guide. The identification codes of the shade tabs were masked to prevent shade memory. ) against another full set of VITA$^{(R)}$ PAN$^{(R)}$ Classical shade guide under similar lighting conditions. Shade selections were randomly repeated five times every week and then the repeatability between dental personnel was evaluated. To compare value perception ability, they were asked to arrange randomly selected five test tabs (Bl, A2, D2, C3, A4) in descending order from the brightest to the darkest. To compare hue determination ability, they were asked to divide selected eight test tabs (n, A3, B2, B3, C2, C3, D2, D3) into four groups by manufacturer as follows : Group A-Reddish brown, Group B-Reddish yellow. Group C-Grey. Group D-Reddish grey. Results and conclusion : The obtained results were as follows : 1. For the value perception ability and hue determination ability. there was no significant difference among 4 groups: prosthodontists, general practitioners, dental students, dental technicians (P>.05). 2. For shade selection ability, the prosthodontists and dental technicians were significantly higher than dental students(P<.05). 3. The repeatability of selected shade in the dental technicians was significantly higher than that of general practitioners and dental students(P<.05). 4. The prosthodontists and dental technicians had significantly higher selection ability than dental students for shade B2 (P<.05).

Study on the Vapor Pressure and Miseibility of R-744/Mineral and POE Oil Mixture (R-744/광유 및 POE 오일 혼합물의 증기압 및 상용성에 관한 연구)

  • Choi, H.S.;Kim, S.;Park, K.K.
    • Proceedings of the KSME Conference
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    • 2003.04a
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    • pp.1672-1677
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    • 2003
  • Carbon dioxide($CO_2$, R-744) has become a very popular issue in application to refrigeration and air conditioning systems as a natural refrigerant. An experimental study has been carried out to investigate the vapor pressure and miscibility of refrigerant R-744 in the presence of lubricant oil. This is of particular interest in the selection of the lubricant oil for the compressor of a refrigeration system or an air conditioning system using the refrigerant R-744. This apparatus consists of the test section, measuring devices, the vacuum pump, the constant temperature bath and relevant connecting pipes made of stainless steel. Two lubricant oils, such as mineral oil(Naphthenic) and polyol ester(POE) oil, are considered in the present study. For this purpose, test runs were conducted with the oil concentration range from 5 to 50 wt%, and the temperature range from -10 to $10^{\circ}C$ with $2^{\circ}C$ intervals. The results are correlated with the vapor pressure. and showed with the miscibility as visualization for the individual text components.

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Development of a SCAR Marker Linked to Male Fertility Traits in 'Jinkyool' (Citrus sunki) ('진귤' (Citrus sunki) 의 웅성가임 연관 SCAR 마커 개발)

  • Chae, Chi-Won;Dutt, Manjul;Yun, Su-Hyun;Park, Jae-Ho;Lee, Dong-Hoon
    • Journal of Life Science
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    • v.21 no.12
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    • pp.1659-1665
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    • 2011
  • In Citrus, an $F_1$ segregation population of 150 plants was constructed from a cross between 'Kiyomi' (C. unshiu ${\times}$ C. sinensis) carrying the male sterility trait and 'Jinkyool' (C. sunki). Sequence-related amplification polymorphism (SRAP) combined with bulked segregant analysis was used to develop markers linked to male fertility. In the $F_1$ population, 66 out of 150 seedlings had aborted anthers and the ratio of male sterile plants to fertile plants in the progenies matched the expected Mendelian segregation ratio of 1:1 ($x^2$ =2.16 at p=0.05). From the profiling of the 197 SRAP primer sets, three SRAP primer sets (F4/R27, F39/R60, and F15/R37) that were closely linked to the target trait were identified and successfully converted into a sequence characterized amplified region (SCAR) marker for selection of male fertility in citrus. The SCAR marker, using the pMS 33U/pMS 1462L primer set specifically, produced a single 1.4-Kb fragment that was linked to male fertility. Our results suggested that this SCAR marker can be useful for marker-assisted selection of male sterile individuals in breeding $F_1$ progenies in Citrus.

Studies on Male Sterile Facilitated. Recurrent Selection in Barley Breeding 1. Development of RSPYB#1 Population and Selection of Pedigree Lines (웅성불임을 이용한 보리의 순환선발 육종에 관한 연구 제1보 보리 순환선발집단 RSPYB#1의 육성과 계통선발에 관하여)

  • Lee, B.H.;Suh, D.Y.;Suh, H.S.;Park, R.K.
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.25 no.1
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    • pp.39-46
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    • 1980
  • A male sterile facilitated recurrent selection population was developed by the barley breeding team of Yeongnam Crop Experiment Station. To breed this population, three composite cross populations and a composite population of breeding lines in our country were used as the materials. This population was developed in order to breed early maturing, wet-soil tolerant and high yielding barley varieties, adapted for double cropping with rice in southern part of Korea. The population was named by RSPYB#l which means Recurrent Selection Population No.1. of Yeongnam Barley.

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