• Title/Summary/Keyword: Genetic Improvement

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A Study on the Prolactin Receptor 3 (PRLR3) Gene and the Retinol-binding Protein 4 (RBP4) Gene as Candidate Genes for Growth and Litter Size Traits of Berkshire in Korea (국내 버크셔 돼지에서 성장 및 산자수의 후보유전자로서 PRLR3와 RBP4에 관한 연구)

  • Do, Chang-Hee;Kim, Seon-Ku;Kang, Han-Suk;Shin, Teak-Soon;Lee, Hong-Gu;Cho, Seong-Keun;Do, Kyung-Tak;Song, Ji-Na;Kim, Tae-Hun;Choi, Bong-Hwan;Sang, Byung-Chan;Joo, Yeong-Kuk;Park, Jun-Kyu;Lee, Sung-Hoon;Lee, Jeong-Ill;Park, Jeong-Suk;Sin, Young-Soo;Kim, Byung-Woo;Cho, Byung-Wook
    • Journal of Life Science
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    • v.20 no.6
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    • pp.825-830
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    • 2010
  • Two diallelic markers at candidate gene loci, the prolactin receptor 3 (PRLR3) gene and the retinol-binding protein 4 (RBP4) gene were evaluated for their association with growth and litter size traits in Berkshire. Genetic evaluation was conducted for 5,919 pigs with pedigree information, which included 3,480 growth performance records and 775 litter size records of 224 sows. From the same herd, genotyping was carried out on 144 and 156 animals for PRLR3 and RBP4, respectively. After assigning a genotype to subjects in which both parents had a homozygous genotype, numbers of genotyped animals increased to 474 and 338, for the PRLR3 gene and RBP4 gene, respectively. The genotype effects of two markers were estimated with breeding values of the genotyped animals. The additive effects of total number of piglets born and number of piglets born alive in the PRLR3 locus were -0.28 and -0.13, respectively. The dominance effect of the RBP4 locus on average daily gain was -10.58 g. However, the polymorphism of the RBP4 locus in total number of piglets born and number of piglets born alive has shown -0.34 and -0.33 of the additive genetic effects. In view of the results, MAS (marker-assisted selection) favoring B alleles of RBP4 and PRLR3 loci could potentially accelerate the rate of the genetic improvement in the litter size traits.

Screening for Fittest Miscellaneous Cereals for Reclaimed Land and Functionality Improvement of Sorghum bicolor Cultivated in Reclaimed Land (간척지 적응성 잡곡 선발 및 간척지 재배 수수의 기능성 향상 효과)

  • Kang, Chan Ho;Lee, In Sok;Kwon, Suk Ju
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.64 no.2
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    • pp.109-126
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    • 2019
  • Genetic resources of 84 species of Setaria italica BEAUVOIS, Sorghum bicolor, and Panicum miliaceum were collected to select the adaptable miscellaneous cereals in Saemangeum reclaimed land. The adaptability of Sorghum bicolor in reclaimed land was the highest among the three cereals cultivated on reclaimed land. The ratio of the average height of Sorghum bicolor plants cultivated in reclaimed land/normal field was 0.82, that of Panicum miliaceum was 0.61, and that of Setaria italica BEAUVOIS was 0.51. Three species of Sorghum bicolor, Satangdajuk, Kkamansusu, and Nampungcharl, were selected as potential genetic resources as they had excellent adaptability to reclaimed land. The yield of Satandaejuk on reclaimed land was 229.4 kg/10a, and the yield ratio of reclaimed land/normal field was 89.3%. The yield of Kkamansusu was 227.4 kg/10a, with reclaimed land/normal field ratio of 87.8%, and yield of Nampungcharl was 239.6 kg/10a, and reclaimed land/normal field ratio of 86%. In order to study the salt tolerance of selected genetic resources, we conducted salinity test. Salinity tolerance of Sorghum bicolor species-Satangdajuk, Kkamansusu, Nampungcharl was excellent compared to that of the other cereals. Among these, Satandaejuk had to highest salt tolerance level. Polyphenols, flavonoids, and detoxification of free radical were also studied. The anti-diabetic property of the cereals was also analyzed by ${\alpha}$-glucosidase inhibitory activity. We confirmed that the functionality of 3 lines in reclaimed land had improved in all the functional analysis categories when compared to that with yield in the normal field. Polyphenol, an antioxidant, increased in the range of 2~26% when cultivated in reclaimed land and the flavonoid content also increased from 8.5 to 55.6%. DPPH elimination capability, the ability to scavenge harmful reactive oxygen, also increased from 16.7 to 47% when cultivated in reclaimed land. The anti-diabetic activity and ${\alpha}$-glucosidase inhibition activity of selected Sorghum bicolor species-Satangdajuk, Kkamansusu, Nampungcharl also increased from 18.4 to 19.9% when cultivated on reclaimed land.

Effect of the Fatty Acid Synthase Gene for Beef Quantity Traits in Hanwoo Breeding Stock (한우 Fatty Acid Synthase (FASN) 유전자 반수체형의 후대검정우 육량 및 육질에 미치는 영향)

  • Kim, Sang-Wook;Lee, Jun-Heon;Kim, Jin-Ho;Won, You-Seog;Kim, Nae-Soo;Kim, Kwan-Suk
    • Journal of Animal Science and Technology
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    • v.52 no.1
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    • pp.9-16
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    • 2010
  • A previous study has shown that the g.17924G>A polymorphism of fatty acid synthase (FASN) is associated with unsaturated fatty acid composition in the Hanwoo beef, hence this study was conducted to evaluate the effect of single nucleotide polymorphisms (SNPs) within FASN gene on the selection phenotypes of Hanwoo breeding stock. A total of 925 progeny test steers were used to genotype g.11280G>A, g.13125T>C, and g.17924G>A polymorphisms and significant associations were found among g.11280G>A, g.17924G>A, and carcass traits, such as carcass weight, backfat thickness, and beef quantity index. No significant association was found between g.13125T>C and carcass traits. Although the degree of linkage disequilibrium (LD) was not strong among g.11280G>A, g.13125T>C, and g.17924G>A in the LD analysis, four major haplotype classes were formed with the genotypic information within the FASN gene; the frequencies of the halpotypeswere -GCG-[0.378], -ATG-[0.301], -GTA-[0.191], and -ACG-[0.063], respectively. Phenotypic association was performed among these haploptypes, and the haplotype 2 (-ATG-)was significantly associated with higher carcass weight when compared to the other haplotypes, i.e. haplotype 1 (-GCG-) and haplotype 3 (-GTA-). A copy number of the FASN haplotype 3 (-GTA-) had also a significant association with carcass weight of subjects. In conclusion, it was observed that two polymorphisms (g.11280G>A and g.17924G>A) and their haplotypes within the FASN gene are consistently associated with carcass traits. Therefore, it is desirable to use the FASN polymorphisms for pre-selection program as genetic marker with improved carcass yield and beef quality of the Hanwoo sire at the Hanwoo Improvement Center as well as for commercial Hanwoo producers, the FASN genotypic information can be used for a part of selecting Hanwoo dam for superior calf production.

Study on the Analysis of β-lactoglobulin and κ-casein Genotypes of Cattle using Polymerase Chain Reaction (PCR 기법을 이용한 축우의 β-lactoglobulin 및 κ-casein 유전자형 분석에 관한 연구)

  • Sang, Byung Chan;Ryoo, Seung Heui;Lee, Sang Hoon;Song, Chi Eun;Nam, Myung Soo;Chon, Byung Soon
    • Korean Journal of Agricultural Science
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    • v.25 no.2
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    • pp.216-224
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    • 1998
  • This study was performed to offer the basic and applicable data for improvement of Korean cattle and dairy cattle, according to finding the genetic construction obtained from analysis of genetic polymorphisms of ${\beta}$-lactoglobulin and ${\kappa}$-casein loci related Korean cattle and Holstein cows using PCR-RFLP. Genomic DNA used in this study was prepared from the blood of 253 individuals of Korean cattle in Korean Native Cattle Improvement Center, NLCF, and the blood of 113 individuals of Holstein cows in National Livestock Research Institute. The results obtained are summarized as follows : 1. This study confirmed amplified products of 530bp and 262bp fragments obtained from the amplification of ${\beta}$-lactoglobulin and ${\kappa}$-casein loci in Korean cattle and Holstein breed by PCR. 2. The ${\beta}$-lactoglobulin AA genotype showed 153bp and 109bp fragments, and ${\beta}$-lactoglobulin AB genotype showed 153bp, 109bp, 79bp and 74bp fragments, and BB genotype showed 109bp, 79bp and 74bp fragments in amplified products of ${\beta}$-lactoglobulin loci with the restricted enzyme digestion of Hae III. 3. The ${\kappa}$-casein AA genotype showed a 530bp fragment, and ${\kappa}$-casein AB genotype showed 530bp, 344bp and 186bp fragments, and BB genotype showed 344bp and 186bp fragments in amplified products of ${\kappa}$-casein loci with the restricted enzyme digestion of Taq I. 4. On ${\beta}$-lactoglobulin genotypes and gene frequencies, Korean cattle were 6.72%, 26.09% and 67.19% for AA, AB and BB genotypes, and ${\beta}$-lactoglobulin A and B alleles were 0.197 and 0.803, and Holstein were 35.40%, 56.64% and 7.96% for AA, AB and BB genotypes, and ${\beta}$-lactoglobulin A and B alleles were 0.637 and 0.363, respectively. 5. On ${\kappa}$-casein genotypes and gene frequencies, Korean cattle were 46.25%, 39.13% and 14.62% for AA, AB and BB genotypes, and ${\kappa}$-casein A and B alleles were 0.658 and 0.342, and Holstein were 60.18% and 38.94% and 0.88% for AA, AB and BB genotypes, and ${\kappa}$-casein A and B alleles were 0.796 and 0.204, respectively. 6. As a consequence, the gene frequency was 0.197 and 0.803 for ${\beta}$-lactoglobulin A and B alleles, and 0.658 and 0.342 for ${\kappa}$-casein A and B alleles in Korea cattle, but was 0.637 and 0.363 for ${\beta}$-lactoglobulin A and B alleles, and 0.796 and 0.204 for ${\kappa}$-casein A and B alleles in Holstein, respectively.

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A Study on the Prediction Model of Stock Price Index Trend based on GA-MSVM that Simultaneously Optimizes Feature and Instance Selection (입력변수 및 학습사례 선정을 동시에 최적화하는 GA-MSVM 기반 주가지수 추세 예측 모형에 관한 연구)

  • Lee, Jong-sik;Ahn, Hyunchul
    • Journal of Intelligence and Information Systems
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    • v.23 no.4
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    • pp.147-168
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    • 2017
  • There have been many studies on accurate stock market forecasting in academia for a long time, and now there are also various forecasting models using various techniques. Recently, many attempts have been made to predict the stock index using various machine learning methods including Deep Learning. Although the fundamental analysis and the technical analysis method are used for the analysis of the traditional stock investment transaction, the technical analysis method is more useful for the application of the short-term transaction prediction or statistical and mathematical techniques. Most of the studies that have been conducted using these technical indicators have studied the model of predicting stock prices by binary classification - rising or falling - of stock market fluctuations in the future market (usually next trading day). However, it is also true that this binary classification has many unfavorable aspects in predicting trends, identifying trading signals, or signaling portfolio rebalancing. In this study, we try to predict the stock index by expanding the stock index trend (upward trend, boxed, downward trend) to the multiple classification system in the existing binary index method. In order to solve this multi-classification problem, a technique such as Multinomial Logistic Regression Analysis (MLOGIT), Multiple Discriminant Analysis (MDA) or Artificial Neural Networks (ANN) we propose an optimization model using Genetic Algorithm as a wrapper for improving the performance of this model using Multi-classification Support Vector Machines (MSVM), which has proved to be superior in prediction performance. In particular, the proposed model named GA-MSVM is designed to maximize model performance by optimizing not only the kernel function parameters of MSVM, but also the optimal selection of input variables (feature selection) as well as instance selection. In order to verify the performance of the proposed model, we applied the proposed method to the real data. The results show that the proposed method is more effective than the conventional multivariate SVM, which has been known to show the best prediction performance up to now, as well as existing artificial intelligence / data mining techniques such as MDA, MLOGIT, CBR, and it is confirmed that the prediction performance is better than this. Especially, it has been confirmed that the 'instance selection' plays a very important role in predicting the stock index trend, and it is confirmed that the improvement effect of the model is more important than other factors. To verify the usefulness of GA-MSVM, we applied it to Korea's real KOSPI200 stock index trend forecast. Our research is primarily aimed at predicting trend segments to capture signal acquisition or short-term trend transition points. The experimental data set includes technical indicators such as the price and volatility index (2004 ~ 2017) and macroeconomic data (interest rate, exchange rate, S&P 500, etc.) of KOSPI200 stock index in Korea. Using a variety of statistical methods including one-way ANOVA and stepwise MDA, 15 indicators were selected as candidate independent variables. The dependent variable, trend classification, was classified into three states: 1 (upward trend), 0 (boxed), and -1 (downward trend). 70% of the total data for each class was used for training and the remaining 30% was used for verifying. To verify the performance of the proposed model, several comparative model experiments such as MDA, MLOGIT, CBR, ANN and MSVM were conducted. MSVM has adopted the One-Against-One (OAO) approach, which is known as the most accurate approach among the various MSVM approaches. Although there are some limitations, the final experimental results demonstrate that the proposed model, GA-MSVM, performs at a significantly higher level than all comparative models.

Improvement of Pregnancy Rate in Preimplantation Genetic Diagnosis with FISH Procedure by the Laboratory Optimization and Experiences (형광직접보합법을 이용한 착상전 유전진단 기법의 최적화와 경험 축적에 의한 임신율의 향상)

  • Lim, Chun-Kyu;Min, Dong-Mi;Lee, Hyoung-Song;Byun, Hye-Kyung;Park, So-Yeon;Ryu, Hyun-Mee;Kim, Jin-Young;Koong, Mi-Kyoung;Kang, Inn-Soo;Jun, Jin-Hyun
    • Clinical and Experimental Reproductive Medicine
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    • v.31 no.1
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    • pp.29-39
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    • 2004
  • Objectives: This study was performed to evaluate the laboratory system for successful PGD using fluorescence in situ hybridization (FISH) and the clinical outcome of PGD cycles in five years experiences. Methods: A total of 181 PGD-FISH cycles of 106 couples were performed, and diagnosed chromosome normality in the preimplantation embryos. The laboratory and clinical data were classified by the following optimization steps, and statistically analyzed. Phase I: Blastomere biopsy with two kinds of pipettes, removal of cytoplasmic proteins without treatment of pepsin and culture of biopsied embryos with single medium; Phase II: Blatomere biopsy with single pipette, removal of cytoplasmic proteins with pepsin and culture of biopsied embryos with single medium; Phase III: Blastomere biopsy with single pipette, removal of cytoplasmic proteins with pepsin and culture of biopsied embryos with sequential media. Results: A total of 3, 209 oocytes were collected, and 83.8% (2, 212/2, 640) of fertilization rate was obtained by ICSI procedure. The successful blastomere biopsies were accomplished in 98.6% (2, 043/2, 071) of embryos, and the successful diagnosis rate of FISH was 94.7% (1, 935/ 2, 043) of blastomeres from overall data. Embryo transfers with normal embryos were conducted in 93.9% (170/181) of started cycles. There was no difference in the successful rate of biopsy and diagnosis among Phase I, II and III. However, the pregnancy rate per embryo transfer of Phase III (38.8%, 26/67) was significantly (p<0.05) higher than those of Phase I (13.9%, 5/36) and Phase II (14.9%, 10/67). Conclusions: The laboratory optimization and experience for the PGD with FISH procedure can increase the pregnancy rate to 38.8% in the human IVF-ET program. Our facility of PGD with FISH provides the great possibility to get a normal pregnancy for the concerned couples by chromosomal aberrations.

Association of SNPs from iNOS and TLR-4 Genes with Economic Trait in Chicken (닭의 iNOS와 TLR-4 유전자 내 변이와 경제 형질 간의 연관성 분석)

  • Lim, Hee Kyong;Han, Jung-Min;Oh, Jae Don;Lee, Hak Kyo;Jeon, Gwang Joo;Lee, Jun Heon;Seo, Dong Won;Cahyadi, Muhammad;Song, Ki Duk;Choi, Kang Duk;Kong, Hong Sik
    • Korean Journal of Poultry Science
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    • v.40 no.2
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    • pp.83-89
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    • 2013
  • iNOS (Inducible nitric oxide synthase) and TLR-4 (Toll-like Receptor-4) play crucial roles in innate immunity of poultry. iNOS has been mapped to chicken chromosome 14 and implicated in a variety of chicken diseases. iNOS possesses potent antimicrobial activity, including the inhibition of microbes replication in vitro. TLR-4 is a pathogen associated molecular-pattern receptor for bacterial product, such as LPS (lipopolysaccharides) found in Gram negative bacteria, that triggers pro-inflammatory cytokine expression after engagement with ligands. In the previous studies, genetic analysis of iNOS and TLR-4 revealed the possible association of mutation in these genes with the intestinal microflora of cecum when infected with Salmonella spp. This study was aimed to augment previous findings, which show the association of iNOS (C14513T) and TLR-4 (G4409T) polymorphisms with economic traits in Korean Native Black (KNB), Rhode Island Red (RIR) and Cornish chickens. Investigation in the effect of SNPs on economic traits (layday, layw, layno, bw150, bw270, layw270) was conducted. iNOS (C14513T) had a significant effect on the average body weight at 270 days of age (p<0.05) in both KNB and RIR, whereas TLR-4 (G4409T) showed no significant correlation with all traits (p>0.05). The results obtained from using the candidate genes can be useful for the genetic improvement of body weight in both KNB and RIR breeds.

Improvement of Selection Efficiency for Bacterial Blight Resistance Using SNP Marker in Rice (SNP 마커를 이용한 벼 흰잎마름병 저항성 선발 효율 증진)

  • Shin, Woon-Chul;Baek, So-Hyeon;Seo, Chun-Sun;Kang, Hyeon-Jung;Kim, Chung-Kon;Shin, Mun-Sik;Lee, Gang-Seob;Hahn, Jang-Ho;Kim, Hyun-Soon
    • Journal of Plant Biotechnology
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    • v.33 no.4
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    • pp.309-313
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    • 2006
  • Discovery of single nucleotide polymorphisms (SNPs), including small insertions and deletions, is one of the hot topics in genetic research. The most common type of sequence variant consists of single base differences or small insertions and deletions at specific nucleotide positions. Significance of SNPs in rice is increasing for genetic research, positional cloning and molecular breeding. $F_2$ 170 lines and $F_3$ 194 lines derived from Sangjuchalbyeo/HR13721-53-3-1-3-3-2-2 Were used for Searching SNP markers related to bacterial blight resistance. Sangjuchalbyeo is susceptible to bacterial blight, but HR13721-53-3-1-3-3-2-2 has Xa1 gene resistant to bacterial blight. Individual lines were inoculated with $K_1$ race of bacterial blight and resistant or susceptible was evaluated after 3 weeks from inoculation. The genotypes of population were analysed by PCR-RFLP for SNP marker developing. The segregation of $F_2\;and\;F_3$ population showed almost 3:1, 1:1 ratio, respectively. Analysis of genotype using SNP marker is capable of confirming resistance for $K_1$ race and genotype through amplifying the gene using 16PFXal primer and digested the PCR product with Eco RV. There were close relation between resistance test for $K_1$ race and SNP marker genotype. Especially, DNA analysis using SNP marker is capable of judging homozygote/heterozygote in $F_2$ population compared with resistant test for Kl race. So, it seems to improve the selection efficiency in disease resistant breeding.

Geographic Variation of Seed Characteristics and 1-year-old Seedling Growth of Zelkova serrata (느티나무 종자특성의 지리적 변이와 1년생 유묘의 생장)

  • Kim, In Sik;Lee, Joo Hwan
    • Korean Journal of Agricultural and Forest Meteorology
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    • v.15 no.4
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    • pp.234-244
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    • 2013
  • This study was conducted to determine the factors affecting to seed characteristics and seedling growth of Zelkova serrata. The seeds were collected from sixteen populations of Z. serrata and the seed characteristics (i.e., seed length, width, weight and full seed rate) were measured. We also measured the 1-year-old seedling growth of each population at nursery. All seed characteristics showed significant differences in population level. Seed length and seed width were positively correlated with latitude, longitude, altitude and distance from coast line of sampling site. Seed length and seed width also negatively correlated with annual mean temperature, mean temperature of growing season (Mar.~Oct.). The ratio of seed length/seed width showed inverse trend in case of seed length and seed width. Seed weight/1,000 grains had no correlation with geographic factors but showed negative correlation with annual mean dryness index. Seed weight/L showed negative correlation with latitude and longitude and positive correlation with mean temperature of growing season of sampling site. Full seed rate showed negative correlation with latitude, longitude and annual mean dryness index of sampling site. There were significant differences among populations, among family within population and among individuals within family in seedling growth. Height and diameter of root collar of seedling showed negative correlation with longitude and mean humidity of growing season of sampling site. Height growth of seedlings was not correlated with any seed characteristics but, diameter at root collar showed low negative correlation with seed weight/1,000 grains and seed weight/L. We discussed the implications of the results in view of tree improvement of Z. serrata.

Single Nucleotide Polymorphisms (SNPs) Discovery in GHSR Gene and Their Association Analysis with Economic Traits in Korean Native Chickens (GHSR 유전자 내 유전변이의 탐색과 한국재래계의 성장 및 산란 특성에 미치는 연관성 분석)

  • Choi, So-Young;Hong, Min-Wook;Yang, Song-Yi;Kim, Chong-Dae;Jeong, Dong Kee;Hong, Yeong Ho;Lee, Sung-Jin
    • Korean Journal of Poultry Science
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    • v.43 no.4
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    • pp.273-279
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    • 2016
  • Recently, it was reported that certain polymorphisms in the growth hormone secretagogue receptor gene (GHSR) are associated with the growth of chickens. However, the correlation between GHSR polymorphisms and economic traits has not been investigated in Korean native chickens (KNCs). Therefore, the objective of this study was to confirm the suitability of the GHSR gene as a candidate for genomic selection and identify a genetic marker for KNCs. A total of 220 KNCs from six breeds raised at the National Institute of Animal Science were genotyped for the c.739+726 SNP in the GHSR gene using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP), and the sequence for a subset of 30 birds was analyzed using direct sequencing. The association between the SNP genotypes and the economic traits of the KNCs was analyzed using the statistical package for the social science (SPSS) software program. The association analysis between the c.739+726T>C SNP and economic traits revealed that the SNP was significantly associated with body weight at 150 and 270 days (BW150 and BW270, respectively) in all KNCs (p<0.01), BW150 in KNC (Gary) (p<0.05), and egg production number in KNC (White, p<0.05). In addition, the SNPs discovered using direct sequencing (513A>G, 517A>T) had a significant effect on the body weight and egg production traits (p<0.05). In conclusion, these results might be useful as a basis for studies on the improvement of KNC breeds. Furthermore, these results suggest that the SNPs (c.739+726T>C, 513A>G, and 517A>T) located in the GHSR gene could be useful molecular genetic markers for KNCs.