Transcriptome Characterization and Single Nucleotide Polymorphism (SNP) Identification in Vicia amurensis Oett. Using Next-Generation Sequencing Technology

( Suresh Sundan ),( Tae Sung Kim ),( Sebastin Raveendar ),( Gyu Taek Cho ),( Jung Sook Sung ),( Yong Gu Cho ),( Sok Young Lee ),( Kyung Ho Ma ),( Jong Wook Chung ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.3

Vicia amurensis is a perennial plant found in Northern China, Japan, and Korea that plays an important role in sustainable agricultural practices due to its ability to fix atmospheric nitrogen in a symbiotic association with rhizobia. 454 sequencing technology was used to sequence the V. amurensis transcriptome which yielded 26.41 Mb from 71,197 reads as a result of 24,959 valid singletons. In addition, 1743 contigs, with the largest contig size being 3534, and 26,702 unigenes were detected. The contig distributions in three non-mutually exclusive Gene Ontology classifications and clusters of orthologous gene classes showed that differentially expressed genes were generally overrepresented in general function and prediction alone (176, 14.47%), and posttranslational modifications, protein turnover, chaperones (162, 13.32%). In total, 12,656 single nucleotide polymorphism (SNP) types were detected; these variants contained 10,585 SNPs, 1513 indels and 558 variants involving more than one nucleotide. The 2383 SNP types with high confidence differences were identified. The present study provides invaluable information on the functional genomic resources and future biological research on V. amurensis. The SNPs identified in this study will provide a material basis for future mapping and marker-assisted breeding analyses.

Development and Evaluation of Core Collection Using Qualitative and Quantitative Trait Descriptor in Sesame (Sesamum indicum L.) Germplasm

Jong-Hyun Park,Sundan Suresh,Sebastin Raveendar,Hyung-Jin Baek,Chung-Kon Kim,Sokyoung Lee,Gyu-Taek Cho,Kyung-Ho Ma,Chul-Won Lee,Jong-Wook Chung 한국작물학회 2015 Korean journal of crop science Vol.60 No.1

Sesame (Sesamum indicum L.) is one of the most important oilseed crops with high oil contents and rich nutrient value. The development of a core collection could facilitate easier access to sesame genetic resources for their use in crop improvement programs and simplify the genebank management. The present study was initiated to the development and evaluation of a core collection of sesame based on 5 qualitative and 10 quantitative trait descriptors on 2,751 sesame accessions. The accessions were different countries of origin. About 10.1 percent of accessions were selected by using the power core program to constitute a core collection consisting of 278 accessions. Mean comparisons using t-test, Nei’s diversity index of 10 morphological descriptors and correlation coefficients among traits indicated that the existing genetic variation for these traits in the entire collection has been preserved in the core collection. The results from this study will provide effective information for future germplasm conservation and improvement programs in sesame.

Selection of RAPD Markers for Investigating Genetic Diversity in Dill (Anethum graveolens L.) Germplasm

Jong-Wook Chung,Suresh Sundan,Jong-Hyun Park,Gi-An Lee,Jung-Sook Sung,Sok-Young Lee,Hyung-Jin Baek,Yeon-Gyu Kim,Gyu-Taek Cho 한국국제농업개발학회 2012 韓國國際農業開發學會誌 Vol.24 No.4

딜에 관한 연구는 대부분이 항산화 물질 및 항암효과 등에 관한 연구가 수행되었으며, 유전적 다양성에 대한 연구는 수행되지 않고 있다. 작물의 유전적 다양성 분석은 자원의 보존, 관리 및 새로운 품종 개발 등에 활용될 수 있는 중요한 정보를제공한다. 본 연구는 Dill 유전자원에 대한 유전적 다양성 분석을 위한 마커 선발을 위해 수행하였다. 1. 유전적 다양성 평가를 위하여 Operon사의 OPA, OPB 그리고 OPC 3 set, 60개 RAPD 마커에 대해서 1차 선발 후, 재현성이 있는 마커를 최종 선발하였다. 선발된 RAPD 마커의 다형성 분석을 위하여 국립농업유전자원센터에서 보유중인 dill 자원 16점을 사용하였다. 2. PCR 산물의 크기가 200 bp에서 3,000 bp 사이에 있는band들을 분석한 결과, 마커 당 평균 7 ~ 14개의 단편들을 나타내었다. 총 band 수는 119개였으며, 그 중 109개가 다형성을보였다. 총 12개의 마커 중 7개의 마커는 모든 band가 다형성을 보였고, 나머지 5개 마커는 70%~ 91%가 다형성 band였다. 각각의 마커에 대한 Nei’s gene diversity(H) 지수는 0.13 ~ 0.28였으며, 평균은 0.214이다. Shannon’s information index(I) 지수는 0.23 ~ 0.44이며, 평균은 0.353이다. 3. UPGMA tree에서는 그루지아 원산 1점을 제외한 15점이 3개 군집으로 나누어졌다. 군집 I은 2점, 군집 II는 11점이 포함되었으며, 군집 III에서는 2점이 포함되었다. 본 실험으로 선발된 RAPD marker들은 dill 유전자원에 대한 유전적 다양성 분석에 활용될 수 있을 것이다. Dill (Anethum graveolens L.), a green leafy vegetable, belongs to the family Apiaceae(Umbelliferae) and is a good source of minerals and vitamins. This investigation was undertaken to assess the genetic diversity of 16 A. graveolens accessions based on random amplified polymorphic DNA markers. Of the 60 random primers used, 12 primers gave reproducible amplification banding patterns for 109 polymorphic bands out of 119 bands scored, accounting for 91.6% of the polymorphism across all the accessions. Seven primers (OPB07, OPB12, OPB13, OPB15, OPB18, OPB20, and OPC01) generated 100% polymorphic patterns. Nei’s genetic diversity and Shannon’s information index had their highest value for primer OPB15 and their lowest value for primer OPC04. Jaccard’s coefficient of similarity varied from 0.00 to 0.64, indicative of a high level of genetic variation among all the studied accessions. UPGMA cluster analysis indicated three clusters denoted as group-1, group-2, and group-3, and one outgroup. Despite the identification of several groups, these dendrograms showed no strong relationship with respect to geographical distribution. The result provides valid guidelines for the collection and conservation of dill genetic resources.

Development and Evaluation of Core Collection Using Qualitative and Quantitative Trait Descriptor in Sesame (Sesamum indicum L.) Germplasm

박종현,Sundan Suresh,Sebastin Raveendar,백형진,김정곤,이석영,조규택,마경호,이철원,정종욱 한국작물학회 2015 한국작물학회지 Vol.60 No.1

Sesame (Sesamum indicum L.) is one of themost important oilseed crops with high oil contents and richnutrient value. The development of a core collection couldfacilitate easier access to sesame genetic resources for theiruse in crop improvement programs and simplify the genebankmanagement. The present study was initiated to the developmentand evaluation of a core collection of sesame basedon 5 qualitative and 10 quantitative trait descriptors on 2,751sesame accessions. The accessions were different countriesof origin. About 10.1 percent of accessions were selectedby using the power core program to constitute a core collectionconsisting of 278 accessions. Mean comparisons using t-test,Nei’s diversity index of 10 morphological descriptors andcorrelation coefficients among traits indicated that the existinggenetic variation for these traits in the entire collection hasbeen preserved in the core collection. The results from thisstudy will provide effective information for future germplasmconservation and improvement programs in sesame. Keywords : core collection, development, evaluation, samplingstrategy, sesame germplasm

연구보문 : 자연과학 ; 딜 유전자원의 다양성 분석을 위한 RAPD 마커 선발

정종욱,Suresh Sundan,박종현,이기안,성정숙,이석영,백형진,김연규,조규택 韓國國際農業開發學會 2012 韓國國際農業開發學會誌 Vol.24 No.4

Dill (Anethum graveolens L.), a green leafy vegetable, belongs to the family Apiaceae (Umbelliferae) and is a good source of minerals and vitamins. This investigation was undertaken to assess the genetic diversity of 16 A. graveolens accessions based on random amplified polymorphic DNA markers. Of the 60 random primers used, 12 primers gave reproducible amplification banding patterns for 109 polymorphic bands out of 119 bands scored, accounting for 91.6% of the polymorphism across all the accessions. Seven primers (OPB07, OPB12, OPB13, OPB15, OPB18, OPB20, and OPC01) generated 100% polymorphic patterns. Nei's genetic diversity and Shannon's information index had their highest value for primer OPB15 and their lowest value for primer OPC04. Jaccard's coefficient of similarity varied from 0.00 to 0.64, indicative of a high level of genetic variation among all the studied accessions. UPGMA cluster analysis indicated three clusters denoted as group-1, group-2, and group-3, and one outgroup. Despite the identification of several groups, these dendrograms showed no strong relationship with respect to geographical distribution. The result provides valid guidelines for the collection and conservation of dill genetic resources.

Selection of RAPD Markers for Investigating Genetic Diversity in Dill (Anethum graveolens L.) Germplasm

정종욱,Suresh Sundan,박종현,이기안,성정숙,이석영,백형진,김연규,조규택 한국국제농업개발학회 2012 韓國國際農業開發學會誌 Vol.24 No.4

Dill (Anethum graveolens L.), a green leafy vegetable, belongs to the family Apiaceae(Umbelliferae) and is a good source of minerals and vitamins. This investigation was undertaken to assess the genetic diversity of 16 A. graveolens accessions based on random amplified polymorphic DNA markers. Of the 60 random primers used, 12 primers gave reproducible amplification banding patterns for 109 polymorphic bands out of 119 bands scored, accounting for 91.6% of the polymorphism across all the accessions. Seven primers (OPB07, OPB12, OPB13, OPB15, OPB18, OPB20, and OPC01) generated 100% polymorphic patterns. Nei’s genetic diversity and Shannon’s information index had their highest value for primer OPB15 and their lowest value for primer OPC04. Jaccard’s coefficient of similarity varied from 0.00 to 0.64, indicative of a high level of genetic variation among all the studied accessions. UPGMA cluster analysis indicated three clusters denoted as group-1, group-2, and group-3, and one outgroup. Despite the identification of several groups, these dendrograms showed no strong relationship with respect to geographical distribution. The result provides valid guidelines for the collection and conservation of dill genetic resources.

Assessment of molecular genetic diversity and population structure of sesame (<i>Sesamum indicum</i> L.) core collection accessions using simple sequence repeat markers

Park, Jong-Hyun,Suresh, Sundan,Cho, Gyu-Taek,Choi, Nag-Gor,Baek, Hyung-Jin,Lee, Chul-Won,Chung, Jong-Wook Cambridge University Press 2014 Plant genetic resources Vol.12 No.1

<P>Sesame (<I>Sesamum indicum</I> L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.</P>

Application of Simple Sequence Repeat (SSR) Markers for the Discrimination of Korean and Chinese Sesame (Sesamum indicum L.) Accessions

( Jong Hyun Park ),( Sundan Suresh ),( Xiang Min Piao ),( Gyu Taek Cho ),( Sok Young Lee ),( Hyung Jin Baek ),( Chul Won Lee ),( Jong Wook Chung ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.1

ABSTRACT Sesame (Sesamum indicum L.) is an ancient oil seed crop that has been referred to as the ‘queen of oilseeds’ by virtue of its high quality oil. Fourteen simple sequence repeat (SSR) markers were used to differentiate 70 sesame (Sesame indicum L) accessions. Forty-three of the accessions were from Korea and 27 were from China. An initial round of analysis using two SSR markers (GBssr-sa-005 and GBssr-sa-182) identified 21 distinct accessions. A second round of analysis using one additional SSR marker (GBssr-sa-108) identified 25 more distinct accessions. Addition of a fourth SSR marker (GBssr-sa-184) for a third round of analysis identified an additional 20 accessions. This study demonstrates differentiation between 43 accessions from Korea and 23 accessions from China by four SSR markers.

Genetic Diversity and Population Structure of Korean Mint Agastache rugosa (Fisch & Meyer) Kuntze (Lamiaceae) Using ISSR Markers

Kang, Man Jung,Sundan, Suresh,Lee, Gi An,Ko, Ho Cheol,Chung, Jong Wook,Huh, Yun Chan,Gwag, Jae Gyun,Oh, Se Jong,Kim, Yeon Gyu,Cho, Gyu Taek The Plant Resources Society of Korea 2013 한국자원식물학회지 Vol.26 No.3

Agastache rugosa, a member of the mint family (Labiatae), is a perennial herb widely distributed in East Asian countries. It is used in traditional medicine for the treatment of cholera, vomiting, and miasma. This study assessed the genetic diversity and population structures on 65 accessions of Korean mint A. rugosa germplasm based on inter simple sequence repeat (ISSR) markers. The selected nine ISSR primers produced reproducible polymorphic banding patterns. In total, 126 bands were scored; 119 (94.4%) were polymorphic. The number of bands generated per primer varied from 7 to 18. A minimum of seven bands was generated by primer 874, while a maximum of 18 bands was generated by the primer 844. Six primers (815, 826, 835, 844, 868, and 874) generated 100% polymorphic bands. This was supported by other parameters such as total gene diversity ($H_T$) values, which ranged from 0.112 to 0.330 with a mean of 0.218. The effective number of alleles ($N_E$) ranged from 1.174 to 1.486 with a mean value of 1.351. Nei's genetic diversity (H) mean value was 0.218, and Shannon's information index (I) mean value was 0.343. The high values for total gene diversity, effective number of alleles, Nei's genetic diversity, and Shannon's information index indicated substantial variations within the population. Cluster analysis showed characteristic grouping, which is not in accordance with their geographical affiliation. The implications of the results of this study in developing a strategy for the conservation and breeding of A. rugosa and other medicinal plant germplasm are discussed.

New cDNA-SSR markers in the narrow-leaved vetch (Vicia sativa subsp. nigra) using 454 pyrosequencing

Chung, Jong-Wook,Kim, Tae Sung,Sundan, Suresh,Lee, Gi-An,Park, Jong-Hyun,Cho, Gyu-Taek,Lee, Ho-Sun,Lee, Jung-Yoon,Lee, Myung-Chul,Baek, Hyung-Jin,Lee, Sok-Young Springer-Verlag 2014 Molecular breeding Vol.33 No.3