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( Kyaw Thu Moe ),( Hao Cui ),정종욱 ( Jong Wook Chung ),라상복 ( Sang Bog Ra ),권순욱 ( Soon Wook Kwon ),박용진 ( Yong Jin Park ) 한국국제농업개발학회 2011 韓國國際農業開發學會誌 Vol.23 No.3
본 연구는 강화도에서 수집한 샤레벼 자원의 유전적 다양성 수준과 집단의 특성을 구명하기 위해 몇몇 Indica(5점), Japonica(8점) 및 통일형(2점) 품종과 재래종(10점) 및 강화도 수집 샤레벼 89점을 포함한 총 114개 벼 자원에 대하여 유전적 다양성과 집단의 구조 분석을 수행하였으며, 이를 통하여 향후 육종을 위한 소재로 활용할 수 있는 기초 정보를 제공하고자 본 실험을 수행하였다. 1. 114점의 벼 자원에 대하여 29개 SSR 마커에 의해 얻어진 allele는 총 243개이고, 마커당 평균 allele 수는 8.4개를 보였다. 유전적 다양성을 나타내는 genetic diversity와 PIC 값의 범위는 각각 0.04~0.87, 0.04~0.86 이였으며, 평균은 각각 0.61, 0.57로 관찰되었다. 2. 유전적 거리와 STURUCTURE를 이용하여 집단의 구조를 분석한 결과 70% 확률로 5개의 subpopulation으로 나눌 수 있었으며, 9.6%는 유전적으로 혼입된 형태를 나타냈다. 3. 강화도에서 수집된 샤레벼 89점 중 11개 자원은 japonica형의 국내육성품종 (8점) 및 재래벼(10점)와 POP4에 속했고, 11개 자원은 혼입된 형태이며, 67개 자원은 POP2(20점), POP3(17점), POP5(30점)에 포함되었다. 강화 수집 샤레벼는 차후 국내 벼 품종의 유전적 다양성을 확대하고, 육종 소재로 활용할 수 있는 중요한 재료가 될 것이다. A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of Korea weedy rice (Oryza sativa L.). A total of 243 alleles were detected with an average of 8.4 per locus among 114 rice accessions. Major allele frequency (MAF) ranged from 0.22 to 0.98 and the average is 0.52. The averages of gene diversity and polymorphic information content (PIC) values were 0.61 and 0.57, with a range from 0.04 (SSS) to 0.87 (RM241) and from 0.04 (SSS) to 0.86 (RM241), respectively. In cluster analysis, 90.4% of accessions (shared > 70% membership with one of five clusters) were classified as members of each cluster, whereas 9.6% accessions showed evidence of mixed population ancestry. The Korea weedy rice, ``Sharei rice`` collected from isolated island, ``Ganghwa`` appears to be a very primitive rice cultivar for being separately grouped from indica and japonica. It might have changed its genetic background along with adaptation to such an isolated region. This result showed that the collected weedy rice accessions have valuable sources of gene diversity for future rice improvement breeding programs.
Trends in genomics and molecular marker systems for the development of some underutilized crops
Kyaw Thu Moe,권순욱,박용진 한국유전학회 2012 Genes & Genomics Vol.34 No.5
The term ‘underutilized’ is often used to characterize the range of plant species whose potential contribution to food security,health, income generation, and environmental services has not yet been fully exploited. To harness unexploited resources, the first step is to prevent them from extinction and to conserve them in- and/or ex-situ. To utilize plant species as crops, plants must be collected, conserved, evaluated, and then if necessary manipulated. In this context, significant international efforts have focused on impeding the erosion of genetic diversity. Thousands of new accessions are introduced into germplasm institutes each year. Assessment of their molecular diversity is necessary to eliminate redundant genotypes. Marker systems have been used not only for genotyping to reduce redundancy and develop a core set, but also for a wide variety of other purposes. The use of markers based on single nucleotide polymorphisms,copy number variation, and insertions/deletions,as well as genotyping by sequencing, is becoming popular for genetic mapping and analyses of quantitative trait loci. This review discusses current marker systems and genomic analyses of a number of underutilized crops.
국화 SSR-enriched Library에서 SSR 반복염기의 분포 및 빈도
( Kyaw Thu Moe ),라상복 ( Sang Bog Ra ),이기안 ( Gi An Lee ),이명철 ( Myung Chul Lee ),박하승 ( Ha Seung Park ),김동찬 ( Dong Chan Kim ),이철휘 ( Cheol Hwi Lee ),최현구 ( Hyun Gu Choi ),전낙범 ( Nak Beom Jeon ),최병준 ( Byung J 한국국제농업개발학회 2011 韓國國際農業開發學會誌 Vol.23 No.5
Chrysanthemums, often called mums or chrysanths, belong to the genus Chrysanthemum, which includes about 30 species of perennial flowering plants in the family Asteraceae. We extracted DNA from Dendranthema grandiflorum (``Smileball``) to construct a simple sequence repeat (SSR)- enriched library, using a modified biotin-streptavidin capture method. GS FLX (Genome Sequencer FLX System which provides the flexibility to perform the broad range of applications) sequencing (at the 1/8 run specification) resulted in 18.83 mega base pairs (Mbp) with an average read length of 280.06 bp. Sequence analyses of all SSR-containing clones revealed a predominance of di-nucleotide motifs (16,375, 61.5%) followed by tri-nucleotide motifs (6,616, 24.8%), tetra-nucleotide motifs (1,674, 6.3%), pentanucleotide motifs (1,283, 4.8%), and hexa-nucleotide motifs (693, 2.6%). Among the di-nucleotide motifs, the AC/CA class was the most frequently identified (93.5% of all di-nucleotide types), followed by the GA/AG class (6.1%), the AT/TA class (0.4%), and the CG/GC class (0.03%). When we analyzed the distribution of different repeat motifs and their respective numbers of repeats, regardless of the motif class, of 100 SSR markers, we found a higher number of di-nucleotide motifs with 70 to 80 repeats; we also found two di-nucleotide motifs with 83 and 89 repeats, respectively, but their product lengths were within optimum size (297 and 300 bp). In future work, we will screen for polymorphisms of possible primer pairs. The results will provide a useful tool for assessing molecular diversity and investigating the population structure among and within Chrysanthemum species.
Kyaw Thu Moe,Sang-Bog Ra,Gi-An Lee,Myung-Chul Lee,Ha-Seung Park,Dong-Chan Kim,Cheol-Hwi Lee,Hyun-Gu Choi,Nak-Beom Jeon,Byung-Jun Choi,Ji-Youn Jung,Kyu-Min Lee,Yong-Jin Park 한국국제농업개발학회 2011 韓國國際農業開發學會誌 Vol.23 No.5
국화과(Compositae)는 현화식물 중 세계에서 가장 넓게 분포하고, 쌍자엽식물 중 가장 진화된 식물분류군이며, 우리나라에는 약 300여종이 존재하는 것으로 알려져 있다. 구절초, 감국, 쑥, 쑥갓, 개미취, 참취, 곰취 등 국화과 식물들은 예로부터 민간에서 약용 및 식용 소재로써 다양하게 사용되어왔다. 본 연구는 국화 및 국화근연종 유용유전자원 선발을 통하여 육종 소재를 확대하고, 중간모본 및 신품종 육성기반을 구축하고자 DNA 마커시스템의 개발을 위해 수행되었다. 1. 화단국인 Smileball(Dendranthema grandiflorum) 품종을 사용하여 SSR-enriched library를 작성하였고, GS FLX 분석을 통해 18.83Mbp의 염기서열 결과를 얻었으며, read의 평균 길이는 280.06bp로 나타났다. 2. 단순반복염기서열(SSR) 부위를 포함하는 26,780개 clones 중 di-nucleotide motifs가 16,375개(61.5%)로 우세하였고, trinucleotide motifs(6,616개, 24.8%), tetra-nucleotide motifs(1,674개, 6.3%), penta-nucleotide motifs(1,283개, 4.8%), hexa-nucleotide motifs(693개, 2.6%) 순으로 나타났다. 3. 얻어진 di-nucleotide motifs들 중에서는, AC/CA class가 93.5%로 대부분이었고, tri-nucleotide motifs에서는 AAC class가 50.5%, tetra-nucleotide motifs는 ACGT class가 43.6%이고, pentanucleotide motif에서는 AACGT class 27.2%이며, hexa-nucleotide motif에서는 ACGATG class 21.8%였다. 4. 얻어진 염기서열 결과를 토대로 다양한 motif를 갖는 100개의 SSR 마커를 제작하였고, 차후 이를 활용하여 국화 유전자원의 다형성 및 유전자형 분석을 통해 분자유전학적 다양성 및 집단의 구조분석이 가능하고, 국화의 분자육종기반 구축을 위한 유용한 도구가 될 것 이다. Chrysanthemums, often called mums or chrysanths, belong to the genus Chrysanthemum, which includes about 30 species of perennial flowering plants in the family Asteraceae. We extracted DNA from Dendranthema grandiflorum (‘Smileball’) to construct a simple sequence repeat (SSR)-enriched library, using a modified biotin-streptavidin capture method. GS FLX (Genome Sequencer FLX System which provides the flexibility to perform the broad range of applications) sequencing (at the 1/8 run specification) resulted in 18.83 mega base pairs (Mbp) with an average read length of 280.06 bp. Sequence analyses of all SSR-containing clones revealed a predominance of di-nucleotide motifs (16,375, 61.5%) followed by tri-nucleotide motifs (6,616, 24.8%), tetra-nucleotide motifs (1,674, 6.3%), pentanucleotide motifs (1,283, 4.8%), and hexa-nucleotide motifs (693, 2.6%). Among the di-nucleotide motifs, the AC/CA class was the most frequently identified (93.5% of all di-nucleotide types), followed by the GA/AG class (6.1%), the AT/TA class (0.4%), and the CG/GC class (0.03%). When we analyzed the distribution of different repeat motifs and their respective numbers of repeats, regardless of the motif class, of 100 SSR markers, we found a higher number of di-nucleotide motifs with 70 to 80 repeats; we also found two di-nucleotide motifs with 83 and 89 repeats, respectively, but their product lengths were within optimum size (297 and 300 bp). In future work, we will screen for polymorphisms of possible primer pairs. The results will provide a useful tool for assessing molecular diversity and investigating the population structure among and within Chrysanthemum species.
SSR analysis revealed that most of Korean ginsengs are derived from di-phylogenic origins
Young-Chang Kim,Kyaw Thu Moe,Soon-Wook Kwon,Kyung-Ho Ma,Yong-Jin Park 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb which is native to Korea and China. Its roots are highly prized for several medicinal properties. Therefore, Ginseng has been a top-ranked subject of many fields of scientific research worldwide. However, very limited number of research work has been published on species authentication using DNA marker system. In this study, 22 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of 167 ginseng cultivars from 11 regions and 10 breed varieties. A total number of 111 alleles were detected, with an average of 5.05 per locus. The average expected heterozygosity and polymorphism information content (PIC) for SSR locus were 0.35 and 0.30, respectively. The model-based structure analysis revealed that 66.5% of all cultivars could be grouped into three populations with inferred value (allele shared >70%) membership. More than 33% of tested cultivars derived from two ancestries, which was basically consistent with clustering based on genetic distance. Almost all of the cultivars shared the ancestry with S1 and S2 except 1 China Jilin and 3 USA cultivars. The result indicated that most of Korean ginsengs are closely interrelated between the two ancestors but USA ginsengs are totally different from Asian cultivars.