Marker-Assisted Mating Applied in In-Situ Conservation of Indigenous Animals in Small Populations : (1) Choosing Mating Schemes for Maximum Heterozygosity

Wu, X.L.,Liu, R.Z.,Shi, Q.S.,Liu, X.C.,Li, X.,Wu, M.S. Asian Australasian Association of Animal Productio 2000 Animal Bioscience Vol.13 No.4

Maintaining maximum genetic variability is of critical importance with in-situ conservation of animal species in small populations. Marker-assisted mating (MAM) was suggested to achieve maximum heterozygosity in offspring populations. The aims of this research was to investigate and decide the effectiveness and promising types of MAM to achieve this goal. Analysis of variance with simulation data revealed that the heterozygosity in offspring populations was significantly determined by sire heterozygosity from mating of non-inbred parent animals, and significantly by sire heterozygosity and percent parental difference in offspring reproduced by inbred parents. Seven types of marker-assisted mating schemes were examined, in which offspring exhibited heterozygosity that was -0.01 to 7.37% below or above that from random mating of non-inbred parent animals, and 0.00 to 16.39% above that from random mating of inbred parent animals. The great increase in offspring heterozygosity was observed with mating by tandem maximizing sire heterozygosity, percent parental difference, and dam heterozygosity. Random mating resulted in fluctuation of offspring heterozygosity. These results suggested that MAM was a promising method for maintaining maximum offspring variability in in-situ conservation of animal species in small populations.

뇌수막종에 대한 분자유전학적 연구 : Loss of Heterozygosity on Chromosome 22

김종현,이승훈,박상윤,이제호 대한신경외과학회 1991 Journal of Korean neurosurgical society Vol.20 No.4

With the methods of restriction fragment length polymorphisms(RFLPS) and Southern blot, we performed a molecular genetic study in 20 cases of intracranial meningiomas. There were four cases of invasive meningiomas, two cases of recurrent meningiomas and one case of central neurofibromatsis. Comparison of the alleles detected by DNA probes in normal versus tumor DNA revealed chromosomal alteration. The following probes were used, ESR(chromosome 6q), pYNZ22. pYNH37.3(chromosome 17p). cEFD52(chromosome 17q). D22S10. IGLC2(chromosome 22q). In seventeen of 20 casess(85%), constitutional heterozygosity was observed for IGLC2 probe on chromosome 22q and loss of heterozygosity was detected in nine of 17 informative cases(53%). There was no loss of heterozygosity for other probes. Three of 4 cases of invasive meningiomas and one case of central neruofibromatosis displayed loss of heterozygosity.

뇌종양에서 17번 염색체 단완부 소실에 관한 분자유전학적 연구

백선하,김은상,김동규,정희원,김현집,조병규,한대희,이승훈,김종현 대한신경외과학회 1992 Journal of Korean neurosurgical society Vol.21 No.1

With the methods of restriction fragment length polymorphisms(RFLPs) and southern blot analysis, gene deletion of chromosome 17p in 16 cases of brain tumors, was investigated. There were 4 cases of glioblastoma multiforme, 1 case of anaplastic astrocytoma, 4 cases of low grade astrocytoma, 3 cases of oligodendroglioma, and 4 cases of meningioma. Among restriction fragment length polymorphism(RFLP) DNA located in chromosome 17p, p144D 6 and p SNZ 22 were imployed as the probes. In eight of 16 cases(50%) constitutional heterozygosity was observed for p144 D6 probe on the short arm of chromosome 17, and in nine of 16 cases(56%) for PYNZ 22.1 probe. With both probes constitutional heterozygosity was observed in thirteen of 16 cases(81%). And the loss of constitutional heterozygosity was detected in two of 14 informative cases. Although, with the malignant gliomas, including 4 cases of glioblastoma multiforme and 1 case of anaplastic astrocytoma, two of 4 informative cases showed loss of constitutional heterozygosity. None of 9 informative cases showed loss of heterozygosity with the other brain tumors(low grade astrocytoma, oligodendroglioma, and meningioma).

SNPchaser:DNA서열의 SNPs 치환 및 Heterozygosity 확인 프로그램

장진우(Jin-Woo Jang),이현철(Hyun-Chul Lee),이명훈(Myung-Hoon Lee),최연식(YeonShik Choi),추동원(Dongwon Choo),박기정(Kiejung Park),이대상(Daesang Lee) 한국생물공학회 2009 KSBB Journal Vol.24 No.4

단염기 다양성 (Single-Nucleotide Polymorphisms, SNPs) 은 핵산수준에서의 개개인의 유전 서열간의 차이를 나타내는 말로 최근 맞춤의약 분야에서 각광 받고 있다. 일반적으로 NPs존재 유무를 확인하는데 주로 사용되는 방법은 ABI automated DNA sequencer와 같은 대용량 염기서열 결정 기계에서 산출되는 결과물 파일로부터 DNA서열을 추출하여 BLAST와 같은 상동성 검색을 수행하는 것이다. 본 논문에서는 사용자로부터 참조서열, AB1파일, SNPs 존재 가능성을 가진 염기의 위치 정보를 입력 값으로 받아 해당 위치에 존재하는 염기의 SNPs 치환 및 heterozygosity 여부를 확인 할 수 있는 프로그램인 SNPchaser를 개발하였다. 특정 유전자 서열 내에서 SNPs를 보이는 염기의 위치에 대한 정보를 사용자가 알고 있는 경우, 전체 유전자 서열에 대해 SNPs유무를 조사할 필요 없이 SNPs를 보인다고 보고된 위치의 염기를 조사하여 SNPs유무를 판단하고, 해당지역의 염기의 chromatogram정보를 사용자에게 제공하는 기능을 가지고 있다. 또한 SNPchaser는 사람과 같은 2배체의 염색체를 가진 생명체에 존재 하는 SNPs지역의 염기에 대한 heterozygosity여부를 사용자가 손쉽게 판별 할 수 있도록 하였다. 본 논문에서 개발한 SNPchaser는 http://www.bioinformatics.ac.kr/SNPchaser에서 사용 가능하다. Single-nucleotide polymorphisms (SNPs) are the DNA sequences difference among the same species in the level of nucleic acids and are widely applied in clinical fields such as personalized medicine. The routine and labor-intensive methods to determine SNPs are performing the sequence homology search by using BLAST and navigating the trace of chromatogram files generated by high-throughput DNA sequencing machine by using Chromas program. In this paper, we developed SNPchaser, a web-based program for detecting SNPs substitution and heterozygosity existence, to improve the labor-intensive method in determining SNPs. NPchaser performed sequence alignment and visualized the suspected region of SNPs by using user"s reference sequence, AB1 files, and positional information of SNPs. It simultaneously provided the results of sequences alignment and chromatogram of relevant area of SNPs to user. In addition, SNPchaser can easily determine existence of heterozygosity in SNPs area. SNPchaser is freely accessible via the web site http://www.bioinformatics.ac.kr/SNPchaser and the source codes are available for academic research purpose.

Development of genic-SSR markers and genetic diversity of Indian lettuce (Lactuca indica L.) in South Korea

Bal Kumari Oliya,김문영,이석하 한국유전학회 2018 Genes & Genomics Vol.40 No.6

Indian lettuce (Lactuca indica L.) is an undomesticated wild plant with high economic potential. We know little about the plant’s genome, such as its DNA markers, making genetic research using this plant difficult. In this study, 100 genic simple sequence repeat (SSR) primers with a 99–250 bp target amplicon were synthesized from L. indica transcriptomic sequences. These primers were examined in 8 diverse L. indica accessions, and 90 polymorphic SSRs were obtained. Twenty-three of the 90 polymorphic SSRs were used to investigate transferability to another two Lactuca species, Lactuca serriola and Lactuca sativa. Genetic diversity was investigated in 77 Lactuca accessions, including 73 L. indica collected from across South Korea, 2 L. serriola, and 2 L. sativa. Our genic-SSR markers were highly polymorphic with a mean polymorphic information content of 0.61 and, on average, 10.83 alleles per locus. The average expected heterozygosity (0.76) was higher than the observed heterozygosity. An analysis of molecular variance revealed that most of the total variance in our population is attributable to genetic variation among accessions, rather than among provinces. STRU CTU RE, unweighted neighborjoining phylogenetic trees, and principal coordinate analyses resulted in three clusters, where northern and central-southern L. indica accessions were grouped into two clusters with some admixture. The L. serriola and L. sativa accessions did not produce a separate cluster due to a small sample size. These results show our SSR markers will be useful in germplasm assessment and genetic studies of L. indica and other Lactuca species.

유전 및 육종 : 초위성체 표지를 이용한 한국재래돼지 집단의 분자유전학적 고찰

연성흠 ( Seong Heum Yeon ),이승수 ( Seung Soo Lee ),조창연 ( Chang Yeon Cho ),진현주 ( Hyun Ju Jin ),유용희 ( Yong Hee Yoo ),이풍연 ( Poong Yeon Lee ),위미순 ( Mi Soon Wee ),고응규 ( Yeoung Gyu Ko ),손준규 ( Jun Kyu Son ) 한국동물자원과학회(구 한국축산학회) 2011 한국축산학회지 Vol.53 No.1

초위성체(MS) 표지를 이용하여 한국재래돼지 집단의 각각의 분자유전학적 특성을 조사하고 그 평가를 통해 한국재래돼지에 대한 품종 및 계통분류의 기초를 마련하고자 본 연구를 수행하였다. 또한, 각 재래돼지 집단 내 및 집단간의 유전적 변이성을 확인하고, 그 분류 및 특성평가를 위한 MS 분석체계를 마련하여 국내 가축유전자원 관리에 활용하고자 하였다. 국내 관리기관 및 농가에서 보유하고 있는 6개 재래돼지 집단을 중국의 4개 재래돼지 집단 및 외래종 돼지 7개 집단과 함께 분석하였다. 도합 17집단 648두를 대상으로 26개 MS 표지로 분석한 결과, 한국재래돼지 집단은 외래종과 중국재래돼지로부터 분자유전학적으로 별개의 집단으로 확연히 구분되는 것을 확인하였다. 한국재래돼지 집단의 기대이형접합도(HE)는 0.65의 값을 보인 두 집단(B, D)을 제외한 나머지에서 0.48~0.55의 수준을 보여 전반적으로 외래종에 비해 낮았다. 한국재래돼지 집단간의 유전거리 또한 0.12~0.34 정도로 비교대상에 비하여 낮았다. 분석대상 한국재래돼지 6집단 중 세 개의 집단은 높은 유전적 균일도를 보였으나, 두 집단에서는 일부 집단의 혼입을, 나머지 하나의 집단에서는 둘 이상의 집단으로부터의 복잡한 혼입이 의심되는 매우 낮은 유전적 균일도를 확인하였다. 본 연구를 통하여 한국재래돼지 집단간의 유전적 차이 및 동질성, 그리고 집단내의 유전적 균일성을 확인하였다. 이러한 결과는 국내유전자원의 고유성을 인정할 수 있는 과학적인 근거로서, 국가수준의 가축유전자원 평가, 관리의 기초자료로 활용될 수 있을 것이다. The study was conducted to select and optimize microsatellite(MS) markers for evaluation of Korean native pig(KNP) populations in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNP populations. A total of 648 pigs from 17 pig populations including six KNP, four Chinese native pig and four commercial pig populations were analyzed with 26 MS markers. KNP populations formed separate cluster from those of Chinese native pig and introduced pig populations. Expected heterozygosity(He) of KNP populations were 0.48~0.55 except two populations with 0.65. Genetic distances between KNP populations were relatively shorter: 0.12-0.34. Among six KNP populations, three showed high genetic uniformity, two showed lower uniformity and one showed high level of impurity and heterozygosity. The results can be used to evaluate and manage animal genetic resources at national scale.

Correlations between Heterozygosity at Microsatellite Loci, Mean d² and Body Weight in a Chinese Native Chicken

Liu, G.Q.,Jiang, X.P.,Wang, J.Y.,Wang, Z.Y. Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.12

A total of two hundred twenty eight half-sib chickens were scored for allele size at 20 microsatellite loci to estimate individual heterozygosity and mean $d^2$. The averages of microsatellite heterozygosity, allele per locus and mean $d^2$ were 0.39, 3.6 and 49, respectively. The body weight was measured biweekly from birth to twelve weeks of age. Gompertz function was assumed to simulate body weight and to estimate the growth model parameters. Due to sex effect on body weight, the regression of body weight on heterozygosity as well as on mean $d^2$ in males and females was analyzed separately in the present study. Positive correlations were found between microsatellite heterozygosity and body weight in males and females (p<0.05). Positive correlation also observed between individual heterozygosity and simulated maximum daily gain estimated from Gompertz function in female chickens (p<0.05). There were no significant correlations between mean $d^2$ and body weight. The results suggest that local effect hypothesis could explain the correlations between heterozygosity and fitness-related traits in the domesticated chicken population, rather than the general effect hypothesis does.

인체 뇌신경교종에서 10번, 13번, 17번 염색체 유전자소실과 p53 유전자 변이 연구

이승훈,김종현,이창훈,강영순,이재호,최길수 대한신경외과학회 1993 Journal of Korean neurosurgical society Vol.22 No.4

Gliomw the most common primary tumors of the human central nervous system. are usually malignant and virtually incurable. They can be classified according to their cellular differentiation : -ma. olig&ndroglloma and ependymoma. The majority of these brain tumors are asmcyt~mas, which typically p-ss through three histopathologically defined stages with the passage of time : one premalignant stage, low-grade astrocytoma and two malignant stages. anaplastic astrocytoma and ghoblastoma multiforme. Recent studies on the molecular mechanisms of carcinogensis have demonstrated a possible role for two classes of genes in neoplastic transformation : tumor suppressor genes and oncogenes. Tumor suppressor genes are wild-type alleles of genes that are believed to function normally in the cell to suppress cellular proliferation. Inactivation of both copies of suppressor gene may contribute to neoplastic transformation by removing a normal constraint to cell growth. The well characterised suppressor genes are RB gene and p53 gene. Gliomas, like most other cancers. are associated with several genetic changes including oncogenes and suppressor genes. In an attempt to hrther our knowledge of tumor suppressor genes contributing ghoma development and progression, restriction fragment length polymorphism(RnP) analysis was done to determine loss of heterozygosity(L0H) on chromosome 10. 13q(RE!I). 17p. and 22q containing putative tumor suppressor genes in 36 cases of human gliomas with various malignancy grades. And to detect p53 gene mutations at exon 5. 6. and 7 in 23 cases of malignant gliomas. polymerase chain reaction-single strand conformation polymorphisms(PCR-SSCP) analysis was performed. Loss of heterozygosity for loci on chromosome 10 were found in four of 5(60% ) informative cases of glioblastoma multiforme and one of 2 6 0 % ) cases of anaplastic astrocytomas. Loss of heterozygosity on chromosome 17p was found in eight of 17(47%) informative cases of malignant gliomas including 2 cases of anaplastic oligodendroglioma. There was no allelic loss of chromosome 10 and 17 in benign gliomas. Deletions on RBI locus were seen in six of 10(60%) informative cases of glioblastoma multifonne and two of 5(40%) informative cases of low-grade astrocytomas. suggesting that RBI gene may have a role associated with the early events in tumorigenesis. In PCR-SSCP analysis six of 23(26%) cases of malignant gliomas including one case of anaplastic oligodendroghoma showed mobility shifts on exon 5 or 7 of p53 gene which suggest point mutations of this gene. There was no LOH at IGLC2 locus on chromosome 22. On the basis of the data presented here, it is possible to associate certain molecular abnormalities with gliomas of increasing grades of malignancy. deletion of RB gene, loss of heterozygosity on chromosome 17p. p53 gene mutation and loss of allele on chromosome 10.

Insignificant effects of loss of heterozygosity in HLA in the efficacy of immune checkpoint blockade treatment

Yang Yohan,Kim Eunyoung,Kim Sangwoo 한국유전학회 2022 Genes & Genomics Vol.44 No.4

Background: It is assumed that loss of heterozygosity and allelic copy loss in HLA gene is associated with poor response rates in immune checkpoint inhibitor treatment. H-owever, the accurate extents or consistency in cancer types have not been explored. Objective: The goal of this study is to investigate quantitative relationship between HLA allelic copy loss and response rates to immune checkpoint inhibitors. Also, tumor microenvironment was computationally assessed in the tumors with HLA copy loss to provide potential mechanisms for the relationships. Method: A total of 282 whole exome sequencing data from three cohorts of patients who received immune checkpoint blockade immunotherapy were analyzed, including Anti-PDL1 treated in metastatic urothelial cancer (N = 216), anti-PD1 treated metastatic melanoma (N = 26), and anti-CTLA4 treated metastatic melanoma (N = 39). The LOHHLA algorithm was used to calculate allelic copy number loss at each HLA-A, -B, and -C locus, and further determine HLA allelic copy loss status. The HLA copy status and ICB response rates were analyzed for association using Fisher's exact test. The CIBERSORT-absolute algorithm was then used to analyze the patient's immune environment, which represented loss of heterozygosity, using paired matched RNA sequencing data. Results: Unlike the general expectation, HLA allelic copy loss was not significantly associated with the ICB responses. Moreover, the relationship showed a reversed relationship in HLA-A in the urothelial cancer (better ICB response in HLA copy loss). Regardless of the HLA copy status, the proportion of cytotoxic immune cells in the immune environment of patients was correlated with ICB response, which was higher in the loss of heterozygosity group in the urothelial cohort. Conclusion: Although the loss of heterozygosity in HLA was generally expected to be an inhibitory factor in the immune treatment response by causing T cell immune evasion, our analysis demonstrates no explicit relationships.

Genomic Polymorphism Analysis using Microsatellite Markers in Gyeongju Donggyeong Dogs

Kim, Seung-Chang,Kim, Lee-Kyung,Choi, Seog-Kyu,Park, Chang-Min,Park, Sun-Ae,Cho, Yong-Min,Lim, Dajeong,Chai, Han-Ha,Lee, Seung-Hwan,Lee, Ji-Woong,Sun, Sang-Soo,Choi, Bong-Hwan The Korean Society of Animal Reproduction 2012 Reproductive & developmental biology Vol.36 No.4

This study was conducted to find a useful marker for gene polymorphism analysis using Microsatellite marker (MS marker) in Gyeongju Donggyeong dog. Twenty three MS marker analyzed the genetic features of DNA using 100 Gyeongju Donggyeong dogs in Gyeongju area. It was performed multiplex PCR with 3 set primer divided 9, 10 and 4 by analysis of conditions among MS markers. The results were calculated heterozygosity, polymorphic information content (PIC), allele frequency and number of allele at each locus using Microsatellite Toolkit software and Cervus 3.0 program. Total 148 alleles were genotyped to determine and average 6.43 alleles was detected. FH3381 had the highest of 15 alleles and FH2834 had the lowest of 2 alleles. Expected heterozygosity had a wide range from 0.282 to 0.876 and had average value of 0.6496. Also, Observed heterozygosity had a more wide range from 0.200 to 0.950 and had average value of 0.6404. PIC had range from 0.262 to 0.859 and average PIC was calculated 0.606. Especially, FH2998 represented the highest rate of observed heterozygosity of 0.950 and FH3381 represented the highest rate of expected heterozygosity of 0.876 and PIC of 0.859. The use of these markers was considered to be useful to study genetic traits of Gyeongju Donggyeong dog.