Verification of hotspots of genetic diversity in Korean population of Grateloupia asiatica and G. jejuensis (Rhodophyta) show low genetic diversity and similar geographic distribution

Yang Mi Yeon,Kim Su Yeon,김명숙 한국유전학회 2021 Genes & Genomics Vol.43 No.12

Background Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecifc diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. Objective The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. Methods Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fxation index, FST. Results Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identifed as a ‘hotspot’ with the highest genetic diversity for both species, whereas Jeju Island is identifed as a ‘cold spot’ with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene fow. Conclusions The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

생물다양성협약과 유전자원 관련 지식재산권 논의와 쟁점

허인 강원대학교 비교법학연구소 2020 환경법과 정책 Vol.24 No.-

Genetic resources and its relation to the protection of intellectual property is a controversial issue which has been one of the agendas of TRIP regarding biological diversity for the last ten years. Most of the nations agree with the protection of genetic resources and related traditional knowledge but the issue is how to do so. In order to resolve this problem, WIPO IGC was established in 2000 and up until now, they are discussing issues including access and benefit sharing and matters over intellectual property rights regarding traditional knowledge and folklore. With the adoption of 「Convention on Biological Diversity(CBD)」 in 1992, balanced stance and practical approach method to genetic resources is defined as a binding regulation. This convention ensures conservation of biological diversity, the sustainable use of its components and the fair and equitable sharing of the benefits arising out of the utilization of genetic resources and sovereignty of countries on Genetic Resources. Facing the year 2010 the year which UN has declared to be the International Year of Biodiversity, has hosted 10th Conference of the Parties(COP) in Nagoya, Japan and adopted the 「Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity」. This is a historic event in the scene of Access and benefit-sharing(ABS) of biodiversity. The adoption of the ABS Protocol and the following new ABS standards are expected to influence the discussion of WIPO IGC and TRIPS Council. In the WIPO ICG conference and the discussion related to having PIC and MAT mandatory in relation to the TRIPS and CBD, considering relevant matters of the ABS in patent-related works will be discussed. However, it should be noted that the purpose of the Convention on Biological Diversity and ABS Protocol is to preserve the biological diversity through the ABS on genetic resources and related traditional knowledge, and to contribute to the sustainable use of its components while the objective of the discussion of WIPO IGC is to protect genetic resources and traditional knowledge or to preserve them as an intellectual property. In the conclusion, minimum standards which were required by global community on access to genetic resources and benefit sharing need to be set forward to ensure stable and long-term protection of domestic genetic resources and its utilization. In the field of genetic resources, there is a possibility that we would be able to solidify our status as a user nation due to the continuous development of the bio-industry which comes after the advancement of biotechnology. Therefore, we should take counter measures on separate issues considering the stance of user nations in global discussions relevant to the field of genetic resources and traditional knowledge. 유전자원의 무분별한 이용과 생태계 파괴, 환경오염 등으로 인하여 생물다양성은 급격히 감소하고 있는 반면, 분자생물학과 유전공학 등의 분야에서 기술이 발전함에 따라 유전자원에 대한 가치는 지속적으로 증가하고 있다. 이러한 이유로 세계 각국은 유전자원을 확보하기 위한 치열한 경쟁을 벌이고 있다. 유전자원을 이용할 수 있는 기술력을 가진 선진국들은 자원확보를 위한 노력과 함께 유전자원을 통해 산출된 산물에 대한 지식재산권의 강화를 주장하고 있는 반면, 다양한 생물유전자원을 보유한 개발도상국들은 자국의 유전자원 이용에 대한 이익의 공유를 주장하고 있어, 유전자원을 둘러싸고 선진국과 개발도상국 간의 첨예한 갈등과 분쟁이 증가하고 있다. 생물다양성협약이 생물유전자원의 접근과 이익공유를 중심으로 진행이 되었다면, WIPO IGC와 TRIPS 협정에서의 논의는 유전자원 출처공개의 특허요건화를 중심으로 진행되고 있다. 우리나라의 입장에서 유전자원 출처공개의 특허요건화는 출처공개에 따른 행정적 비용 및 출원인의 부담을 증가시켜 국내 생명공학 관련 연구를 위축시킬 수 있다는 견해가 지배적이다. 그러나 국제적 관계 속에서 개발도상국의 입장을 무시할 수는 없는 것이 사실이므로 국제적 동향을 예의주시하고 그 대응을 철저하게 준비할 필요가 있다.

연구보문 : SSR 마커를 이용한 녹두 수집자원의 유전적 다양성 분석

( Li Gang ),권순욱 ( Soon Wook Kwon ),최유미 ( Yu Mi Choi ),박용진 ( Yong Jin Park ) 한국국제농업개발학회 2011 韓國國際農業開發學會誌 Vol.23 No.2

본 연구는 중앙아메리카의 니카라과를 포함하여 동아시아, 중앙아시아 지역의 6개 국가에서 수집한 66개 녹두 유전자원에 대하여 15개 SSR marker를 이용하여 유전적 다양성 및 집단의 구조 분석을 통하여 자원보존 및 육종 소재로서의 활용을 위한 기초정보를 제공하고자 본 실험을 수행하였다. 1. 66점의 녹두 자원에 대하여 15개 SSR 마커에 의해 관찰된 allele수는 총 52개로 나타났고, 평균 allele 수는 3.5개 였다. 이들의 gene diversity와 PIC 값은 각각 0.12~0.66, 0.11~0.60 였으며, 평균은 0.35와 0.31로 나타났다. 2. 유전적 다양성을 나타내는 genetic diversity는 국가별로 중국 > 아프가니스탄 > 한국 > 우즈베키스탄 > 일본 > 니카라과 순으로 각각 0.37, 0.36, 0.31, 0.28, 0.24, 0.23으로 나타났으며, 지역적으로 분석한 결과 동아시아지역에서 평균적으로 가장 높은 genetic diversity를 나타났으며, 그 다음으로 중앙아시아, 중앙아 메리카 순으로 나타났다. 3. STRUCTURE를 이용하여 집단의 구조를 분석한 결과, 66 자원 중 54 점(81.8%)이 70%의 확률로 4개의 subpopulation으로 분류되었으며, 12 자원(18.2%)은 혼입된 형태로 분류되었다. 4. Subpopulation의 유전다양성은 4개 나라에서 수집된 7개 자원을 포함하는 S4에서 가장 높게(0.25) 나타났으며, 한국 수집자원 10점과 우즈베키스탄에 수집된 1개 자원이 포함한 S3에서 가장 낮게 나타났다. 5. 각각의 subpopulation은 수집국가에 대한 특성은 가지고 있지 않았으며, S3에서는 한국 수집자원이 다수 포함된 형태로 나타났으나, 대부분의 자원들은 불규칙적으로 분포되었다. This study was conducted to assess the genetic diversity and population structure of 66 mungbean accessions collected from Korea, China, Japan, Afghanistan, Uzbekistan and Nicaragua using 15 simple sequence repeat (SSR) markers. In total, 52 alleles were detected among 66 accessions at all loci with an average of 3.5 alleles per locus. All microsatellite loci were found to be polymorphic. The expected heterozygosity (HE) and polymorphism information content (PIC) ranged from 0.12 to 0.65 (mean = 0.36) and from 0.11 to 0.60 (mean = 0.31). The mean genetic diversity in Korea, China, Japan, Uzbekistan, Afghanistan, and Nicaragua were 0.31, 0.37, 0.24, 0.28, 0.36, and 0.23, respectively. The average genetic diversity showed the following country-wide trend, China > Afghanistan > Korea > Uzbekistan > Japan > Nicaragua. In addition, the region-wide analysis showed that accessions from East Asia possessed the highest average genetic diversity, followed by Central Asia, and Central America. The model-based structure analysis revealed the presence of four subpopulations, which was essentially consistent with clustering based on genetic distance. Fifty-four accessions (81.8%) showed a clear relation to each cluster with their inferred value (> 70%), while, the other 12 accessions (18.2%) were categorized as admixtures. The results explored the genetic diversity of East and Central Asia which will be useful for future germplasm preservation, conservation, and crossbreeding programs for mungbean.

Genetic diversity and population structure of Mongolian regional horses with 14 microsatellite markers

윤지혜,Oyungerel Baatartsogt,공홍식 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.8

Objective: This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers. Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei’s DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure. Results: On average, the number of alleles, expected heterozygosity (HExp), observed heterozygosity (HObs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei’s DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation. Conclusion: Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships. Objective: This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers.Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei’s DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure.Results: On average, the number of alleles, expected heterozygosity (H_Exp), observed heterozygosity (H_Obs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei’s DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation.Conclusion: Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships.

유전자원 보호와 활용을 위한 국제적 논의와 쟁점에 관한 소고

허인(HUH, In),심현주(SHIM, Hyunjoo) 세창출판사 2013 창작과 권리 Vol.- No.71

Genetic resources and its relation to the protection of intellectual property is a controversial issue which has been one of the agendas of TRIP regarding biological diversity for the last ten years. Most of the nations agree with the protection of genetic resources and related traditional knowledge but the issue is how to do so. In order to resolve this problem, WIPO IGC was established in 2000 and up until now, they are discussing issues including access and benefit sharing and matters over intellectual property rights regarding traditional knowledge and folklore. With the adoption of 「Convention on Biological Diversity(CBD)」 in 1992, balanced stance and practical approach method to genetic resources is defined as a binding regulation. This convention ensures conservation of biological diversity, the sustainable use of its components and the fair and equitable sharing of the benefits arising out of the utilization of genetic resources and sovereignty of countries on Genetic Resources. Facing the year 2010 the year which UN has declared to be the International Year of Biodiversity, has hosted 10th Conference of the Parties(COP) in Nagoya, Japan and adopted the 「Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity」. This is a historic event in the scene of Access and benefit-sharing(ABS) of biodiversity. The adoption of the ABS Protocol and the following new ABS standards are expected to influence the discussion of WIPO IGC and TRIPS Council. In the WIPO ICG conference and the discussion related to having PIC and MAT mandatory in relation to the TRIPS and CBD, considering relevant matters of the ABS in patent-related works will be discussed. However, it should be noted that the purpose of the Convention on Biological Diversity and ABS Protocol is to preserve the biological diversity through the ABS on genetic resources and related traditional knowledge, and to contribute to the sustainable use of its components while the objective of the discussion of WIPO IGC is to protect genetic resources and traditional knowledge or to preserve them as an intellectual property. In the conclusion, minimum standards which were required by global community on access to genetic resources and benefit sharing need to be set forward to ensure stable and long-term protection of domestic genetic resources and its utilization. In the field of genetic resources, there is a possibility that we would be able to solidify our status as a user nation due to the continuous development of the bio-industry which comes after the advancement of biotechnology. Therefore, we should take counter measures on separate issues considering the stance of user nations in global discussions relevant to the field of genetic resources and traditional knowledge.

Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers

Yan‐xin Zhang,Wei Hua,Lin‐han Wang,Zhuo Che,Xiu‐rong Zhang 한국유전학회 2010 Genes & Genomics Vol.32 No.3

The molecular genetic diversity of 404 indigenous landraces from sesame core collection in China were evaluated by 11SRAP and 3 SSR markers, 175 fragments were generated, of which 126 were polymorphic with an average polymorphism rate of 72%. Jaccard’s genetic similarity coefficients (GS=0.7130), Nei's gene diversity (h=0.2418) and Shannon's Information index (I=0.3847) were calculated, a dendrogram of the 404 landraces was made, landraces from various zones were distributed throughout the dendrogram, accessions from different agro‐ecological zones were indistinguishable by cluster analysis, geographical separation did not generally result in greater genetic distance, a similar pattern was obtained using principal coordinates (PCO) analysis. As to seven agro‐ecological zones, the maximum Nei’s gene diversity (h = 0.2613)and Shannon index (I = 0.3980) values in zone VII indicated that they were genetically more diverse than those in other zones, while the least genetically diverse region was zone III (h = 0.1772, I = 0.2858). Nei's genetic identity and genetic distance among landraces from seven agro‐ecological zones were also analyzed, the genetic relationship of seven zones was inferred using the UPGMA method. This study demonstrated that SRAP and SSR markers were appropriate for evaluation of sesame genetic diversities. There existed extensive genetic diverse among indigenous landraces and the abundance of genetic diversity of landraces in different agro‐ecological zones was various. Understanding of these characteristics of indigenous landraces in China can provide theoretical foundation for further collection, effective protection and reasonable utilization of these sesame landraces in breeding.

Populations of Asarum mandshuricum are Strongly Differentiated Despite a High Outcrossing Rate

Jeong Hyeon Jin,김재근 한국식물학회 2022 Journal of Plant Biology Vol.65 No.3

Asarum mandshuricum is a perennial herb that inhabits the herb layer of a forest. This species has life-history traits and distribution patterns that could negatively affect genetic diversity such as small population size, sparse distribution of populations, self-compatible flower, and short seed dispersal distance. Due to these traits, there are concerns about genetic drift and fragmentation by restricted gene flow, thus decreasing the fitness of the population. To identify genetic structures of A. mandshuricum and suggest main factors that determine its genetic structures, outcrossing rate and inhabitation pattern were investigated. Population size of this species was very small (15.2 individuals). Its outcrossing rate was high (tm: 0.980). Genetic diversity of population was also high (h: 0.275, I: 0.421). Its cross-pollination rate, rather than distribution traits such as population size and insufficient connectivity among populations, was the main factor in determining genetic diversity. Despite high outcrossing rate, populations of A. mandshuricum were strongly differentiated (Gst: 0.492). Inhabitation with a limited gene flow through generation in the same place might have caused A. mandshuricum populations to have differentiated genetic structure. To preserve its populations and maintain genetic diversity, conservative efforts such as retaining population size and establishing connections between subpopulations are needed.

A double-labeling marker-based method for estimating inbreeding and parental genomic components in a population under conservation

Li, Wenting,Zhang, Mengmeng,Wang, Kejun,Lu, Yunfeng,Tang, Hui,Wu, Keliang Asian Australasian Association of Animal Productio 2020 Animal Bioscience Vol.33 No.1

Objective: The objective of a conservation program is to maintain maximum genetic diversity and preserve the viability of a breed. However, the efficiency of a program is influenced by the ability to accurately measure and predict genetic diversity. Methods: To examine this question, we conducted a simulation in which common measures (i.e. heterozygosity) and novel measures (identity-by-descent probabilities and parental genomic components) were used to estimate genetic diversity within a conserved population using double-labeled single nucleotide polymorphism markers. Results: The results showed that the accuracy and sensitivity of identity-by-state probabilities and heterozygosity were close to identity by descent (IBD) probabilities, which reflect the true genetic diversity. Expected heterozygosity most closely aligned with IBD. All common measures suggested that practices used in the current Chinese pig conservation program result in a ~5% loss in genetic diversity every 10 generations. Parental genomic components were also analyzed to monitor real-time changes in genomic components for each male and female ancestor. The analysis showed that ~7.5% of male families and ~30% of female families were lost every 5 generations. After 50 generations of simulated conservation, 4 male families lost ~50% of their initial genomic components, and the genomic components for 24.8% of the female families were lost entirely. Conclusion: In summary, compared with the true genetic diversity value obtained using double-labeled markers, expected heterozygosity appears to be the optimal indicator. Parental genomic components analysis provides a more detailed picture of genetic diversity and can be used to guide conservation management practices.

Genetic diversity among cultivated and wild Panax ginseng populations revealed by high-resolution microsatellite markers

장우종,장예은,김남훈,Nomar Espinosa Waminal,Young-Chang Kim,Jung Woo Lee,Tae Jin Yang 고려인삼학회 2020 Journal of Ginseng Research Vol.44 No.4

Background: Ginseng (Panax ginseng Meyer) is one of the world’s most valuable medicinal plants withnumerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collectionsfor a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is notfully understood. Methods: We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci toelucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars,breeding lines, and wild populations in Korea and neighboring countries. Results: Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication,which causes confusion in interpretation of their target locus. The five high-resolution markers revealed3 to 8 alleles from each single locus. The proportion of heterozygosity (He) ranged from 0.027 to 0.190,with an average of 0.132, which is notably lower than that of previous studies. Polymorphism informationcontent of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was nostatistically significant difference in genetic diversity between cultivated and wild ginseng groups, andthey showed intermingled positioning in the phylogenetic relationship. Conclusion: Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups havesimilar levels of genetic diversity. Collectively, our data demonstrate that current breeding populationshave abundant genetic diversity for breeding of elite ginseng cultivars.

Genetic Diversity of Plasmodium vivax in Clinical Isolates from Southern Thailand using PvMSP1, PvMSP3 (PvMSP3α, PvMSP3β) Genes and Eight Microsatellite Markers

Supinya Thanapongpichat,Thunchanok Khammanee,Nongyao Sawangjaroen,Hansuk Buncherd,Aung Win Tun 대한기생충학ㆍ열대의학회 2019 The Korean Journal of Parasitology Vol.57 No.5

Plasmodium vivax is usually considered morbidity in endemic areas of Asia, Central and South America, and some part of Africa. In Thailand, previous studies indicated the genetic diversity of P. vivax in malaria-endemic regions such as the western part of Thailand bordering with Myanmar. The objective of the study is to investigate the genetic diversity of P. vivax circulating in Southern Thailand by using 3 antigenic markers and 8 microsatellite markers. Dried blood spots were collected from Chumphon, Phang Nga, Ranong and, Surat Thani provinces of Thailand. By PCR, 3 distinct sizes of PvMSP3α, 2 sizes of PvMSP3β and 2 sizes of PvMSP1 F2 were detected based on the length of PCR products, respectively. PCR/RFLP analyses of these antigen genes revealed high levels of genetic diversity. The genotyping of 8 microsatellite loci showed high genetic diversity as indicated by high alleles per locus and high expected heterozygosity (HE). The genotyping markers also showed multiple-clones of infection. Mixed genotypes were detected in 4.8% of PvMSP3α, 29.1% in PvMSP3β and 55.3% of microsatellite markers. These results showed that there was high genetic diversity of P. vivax isolated from Southern Thailand, indicating that the genetic diversity of P. vivax in this region was comparable to those observed other areas of Thailand.