• Fisheries and Aquatic Sciences
• /
• 제16권4호
• /
• pp.303-309
• /
• 2013

Microsatellite markers are important for gene mapping and for marker-assisted selection. Sixty-five polymorphic microsatellite markers were developed with an enriched partial genomic library from olive flounder Paralichthys olivaceus an important commercial fish species in Korea. The variability of these markers was tested in 30 individuals collected from the East Sea (Korea). The number of alleles for each locus ranged from 2 to 33 (mean, 17.1). Observed and expected heterozygosity as well as polymorphism information content varied from 0.313 to 1.000 (mean, 0.788), from 0.323 to 0.977 (mean, 0.820), and from 0.277 to 0.960 (mean, 0.787), respectively. Nine loci showed significant deviation from the Hardy-Weinberg equilibrium after sequential Bonferroni correction. Analysis with MICROCHECKER suggested the presence of null alleles at five of these loci with estimated null allele frequencies of 0.126-0.285. These new microsatellite markers from genomic libraries will be useful for constructing a P. olivaceus linkage map.

• Weed & Turfgrass Science
• /
• 제2권3호
• /
• pp.230-235
• /
• 2013

Amaranths (Amaranthus sp.), an endemic American crop, are now grown widely across the world. This study used 14 simple sequence repeat (SSR) markers to analyze the genetic diversity of 74 amaranth accessions from the United States, with eight accessions from Australia as controls. One hundred twenty-two alleles, averaging eight alleles per locus, were observed. The average major allele frequency, expected heterozygosity, and polymorphism information content (PIC) were 0.44, 0.69, and 0.65, respectively. The structure analysis based on genetic distance classified 77 accessions (94%) into three clusters, while five accessions (6%) were admixtures. Among the three clusters, Cluster 3 had the highest allele number and PIC values, while Cluster 2 had the lowest. The lowest FST was between Clusters 1 and 3, indicating that these two clusters have higher gene flow between them compared to the others. This finding was reasonable because Cluster 2 included most of the Australian accessions. These results indicated satisfactory genetic diversity among U.S. amaranths. These findings can be used to design effective breeding programs involving different plant characteristics.

• Journal of Plant Biotechnology
• /
• 제46권2호
• /
• pp.61-70
• /
• 2019

There is vast genetic diversity of Myanmar Mangoes. This study mainly focused on indigenous thirteen different mango landraces cultivated in central area of Myanmar, Kyauk-se District and their fruit characteristics by 18 descriptors together with genetic relationship among them by 12 SSR markers. Based on the morpho-physical characters, a wide variation among accessions was found. Genetic characterization of thirteen mango genotypes resulted in the detection of 302 scorable polymorphic bands with an average of 4.33 alleles per locus and an average polymorphism information content (PIC) of 0.7. All the genotypes were grouped into two major clusters by UPGMA cluster analysis and a genetic similarity was observed in a range of 61 ~ 85%. This study may somehow contribute insights into the identification of regional mango diversity in Myanmar and would be useful for future mango breeding program.

• Journal of Animal Science and Technology
• /
• 제63권1호
• /
• pp.25-35
• /
• 2021

The purpose of this study is to estimate the single nucleotide polymorphism (SNP) effect for pH values affecting Berkshire meat quality. A total of 39,603 SNPs from 1,978 heads after quality control and 882 pH values were used estimate SNP effect by single step genomic best linear unbiased prediction (ssGBLUP) method. The average physical distance between adjacent SNP pairs was 61.7kbp and the number and proportion of SNPs whose minor allele frequency was below 10% were 9,573 and 24.2%, respectively. The average of observed heterozygosity and polymorphic information content was 0.32 ± 0.16 and 0.26 ± 0.11, respectively and the estimate for average linkage disequilibrium was 0.40. The heritability of pH45m and pH24h were 0.10 and 0.15 respectively. SNPs with an absolute value more than 4 standard deviations from the mean were selected as threshold markers, among the selected SNPs, protein-coding genes of pH45m and pH24h were detected in 6 and 4 SNPs, respectively. The distribution of coding genes were detected at pH45m and were detected at pH24h.

• 한국작물학회:학술대회논문집
• /
• 한국작물학회 2022년도 춘계학술대회
• /
• pp.110-110
• /
• 2022

Rice is the world's most important food crop and a major source of nutrition for about two thirds of populations. Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Most interestingly, analysis of molecular variance (AMOVA) found genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. More emphasis was given to provide signatures and infer explanations about the role of geographical isolation and environmental heterogeneity in genetic differentiation among regions in landraces from northern Vietnam. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

• 한국균학회지
• /
• 제42권2호
• /
• pp.159-164
• /
• 2014

큰느타리 품종구분을 위한 마커의 개발을 위하여 큰느타리 전체 유전자 염기서열을 바탕으로 제작한 484개의 SSR마커를 사용하여 다형성 분석을 실시하였다. 그 결과 각 275개의 primer에서 다형성이 관찰되었다. 이 중 품종간에 다양한 패턴을 나타내는 5개의 마커를 최종 선발하였다. 이들 마커의 PIC 값은 0.6627에서 0.6848로 나타났고, 평균값은 0.6775였다. 이 결과를 밴드 이미지 인식 방법으로 dendrogram을 작성하였다. UPGMA 집괴분석 결과, 큰느타리 품종은 크게 Cluster 1과 Cluster 2로 구분되었다. SSR primer를 이용한 PCR 결과 나타나는 품종별 고유의 DNA 밴드를 품종특이적 마커로 개발하기 위하여, 선발된 마커중에서 SSR312과 SSR366, SSR178과 SSR 277 마커를 조합하여 초위성체 유래 다중 표지 세트를 개발하였다. Multiplex-SSR 마커의 사용을 통해 두번의 PCR 반응만으로 본 연구에서 사용된 12개의 큰느타리 품종을 구분할 수 있었다.

• 동물자원연구
• /
• 제29권4호
• /
• pp.142-149
• /
• 2018

본 연구는 한우 보증씨수소 844두를 출생년도를 기준으로 8개 집단으로 분류하고, 각 개체들의 친자확인용 유전자 마커정보를 농협경제지주 한우개량사업소 홈페이지에서 제공 받아 유전적 다양성 및 구조 변화 분석에 활용하였다. 한우 보증씨수소 전체 집단의 대립유전자수(number of alleles)의 평균은 10.54개, 기대 및 관측 이형접합율($H_{ex}$, $H_{ob}$)의 평균은 각각 0.764, 0.773, 다형성 정보량 지수(PIC)의 평균은 0.727 그리고 $F_{is}$의 평균은 -0.014로 확인되었다. 한우 보증씨수소 집단을 출생년도 별로 구분한 8개 집단의 유전적 다양성 및 구조 분석 결과, D집단(2005-2004년)의 기대이형접합율(0.777), 관측이형접합율(0.792) 그리고 다형성정보지수(0.740)가 가장 높은 것으로 확인되었다. C집단(2003-2004년)과 E집단(2007-2008년)에서는 기대이형접합율이 관측이형접합율 보다 큰 것으로 확인되었고, 나머지 그룹 모두에서는 관측이형접합율이 기대이형접합율 보다 큰 것으로 확인되었다. 대립유전자 출현빈도를 기반으로 유전적 조성과 구조를 추론하기 위해 STRUCTURE software를 이용하여 분석한 결과 세대가 지남에 따라 특정 유전적 성분의 변화 또는 비중의 증감을 확인 할 수 있었다. 이는 개량 목표를 설정하고 지속적으로 추진되고 있는 개량 사업이 한우 씨수소 집단의 유전적 구조 변화에 영향을 미치고 있음을 확인 할 수 있는 중요한 자료로, 한우 개량 사업의 효율적인 추진을 위해 유용하게 활용 될 것으로 사료된다.

• Journal of the Korean Data and Information Science Society
• /
• 제28권5호
• /
• pp.1043-1053
• /
• 2017

본 연구는 산양 7 품종을 대상으로 (Saanen (88), Laoshan (67), Toggenburg (32), Alpine (12), Anglonubian (9), Jamnapari (7), Black Bengal (4)) 13종의 초위성체 마커 (microsatellite marker)를 활용하여 유전적 다형성 분석을 실시하였다. 대립유전자 수는 4개 (INRA005) 부터 18개 (SRCRSP23)까지 확인되었으며, 관측이형접합율 ($H_{obs}$)과 기대이형접합율 ($H_{\exp}$) 그리고 다형성 정보지수 (PIC) 값은 각각 0.482 ~ 0.786, 0.476 ~ 0.923 그리고 0.392 ~ 0.915로 나타났다. 품종별 유전적 거리를 확인하기 위하여 실시한 주성분분석 (PCoA) 결과는 요인대응분석 (FCA) 분석과 유사한 결과를 보였으며, 동일개체출현빈도는 $2.47{\times}10^{-15}$으로 확인되었다. 따라서 본 연구 결과는 산양 품종 개량 및 보존에 있어 기초자료로써 유용한 자료로 활용 가능 할 것으로 사료된다.

• 한국작물학회지
• /
• 제63권1호
• /
• pp.1-7
• /
• 2018

Information on the patterns of genetic diversity and population structure is essential for the rational use and efficient management of germplasms; accurate information aids in monitoring germplasms, and can also be used to predict potential genetic gains. In this study, we assessed genetic diversity, focusing on Korean rice accessions for theand their sustainable conserved diversity. Using DNA profiling with 12 simple sequence repeat (SSR) markers, we detected a total of 333 alleles among 2,016 accessions. The number of alleles ranged from 21 to 53, with an average of 27.8. Average polymorphism information content was 0.797, with the lowest being 0.667 and the highest 0.940. CA cluster analysis and the model-based population structure revealed two main groups that could be subdivided into five subgroups. Analysis of the molecular variance study based on the SSR profile data showed 5% variance among the profiles, whereas we recorded 93% variance among individuals and 2% variance within individuals. Specifically, the utilized diversity for of the breeding program is restricted in that cultivars were located in limited clades. These results revealed that preserving the diversity of Korean landraces could be useful sources for breeding new rice cultivars, and cwould be the basis for the sustainable conservation and utilization of a Korean rice germplasm.

• Asian-Australasian Journal of Animal Sciences
• /
• 제27권11호
• /
• pp.1548-1553
• /
• 2014

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.