AFLP Marker를 이용한 한국 재래돼지의 유전적 다양성 및 품종식별

정의룡,김우태,김연수,이정구,한상기 한국동물자원과학회 2001 한국축산학회지 Vol.43 No.6

본 연구는 한국재래돼지의 순수 혈통정립 및 유전자원 보존을 목적으로 AFLP 다형성을 분석하고 이를 유전적 표지인자로 이용하여 재래돼지의 유전적 특성을 분자 수준에서 규명하고 품종 집단내 유전적 변이성과 품종 특이적인 DNA marker를 탐색하며 동시에 타품종들과의 유전적 근연관계를 추정하기 위해 수행하였다. 13종류의 selective primer 조합형을 이용하여 분석한 결과 총 band의 수는 611개로 각 조합형 당 평균 47개의 band가 확인되었으며 이 가운데 다형적 band가 152개로 다형성 수준은 약24.5%였다. 한국 재래돼지의 다형율과 유전적 다양성 값은 각각 29.8%와 2.9로 개량종에 비해서 다소 높은 경향이었다. 한편, 13종류의 primer 조합형 가운데 E35/T38 및 E38/H13 primer 조합형에서 품종간의 차이를 나타내는 DNA marker가 확인되었다. 특히, 재래돼지에서 검출된 E35/T38 primer 조합형의 0.50kb, 0.25kb 및 0.38kb의 DNA band는 개량종과 명확히 구별되어 이들 품종 특이적 DNA band는 한국 재래돼지의 품종식별에 유용한 표지인자로 이용 가능할 것으로 기대된다. 품종간 유전적 근연관계에서 한국 재래돼지는 Hampshire종과 유전적 유사성이 가장 높은 것으로 추정되었다. 본 연구에서 검출한 한국 재래돼지의 AFLP 유전자 지문은 재래돼지 집단의 유전적 변이성 및 타 품종과의 근연관계 분석뿐만 아니라 경제형질과 연관된 marker 개발에 유용한 DNA 표지인자로 활용할 수 있을 것으로 기대된다. For the purpose of genetic conversation and utilization of Korean native pig(KNP) as a valuable animal genetic resource, DNA polymorphisms of AFLP (amplified fragment length polymorphisms) as genetic markers were analyzed in KNP and foreign pig breeds (Landrace, Duroc, Hamphsire and Yorkshire). Using these AFLP markers, the genetic structure and characteristics of KNP population were analyzed at the DNA level and the genetic variability and diversity within and between breed population were evaluated. Breed-specific DNA marker for KNP was screened, and phylogenetic relationship within and among breeds were estimated. A total of 611 AFLP markers were amplified by 13 selective primer combinations, and the average number of bands per primer combination was 47.0. Among them 152 bands were polymorphic (24.5%). The rate of polymorphisms and genetic diversity values of KNP (29.8% and 2.90) was higher than these of other foregin breeds. E35/T38 and E38/H13 primer combinations produced AFLP banding patterns which clearly discriminated between KNP and other foreign pig breeds. Three bands(0.50kb, 0.25kb and 0.20kb) identified in E35/T38 and two bands(0.45kb and 0.38kb) identified in E38/H13 primer combinations were present in all of the KNP examined, but not present in the foreign pig breeds. Therefore, these two primer combinations could be used as breed-specific DNA markers for breed identification of KNP. In comparison of genetic distances among pig breeds, KNP was the most closely related to the Hampshire breed. AFLP fingerprints may be useful for genetic variability and relationships and development of breed-specific DNA markers in pig breeds.

Distribution of MITE Transposons in a Rice Genetic Map

박경철,이주경,권순재,신지현,이점호,양찬인,김남수 한국육종학회 2004 한국육종학회지 Vol.36 No.2

Molecular genetic markers have wide applicability for a various genetic analyses, and genetic mapping with PCR-based markers has identified many loci in the rice genome. This study was conducted to develop a genetic map of rice based on SSR and MITE-AFLP markers. The F2 mapping population was established from a cross between Oryza sativa var. Ilpoombyeo (Japonica type variety) and O. rufipogon W259. A total of 334 markers, including 54 SSR and 280 MITE-AFLP markers, were mapped on rice chromosomes using an F2 population. Of these, 280 markers, including 226 MITE-AFLP and 54 SSR markers were found to be genetically linked to form 12 linkage groups. The size of framework map spanned 2899.7 cM of the 12 linkage groups. The average linkage distance between markers among all linkage groups was 10.4 cM. The number of markers per linkage group ranged from 15 to 37. Most of MITE-AFLP markers were well distributed through the twelve rice chromosomes. In this study, we have exploited the MITE-AFLP markers to develop a new class of molecular markers for rice genome study. These new markers are expected to provide valuable resources for map-based studies, such as marker-assisted selection, gene tagging, and the analysis of quantitative trait loci (QTLs) in rice genome research program.

Identification and Monitoring of Lactobacillus delbrueckii Subspecies Using Pangenomic-Based Novel Genetic Markers

( Eiseul Kim ),( Eun-ji Cho ),( Seung-min Yang ),( Hae-yeong Kim ) 한국미생물생명공학회(구 한국산업미생물학회) 2021 Journal of microbiology and biotechnology Vol.31 No.2

Genetic markers currently used for the discrimination of Lactobacillus delbrueckii subspecies have low efficiency for identification at subspecies level. Therefore, our objective in this study was to select novel genetic markers for accurate identification and discrimination of six L. delbrueckii subspecies based on pangenome analysis. We evaluated L. delbrueckii genomes to avoid making incorrect conclusions in the process of selecting genetic markers due to mislabeled genomes. Genome analysis showed that two genomes of L. delbrueckii subspecies deposited at NCBI were misidentified. Based on these results, subspecies-specific genetic markers were selected by comparing the core and pangenomes. Genetic markers were confirmed to be specific for 59,196,562 genome sequences via in silico analysis. They were found in all strains of the same subspecies, but not in other subspecies or bacterial strains. These genetic markers also could be used to accurately identify genomes at the subspecies level for genomes known at the species level. A real-time PCR method for detecting three main subspecies (L. delbrueckii subsp. delbrueckii, lactis, and bulgaricus) was developed to cost-effectively identify them using genetic markers. Results showed 100% specificity for each subspecies. These genetic markers could differentiate each subspecies from 44 other lactic acid bacteria. This real-time PCR method was then applied to monitor 26 probiotics and dairy products. It was also used to identify 64 unknown strains isolated from raw milk samples and dairy products. Results confirmed that unknown isolates and subspecies contained in the product could be accurately identified using this real-time PCR method.

Microsatellite DNA를 이용한 말 집단의 유전적 특성 및 유연 관계

조길재,Cho, Gil-Jae 한국생명과학회 2007 생명과학회지 Vol.17 No.5

말 6개 품종 192두를 대상으로 17개의 microsatellite DNA marker를 이용하여 유전자(DNA)형을 분석하여 비교한 결과 제주마에서 각 marker별로 대립유전자의 수는 5-10개(평균 7.35개)로 분포하였고 제주마에서 관찰된 대립유전자는 총 125개가 관찰되어 평균 좌위 당 7.35개로서 몽고마의 130개(평균 7.65개)보다는 낮은 수치였다. 또한 AHT5 marker에서 대립유전자 P, ASB23 marker에서 대립유전자 Q와 R, CA425 marker에서 대립유전자 H, HMS3 marker에서 대립유전자 S, HTG10 marker에서 대립유전자 J, LEX3 marker에서 대립유전자 J 등 6개 marker에서 7개의 특이 대립유전자가 관찰되었다. 관찰된 이형접합성(observed heterozygosity)과 기대된 이형접합성(expected heterozygosity)은 각각 0.429-0.905(평균 0.703)와 0.387-0.841(평균 0.702)로 관찰되었고 다량정보량(PIC)은 0.354(HTG6)-0.816(LEX3)로서 평균 0.659로 나타났으며 17개 marker중 AHT4, AHT5, CA425, HMS2, HMS3, HTG10, LEX3, VHL20 marker 등이 다량정보량(PIC) 0.7 이상을 나타내었다. 17개 marker에 대한 전체 부권부정율(친부마 혹은 친모마 하나의 유전자형을 알고 있을 경우)을 제주마에 적용 시 99.99%로 나타났다. 말 6개 품종별로 분석하였을 때 평균 대립유전자의 수는 7.64개(몽고마)-4.23개(미니츄어 말)로 분포하였고 17개 marker 전체에서는 153개의 대립유전자가 검출되었다. 품종별로 분석한 결과 기대된 이형접합성(expected heterozygosity)과 관찰된 이형접합성(observed heterozygosity)은 각각 0.7950$\pm$0.0141(몽고마)-0.6751$\pm$0.0378(미니츄어 말), 0.7135$\pm$0.0180(제주경주마)-0.5621$\pm$0.0401(미니츄어 말)로 나타났다. 말 6개 품종을 17개 microsatellite marker로 분석한 결과 몽고마, 제주마, 제주경주마 등의 순으로 높은 유전적 다양성을 보였다. 제주마와 가장 가까운 유전적 유연 관계를 나타낸 집단은 몽고마로서 Da genetic distance에서 0.1517로 나타났고, 제주경주마와는 0.2628의 유전적 거리를 보였다. The present study was conducted to investigate the genetic characteristic and to establish the parentage verification system of the Korean native horse(KNH). A total number of 192 horses from six horse breeds including the KNH were genotyped using 17 microsatellite loci. This method consisted of multiplexing PCR procedure. The number of alleles per locus varied from 5 to 10 with a mean value of 7.35 in KNH. The expected heterozygosity and observed heterozygosity were ranged from 0.387 to 0.841(mean 0.702) and from 0.429 to 0.905(mean 0.703), respectively. The total exclusion probability of 17 microsatellite loci was 0.9999. Of the 17 markers, AHT4, AHT5, CA425, HMS2, HMS3, HTG10, LEX3 and VHL20 marker have relatively high PIC value(>0.7). This study found that there were specific alleles, P allele at AHT5, Q allele and R allele at ASB23, H allele at CA425, S allele at HMS3, J allele at HTG10 and J allele at LEX3 marker in KNH when compared with other horse populations. Also, the results showed two distinct clusters: the Korean native horse cluster(Korean native horse, Mongolian horse), and the European cluster(Jeju racing horse, Thoroughbred horse). These results present basic information for detecting the genetic markers of the KNH, and has high potential for parentage verification and individual identification of the KNH.

A Genetic Linkage Map of Soybean with RFLP, RAPD, SSR and Morphological Markers

Hong-Sik Kim,Suk-Ha Lee,Yeong-Ho Lee 韓國作物學會 2000 Korean journal of crop science Vol.45 No.2

The objective of this study was to develop a linkage map of soybean under the genetic background of Korean soybean. A set of 89 F/sub 5/ lines was developed from a cross between 'Pureunkong', which was released for soy-bean sprout, and 'Jinpumkong 2', which had no beany taste in seed due to lack of lipoxygenase 1, 2, and 3. A linkage map was constructed for this population with a set of 113 genetic markers including 7 restriction fragment length polymorphism (RFLP) markers, 79 randomly amplified polymorphic DNA (RAPD) markers, 24 simple sequence repeat(SSR) markers, and 3 morphological markers. The map defined approximately 807.4 cM of the soybean genome comprising 25 linkage groups with 98 polymorphic markers. Fifteen markers remained unlinked. Seventeen linkage groups identified here could be assigned to the respective 13 linkage groups in the USDA soybean genetic map. RFLP and SSR markers segregated at only single genetic loci. Fourteen of the 25 linkage groups contained at least one SSR marker locus. Map positions of most of the SSR loci and their linkages with RFLP markers were consistent with previous reports of the USDA soybean linkage groups. For RAPD, banding patterns of 13 decamer primers showed independent segregations at two or more marker loci for each primer. Only the segregation at op Y07 locus was expressed with codominant manner among all RAPD loci. As the soybean genetic map in our study is more updated, molecular approaches of agronomically important genes would be useful to improve Korean soybean improvement.

A Genetic Linkage Map of Soybean with RFLP, RAPD, SSR and Morphological Markers

Kim, Hong-Sik,Lee, Suk-Ha,Lee, Yeong-Ho The Korean Society of Crop Science 2000 Korean journal of crop science Vol.45 No.2

The objective of this study was to develop a linkage map of soybean under the genetic background of Korean soybean. A set of 89 F/sub 5/ lines was developed from a cross between 'Pureunkong', which was released for soy-bean sprout, and 'Jinpumkong 2', which had no beany taste in seed due to lack of lipoxygenase 1, 2, and 3. A linkage map was constructed for this population with a set of 113 genetic markers including 7 restriction fragment length polymorphism (RFLP) markers, 79 randomly amplified polymorphic DNA (RAPD) markers, 24 simple sequence repeat(SSR) markers, and 3 morphological markers. The map defined approximately 807.4 cM of the soybean genome comprising 25 linkage groups with 98 polymorphic markers. Fifteen markers remained unlinked. Seventeen linkage groups identified here could be assigned to the respective 13 linkage groups in the USDA soybean genetic map. RFLP and SSR markers segregated at only single genetic loci. Fourteen of the 25 linkage groups contained at least one SSR marker locus. Map positions of most of the SSR loci and their linkages with RFLP markers were consistent with previous reports of the USDA soybean linkage groups. For RAPD, banding patterns of 13 decamer primers showed independent segregations at two or more marker loci for each primer. Only the segregation at op Y07 locus was expressed with codominant manner among all RAPD loci. As the soybean genetic map in our study is more updated, molecular approaches of agronomically important genes would be useful to improve Korean soybean improvement.

Uncovering microsatellite markers associated with agronomic traits of South Sudan landrace maize

Mathiang Emmanuel Andrea,Park Hyeon,Jang So Jung,Cho Jungeun,Heo Tae Hyeon,Lee Ju Kyong 한국유전학회 2023 Genes & Genomics Vol.45 No.12

Background Maize has great importance in South Sudan as the most cultivated cereal after sorghum; however, numerous challenges are encountered in its production. To raise maize production, it is critical to exploit the wealth of its genetic variation for grain yield enhancement. Objective This study aimed to conduct association analysis to identify specific simple sequence repeat (SSR) markers associated with quantitative agronomic traits. Methods Genetic variation and population structure were investigated among 31 maize accessions by association analysis using 50 SSR markers and seven quantitative agronomic traits. Results The genotypes exhibited abundant genetic variation, and 418 alleles were detected with an average of 8.4 alleles per locus. The average genetic diversity, major allele frequency, and polymorphic information content were 0.754, 0.373, and 0.725, respectively. The population structure based on 50 SSR markers divided the maize accessions into two main groups and an admixed group without considering their descent. Association analysis was performed using a general linear model (Q GLM) and a mixed linear model (Q + K MLM). Q GLM detected 44 trait-marker associations involving 23 SSR markers. Q + K MLM detected four marker-trait associations involving three SSR markers (umc2286, umc1303, umc1429) associated with days to tasseling, days to silking, leaf length, and leaf width. Conclusions The detected significant SSR markers related to agronomic traits could be useful for future genetic studies. Additionally, markers affecting several agronomic traits and overlapped SSR markers require further testing on a wide range of genotypes prior to their consideration as candidate markers for marker assisted selection for South Sudan maize improvement.

Population Genetic Studies on Indigenous Conifers in Korea

이석우,홍용표,권해연,김진수 한국산림과학회 2006 Forest Science And Technology Vol.2 No.2

Studies on the genetic variation in tree populations have been greatly facilitated by the development of molecular markers. Allozyme and DNA markers have been employed to estimate the level of genetic diversity and characterize the distribution patterns of genetic variation within and among populations. They have also been applied to examine the dispersal patterns and mating systems influencing the degree of population differentiation. We reviewed 18 population genetic studies on 8 native Korean conifers (Pinus densiflora, P. thunbergii, P. koraiensis, P. pumila, Abies holophylla, A. koreana, Taxus cuspidata, and Torreya nucifera), which appeared in the literature between 1992 and 2005. The level and distribution patterns of genetic variation observed in the 8 conifers were comparable with those reported in studies on other conifers. From studies on allozyme markers, the expected heterozygosity ranged from 0.168 to 0.262 for Taxus cuspidata and Pinus densiflora, and the degree of genetic differentiation between populations (GST) ranged from 0.031 to 0.067 for Pinus densiflora and Taxus cuspidata, respectively. From studies on the DNA markers of I-SSR, the genetic diversity (Shannon’s Index) ranged from 0.306 to 0.478 for Pinus koraiensis and Taxus cuspidata, respectively, and most of genetic variations were allocated within populations with ΦST values (i.e., degree of population differentiation) ranging from 0.066 to 0.198 for Pinus densiflora and Abies holophylla, respectively. Although the multilocus outcrossing rate (tm) of Pinus densiflora was 0.860, based on allozymes, suggesting a high level of outcrossing, highly correlated outcrossed paternity (rp=0.874) and evidence of biparental inbreeding (tm–ts=0.115) were also verified. A study on the spatial autocorrelation of a scattered Korean pine (Pinus koraiensis) stand with relatively low density revealed a significant spatial genetic structure at distances between 24 and 32 m. At the allozyme level, the species with limited distributions tended to show less genetic diversity, but a higher level of genetic differentiation (GST). For DNA markers, this tendency was not marked.

EST로부터 개발된 SSR 마커를 이용한 상추 유전자원 및 유통품종의 식별

홍지화(Jee-Hwa Hong),권용삼(Yong-Sham Kwon),최근진(Keun-Jin Choi),Raghvendra Kumar Mishra,김두환(Doo Hwan Kim) 한국원예학회 2013 원예과학기술지 Vol.31 No.6

본 연구의 목적은 상추(Lactuca sativa)의 expressed sequence tag(EST)로부터 simple sequence repeat(SSR) 마커를 개발하고, 개발된 EST-SSR 마커를 이용하여 상추의 3가지 야생종의 유전자원 9점과 61개의 유통품종을 식별하는 것이다. NCBI 데이터베이스로부터 총 81,330개의 상추 EST를 대상으로 SSR을 탐색하였고, 총 4,229개의 SSR을 발견하였다. SSR의 반복 motif 중 trinucleotide(59.12%, 2,500개)가 가장 많았고, 그 다음으로 dinucleotide(29.70%, 1,256개), hexanucleotide(6.62%, 280개) 순의 분포를 나타내었다. EST로부터 총 474개의 EST-SSR primers를 개발하였고, 이 중 267개의 primer를 9점의 유전자원과 61품종에 대한 유전적 다양성 평가에 활용하였다. 267개의 마커 중 47개의 EST-SSR 마커가 7개 품종 내에서 다형성을 보였으며, 이 중 다형성 정도와 반복 재현성 및 밴드의 선명성을 고려하여 26개의 EST-SSR 마커를 선발하였다. 최종 선발된 26개의 SSR 마커를 이용하여 70개 공시재료를 분석한 결과 대립유전자 수는 총 127개였으며, 최소 2개에서 9개의 분포를 나타내었으며 마커당 평균 대립유전자 수는 4.88개를 나타내었다. PIC 평균값은 0.542로 나타났으며, 0.269-0.768의 범위를 나타내었다. 70개 공시재료의 유전적 거리는 0.05-0.94로 나타났으며, 유사도 지수 0.34를 기준으로 할 때 7개의 주요 그룹으로 나누어졌다. 26개의 EST-SSR 마커를 이용한 유전적 다양성 분석 결과 9점의 유전자원과 61개의 유통품종이 마커의 유전자형에 의해 모두 식별이 되었다. 본 연구를 통해 신규 개발된 EST-SSR 마커는 상추의 품종식별과 구별성, 균일성, 안정성 검정에 유용하게 활용될 수 있을 것으로 사료된다. The objective of this study was to develop simple sequence repeat (SSR) markers from expressed sequence tags (EST) of lettuce (Lactuca sativa) and identify 9 germplasms from 3 wild species of lettuce and 61 commercial cultivars using the developed EST-SSR markers. A total of 81,330 lettuce ESTs from NCBI databases were used to search for SSR and 4,229 SSR loci were identified. The highest proportion (59.12%, 2500) was represented by trinucleotide, followed by dinucleotide (29.70%, 1256) and hexanucleotide (6.62%, 280) among SSR repeat motifs. Totally 474 EST-SSR primers were developed from EST and a random set of 267 primers was used to assess the genetic diversity among 9 germplasms and 61 cultivars. Out of 267 primers, 47 EST-SSR markers showed polymorphism between 7 cultivars. Twenty-six EST-SSR markers among 47 EST-SSR markers showed high polymorphism, reproducibility, and band clearance. The relationship between 26 markers genotypes and 70 accessions was analyzed. Totally 127 polymorphic amplified fragments were obtained by 26 EST-SSR markers and two to nine SSR alleles were detected for each locus with an average of 4.88 alleles per locus. Average polymorphism information content was 0.542, ranging from 0.269 to 0.768. Genetic distance of clusters ranged from 0.05 to 0.94 between 70 accessions and dendrogram at a similarity of 0.34 gave 7 main clusters. Analysis of genetic diversity revealed by these 26 EST-SSR markers showed that the 9 germplasms and 61 commercial cultivars were discriminated by marker genotypes. These newly developed EST-SSR markers will be useful for cultivar identification and distinctness, uniformity and stability test of lettuce.

Genetic diversity and population relationships in wild Korean black raspberry (Rubus coreanus Miq.) based on microsatellite markers: establishing a fruit tree breeding strategy

Han Sung-Kyung,Shin Hanna,Lee Jei-Wan,Hong Kyung-Nak,Ahn Ji-Young 한국원예학회 2024 Horticulture, Environment, and Biotechnology Vol.65 No.2

The importance of involving genetic diversity in breeding has been emphasized for the sustainable and stable utilization of crop genetic resources and preparation for unpredictable future environments. The black raspberry fruit from the genus Rubus is highly consumed owing its fl avor and health benefi ts, but the genetic basis of its cultivars is very limited with insuffi cient genetic information available. Therefore, breeding programs must focus on the exploitation of genetic diversity of wild crop relatives. We assessed the genetic diversity, population diff erentiation, and genetic structure of 11 wild rela tives of R. coreanus Miq. using 10 microsatellite markers to collect valuable genetic information and propose enhanced strategies for development of breeding populations. The observed and expected heterozygosity were 0.493 and 0.520, respectively. Genetic diff erentiation among the populations was 0.109. The Mantel test confi rmed that wild R. coreanus populations diff erentiated following isolation by distance. Moreover, Bayesian clustering analysis showed that R. coreanus populations consisted of three genetic clusters, distribution of those showed a geographical tendency. Based on the genetic diversity, private allele frequency, and genetic structure results, we suggest to preferentially include the Chiak, Hamyang, and Jeju populations for construction of a breeding population of the Korean black raspberry.