• 한국육종학회지
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• 제40권3호
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• pp.250-257
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• 2008

Knowledge of genetic diversity and of the genetic relationships among elite breeding materials has had a significant impact on the improvement of crops. In maize, this information is particularly useful in i) planning crosses for hybrid and line development, ii) in assigning lines to heterotic groups and iii) in plant variety protection. We have used the SSR technique to study the genetic diversity and genetic relationships among 76 Korean waxy corn accessions, representing a diverse collection from throughout Korea. Assessment of genetic diversity among members of this group was conducted using 30 microsatellite markers. Among these 30 microsatellite markers, we identified a total of 127 alleles (with an average of 4.2 and a range of between 2 and 9 alleles per locus). Gene diversity at these 30 microsatellite loci varied from 0.125 to 0.795 with an average of 0.507. The cluster tree generated with the described microsatellite markers recognized two major groups with 36.5% genetic similarity. Group I includes 63 inbred lines, with similarity coefficients of between 0.365 and 0.99. Group II includes 13 inbred lines, with similarity coefficients of between 0.45 and 0.85. The present study indicates that the 30 microsatellite loci chosen for this analysis are effective molecular markers for the assessment of genetic diversity and genetic relationships between Korean waxy corn accessions. Specifically, this study's assessment of genetic diversity and relationships between a set of 76 Korean waxy corn inbred lines will be helpful for such activities as planning crosses for hybrid and line development and association mapping analyses of maize breeding programs in Korea.

• Journal of Animal Science and Technology
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• 제54권6호
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• pp.401-409
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• 2012

The objective of this study was to determine genetic variation of five Korean native chicken lines using 30 microsatellite (MS) markers, which were previously recommended by ISAG (International Society for Animal Genetics). The initial study indicated that two microsatellite markers, MCW0284 and LEI0192, were not amplified in these lines and excluded for further analysis. Twenty eight microsatellite markers were investigated in 83 birds from five Korean native chicken lines. The identified mean number of alleles was 4.57. Also, the expected, observed heterozygosity (He, Ho) and polymorphism information content (PIC) values were estimated in these markers and they ranged from 0.31~0.868, 0.145~0.699, and 0.268~0.847, respectively. The results were used for the discrimination of five chicken lines using genetic distance values and also neighbor-joining phylogenetic tree was constructed. Based on the He and PIC values, eighteen markers are enough for the discrimination of these Korean native chicken lines for the expected probability of identity values among genotypes of random individuals (PI), random half sibs ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$). Taken together, these results will help the decision of conservation strategies and establishment of traceability system in this native chicken breed. Also, the use of ISAG-recommended microsatellite markers may indicate that the global comparison with other chicken breeds is possible.

• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1355-1359
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• 2004

Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree nformation. Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree information.

• Asian-Australasian Journal of Animal Sciences
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• 제20권1호
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• pp.25-30
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• 2007

The capability of microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in two Indian horse breeds. The strength of these individual assignment methods was also evaluated by increasing the number of loci in increments of five. The probability of identity of two random horses from the two breeds at all twenty five studied loci was as low as $1.08{\times}10^{-32}$ showing their suitability to distinguish between individual horses and their products. In the phylogenetic approach for individual assignment using Nei's genetic distances, 10.81% of horses associated with breed other than the major cluster of the source breed horses when all twenty five microsatellite loci were implemented. Similar results were obtained when the maximum likelihood approach for individual assignment was used. Based on these results it is proposed that, although microsatellite markers may prove very useful for individual identification, their utility for breed assignment of horses needs further evaluation.

• 대한수의학회지
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• 제47권4호
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• pp.457-460
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• 2007

The objective of the study was to establish routine parentage testing system in Beagle dogs using 22 ISAG (International Society for Animal Genetics) canine microsatellite markers (2005). Blood collections were obtained from a mother dog, 4 candidate father dogs and 3 offspring (n = 8). Genomic DNA samples were extracted from 8 Beagle dogs blood for PCR analysis. PCR products for the allele were analyzed by ABI 3130 DNA Sequencer and GeneScan (Ver 3.0) analysis and Genotyper (Ver. 2.1) software. The genetic relationship of mother and 3 offspring as well as one father dog among 4 candidate father dogs was confirmed by microsatellite allele analysis. The results of locus for amelogenin, which was designed for sexing, were matching with real gender among 8 Beagle dogs (female; 217/217 homozygosity, male; 179/217 heterozygosity). Twenty two ISAG microsatellite markers are useful the parentage test of Beagle dogs. In addition, amelogenin is an applicable marker to detecting real sex in dogs.

• Communications for Statistical Applications and Methods
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• 제13권3호
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• pp.525-535
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• 2006

We describe tests for detecting and locating quantitative traits loci (QTL) for traits in Hanwoo. Lod scores and a permutation test have been described. From results of a permutation test to detect QTL, we select major DNA markers of ILSTS098 microsatellite locus in Hanwoo chromosome 2 for further analysis. K-means clustering analysis applied to four traits and eight DNA markers in ILSTS098 resulted in three cluster groups. We conclude that the major DNA markers of BMS1167 microsatellite locus in Hanwoo chromosome 2 are markers 105bp, 113bp and 115bp. Finally, bootstrap testing method has been adapted to calculate confidence intervals and for finding major DNA Markers.

• Communications for Statistical Applications and Methods
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• 제13권3호
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• pp.733-743
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• 2006

To apply and evaluate the effectiveness of genetic markers on Hanwoo traceability systems, samples of 33 Hanwoo individuals from Korean elite sire families were used, and five microsatellite markers were selected finally, which were located on chromosomes different chromosomes with the end sequencing of 100 HW-YUBAC that were recorded in the NCBI by Yeungnam University. Ten major microsatellite markers were selected from alleles amplified, their frequencies, H(Heterozygosity) and PIC(Polymorphism information content) with Hardy-Weinberg equilibrium. Next, in order to evaluate the power of the markers selected on the individual animal identification, the match probability(MP) and the relatedness coefficient(R) were computed.

• 한국양식학회지
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• 제18권2호
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• pp.130-132
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• 2005

Genomics research has two ultimate applied goals: to Isolate and clone genes of economic importance for bio-technology and gene-assisted selection (GAS), and to locate and use markers for marker-assisted selection (MAS) in selective breeding programs. To this end, we have identified linked markers for feed conversion efficiency growth rate, and disease resistance to enteric septicemia of catfish (ESC). Three microsatellite markers Ip266, Ip384, and Ip607 were identified to be linked to feed conversion efficiency. Similarly one marker each was identified to be linked to growth rate (Ip607) and disease resistance to ESC (Ip477). Ip607 marker linked to both growth rate and feed conversion efficiency, indicating that the QTL for both growth rate and feed conversion efficiency may either be the same or located in the same chromosomal region in the catfish genome. On phenotypic evaluation, certain traits such as growth rate can be accurately evaluated by body weight evaluation while other traits such as disease resistance can be quite complex. The linked DNA markers will be highly useful for MAS programs and for directing further efforts of genomic mapping for important quantitative traits.

• 생명과학회지
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• 제33권8호
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• pp.623-631
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• 2023

본 연구는 차세대 염기서열 분석법(NGS)을 사용하여 벤자리의 microsatellite 마커를 개발하고, 개발한 마커를 사용하여 벤자리 집단의 유전학적 특성을 분석하기 위해 수행되었다. 차세대 염기서열 분석 장비인 Illumina Hiseq X ten을 사용하여 총 402,244,934개의 read들을 얻어 assembly를 실행한 결과, 전체의 약 0.33%에 해당하는 1,320,995개의 read들이 assembly 되었으며, 이 read들의 총 길이는 705,613,658 bp로 확인되었다. 크기가 640 bp 이상이 되는 contig는 952,326개로 나타났으며, 이 중 microsatellite 영역을 포함하는 contig를 151개(0.016%)로 1차 선별하고, PCR 증폭 여부를 통해 microsatellite 후보 34개를 2차로 선별하였다. 그 중 벤자리 집단의 마커로서 유용한 15개의 microsatellite 마커를 최종 선택하였다. 새로 개발한 15개의 microsatellite 마커를 사용하여 벤자리 집단을 대상으로 분석한 결과, 관찰된 유효 대립유전자 수(N_A)는 평균 12(6~25)로 나타났다. 평균 관측치 이형접합도(H_O)와 평균 기대치 이형접합도(H_E)는 각각 0.750(0.530-0.873)와 0.793 (0.647-0.895)으로 나타냈으며, 이는 해산어의 평균 값인 0.79와 유사한 수치를 나타내었다. 따라서 본 연구에서 개발한 15개의 microsatellite 마커는 벤자리 집단의 유전학적 특성 분석에 유용할 것으로 사료된다.

• 한국어병학회지
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• 제34권1호
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• pp.9-15
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• 2021

Rock bream (Oplegnathus fasciatus) is a highly valued aquaculture species in Korea. However, the aquaculture industry suffers huge economic losses due to rock bream iridovirus (RBIV) infection in summer. The objective of this study was to determine genetic diversity and relationships of DNAs isolated from two groups of rock bream after RBIV infection using five microsatellite (MS) markers. The first group of fish died early and the second group of fish died later after RBIV infection. In this experiment, 90 fish (5.1±1.0 cm and 4.1±1.3 g) were injected with 50 μl of RBIV (10⁴ TCID⁵⁰/ml) and maintained at 26℃ for 15 days. Genomic DNAs were extracted from fins of 20 fish that died earlier or later after RBIV infection. These DNAs were subjected to genotyping using five MS markers (CA-03, CA3-05, CA3-06, CA-10, and CA3-36). Of these markers, CA3-05 (early death group), CA3-06 (late death group), and CA3-36 (both early and late death groups) showed different alleles distribution rates. In-depth studies are needed to provide valuable information for selecting RBIV-resistant fish. In conclusion, microsatellite marker distribution pattern differences between early- and late- death groups of rock bream after RBIV infection showing different RBIV susceptibilities were determined using MS markers and genotyping. Results of this study suggest that MS markers could be used to facilitate the selection of RBIV resistant rock bream.