당근(Daucus carota var. sativa) 종자모 형질 관련 RAPD-SCAR 분자표지 개발

심은조(Eun-Jo Shim),박성관(Sung-Kwan Park),오규동(Gyu-Dong Oh),전상진(Sang-Jin Jun),박영두(Young-Doo Park) 한국원예학회 2013 원예과학기술지 Vol.31 No.6

Mechanical hair removal of carrot seed causes seed injuries and suppresses the germination in carrot cultivation. This study was performed to develop molecular markers for breeding high quality cultivars with short-hair seed. To meet this objective, random amplified polymorphic DNA (RAPD)-sequence characterized amplified region (SCAR) markers specifically linked to seed-hair characteristic were identified using CT-SMR 616 OP 389-1 line with short-haired seed and CT-SMR 616 OP 616-33 line with long-haired seed, bred by self-pollination for 6 years from 2008 to 2013, as parents. After seed hair lengths of these lines were analyzed using microscope, next generations were advanced and compared with the molecular markers polymorphism. From RAPD analysis using fixed lines in 2011, twelve RAPD primers showing polymorphic bands specific between the two lines were identified from 80 random primers. To develop RAPD-SACR marker, SCAR primers were designed based on sequence analysis of these specific RAPD bands and more than three combinations of primers were tested. As a result, it was found that the SCA21.2 amplified single polymorphic band from short-haired seed line. To confirm this result, SCA21.2 marker was retested by applying to the 2012 and 2013 progenies. Finally, it was concluded that the developed SCA21.2 marker distinguished short-haired line from long-haired seed line. Therefore, SCAR marker, SCA21.2 is expected to be utilized for breeding of the short-haired seed cultivars.

국내에서 수집된 국화 품종에 대한 SSR 분자표지 Database 구축

심은조(Eun-Jo Shim),허은정(Eun-Jung Heo),윤무경(Moo-Kyoung Yoon),소은희(Eun-Hee Soh),홍지화(Jee-Hwa Hong) 한국육종학회 2015 한국육종학회지 Vol.47 No.4

Chrysanthemum (Dendranthema grandiflourm Kitamura) is a member of the Asteraceae and one of the important horticultural crops. The objective of this study was to construct a DNA profile database for identification of chrysanthemum varieties using simple sequence repeat (SSR) markers. In order to select SSR markers for the variety identification, we screened 587 SSR primers using 20 varieties. Among them, 27 SSR markers showed polymorphism. We finally selected 14 SSR markers showing peak clearance, high polymorphism and reproducibility in 20 varieties. In conclusion, DNA profile database for 147 chrysanthemum varieties were constructed by 14 SSR markers. A total of 79 SSR alleles were detected and three to ten alleles were detected with an average of 5.6 alleles per locus. The polymorphism information content value ranged 0.287 ~ 0.785 with an average of 0.598. Genetic relationship revealed that genetic distance of 147 varieties ranged from 0.44 to 1.00. The 143 varieties among 147 varieties were distinguished by 14 SSR markers but the 2 varieties developed by mutation breeding and natural variation were not distinguished from original varieties. These constructed SSR profile database will be useful for the selection of similar varieties for candidate variety and for solving problem relating to seed dispute and infringement of plant breeder’s right.

EST profiling을 통한 당근(Daucus carota var. sativa)의 종모 형성에 관련된 유전자 분석

황은미(Eun-Mi Hwang),오규동(Gyu-Dong Oh),심은조(Eun-Jo Shim),전상진(Sang-Jin Jeon),박영두(Young-Doo Park) 한국원예학회 2010 원예과학기술지 Vol.28 No.6

Carrot is one of the useful crops used abundantly in cooking in Western as well as Asia regions such as China and Korea. However, seed coats have hairs which should be removed to increase germination rate. Furthermore, because of seed hairs, farmers face several additional losses, such as time consumption, manpower, capital and so on, for seed handling. To prevent these problems, study of gene related hair formation using short-hair seed lines is required. We analyzed genes related to hair formation from seed through expressed sequenced tag (EST) profiling, based on the fact that the development of carrot seed hair is related to cellulose synthesis pathway in secondary cell wall synthesis stage. To study the gene expression related to hair formation of the carrot seed, a cDNA library was constructed by using the early maturation stage of the short-hair line (659-1) and hairy seed line (677-14). In short-hair (659-1) and hairy seed (677-14) lines, results from of EST profiling through BLASTX search analysis using the NCBI database showed that 172 and 224 unigenes had significant homology with known protein sequences, whereas 233 and 192 unigenes were not, respectively. All ESTs were grouped into 16 categories according to their putative functions. Twenty nine unigenes among all ESTs were considered to be genes regulating seed hair development from cellulose synthesis pathway during secondary cell wall synthesis stage; in results, 14 unigenes related to seed hair development were found only in hairy seed line.

배 품종 및 유전자원에 대한 Microsatellite DNA 프로파일 데이터베이스 구축

홍지화(Jee-Hwa Hong),심은조(Eun-Jo Shim),권용삼(Yong-Sham Kwon) 한국원예학회 2017 원예과학기술지 Vol.35 No.1

A DNA profile database was constructed to investigate the genetic relatedness of 72 germplasm samples of Pyrus and related cultivars using microsatellite markers. Three P. pyrifolia , four P. commus , and one P. betulifolia cultivars with different morphological traits were screened using 387 pairs of microsatellite primers. A core set of 11 primer pairs was selected to obtain 133 polymorphic amplified fragments meeting three criteria: high polymorphism information contents (PIC), high repeatability, and distinct allele patterns. The number of alleles per locus ranged between 4 and 22. Average PIC was 0.743 (range: 0.557 - 0.879). Cluster analysis using the unweighted pair - group method with arithmetical average (UPGMA) separated the 72 pear cultivars and germplasm samples into four major groups: Chinese, European pears, and a cluster of 55 Asian pears that could be reclassify into two subcluster, I - 1st and II - 2nd, according to pedigree information. Almost all of the cultivars were discriminated by 11 microsatellite marker genotypes. The microsatellite DNA profile database may be utilized as tool to verify distinctness, uniformity, and stability between candidate cultivar, and to verify in the distinctness of existing cultivars.

당근 종모 형질 관련 cDNA Library 작성 및 EST 분석

오규동(Gyu-Dong Oh),심은조(Eun-Jo Shim),전상진(Sang-Jin Jun),박영두(Young-Doo Park) 한국원예학회 2013 원예과학기술지 Vol.31 No.6

Carrot (Daucus carota L. var. sativa) is one of the most widely used crops in the world and is nutritionally important crop. However, seed-hair which is generated in epidermal cell of seeds causes the difficulty of the seedling process, because of the seed germination and absorption inhibitions. For these reasons, carrot seeds are commercialized after mechanical hair removal process. However, in this process, various damage and seed loss occur and breeding of hairless-seed carrot cultivar is needed to overcome these various weaknesses and additional seed production costs. In this study, cDNA libraries using 2 combinations, which were composed of short-hair seed CT-ATR 615 OP 666-13 & long-hair seed CT-ATR 615 OP 671-9, and short-hair seed CT-SMR 616 OP 659-1 & long-hair seed CT-SMR 616 OP 677-14, were constructed and EST sequences of each individuals were analyzed to reveal carrot seed-hair characteristics. Firstly, analyzed EST sequences were classified into FunCat functional categories. As a result, significant differences have been identified in metabolism category, protein folding and stabilization, protein binding, C-compound binding category from both of two combinations. Secondly, several candidate EST sequences related to seed trichome differentiation and cellulose biosynthetic process were selected based on GO data of EST sequences. These differences based on FunCat categories and candidate EST obtained by GO data analysis are thought to be involved in the formation of carrot seed hair. Finally, 741 SSR sites and 33 SNP sites were identified from analyzed EST sequences of two combinations. Then we designed SNP and SSR primer sets to develop molecular markers. These molecular markers will be used for classification of carrot cultivars and study seed-hair characteristic.

참나리(Lilium lancifolium Thunb.) 2배체와 3배체의 형태적 변이

장원석(Won Seok Jang),심은조(Eun Jo Shim),배선주(Sun Ju Bae),강중필(Jung Phil Gang),이주경(Ju Kyong Lee),김종화(Jong Hwa Kim) 한국원예학회 2004 한국원예학회 학술발표요지 Vol.2004 No.10

국내에서 수집된 자두의 품종식별을 위한 SSR Profile 데이터베이스 구축

홍지화(Jee-Hwa Hong),심은조(Eun-Jo Shim),박원흠(Won-Heum Park),소은희(Eun-Hee Soh) 한국육종학회 2015 한국육종학회지 Vol.47 No.2

This study was conducted to construct a DNA marker database for 38 plum varieties collected in Korea using simple sequence repeat (SSR) markers. A set of 61 SSR primer pairs was tested to select polymorphic SSR markers between 8 varieties. Among the 61 primer pairs, 21 showed polymorphism, reproducibility and easy scoring. The genetic relationship between the 21 SSR markers and 38 varieties was analyzed. A total of 210 polymorphic amplified fragments were obtained with the 21 SSR markers. Three to seventeen SSR alleles were detected for each locus, with an average of 10.0 alleles per locus. Average polymorphism information content (PIC) was 0.758, with a range from 0.549 to 0.870. A total of 210 SSR marker loci were used to calculate Jaccard’s distance coefficients for cluster analysis by an unweighted pair-group method with arithmetical average (UPGMA). The genetic distance ranged from 0.06 to 1.00 in 38 varieties. Out of 38 plum varieties, 32 were identified using the 21 SSR markers. Therefore, these SSR markers may be employed to complement distinctness, uniformity, and stability (DUS) tests or as potential tools to solve seed disputes regarding plums.

당근 EST 염기서열을 이용한 종자모 형질 관련 SNP 분자표지 개발

오규동(Gyu-Dong Oh),심은조(Eun-Jo Shim),전상진(Sang-Jin Jun),박영두(Young-Doo Park) 한국원예학회 2013 원예과학기술지 Vol.31 No.1

Carrot (Daucus carota L. var. sativa) is one of the most extensively used vegetable crops in the world and a significant source of nutrient because of its high content of β-carotene, well known as the precursor of vitamin A carotenoid. However, seed-hairs generated and elongated from the epidermal cell of seeds inhibit absorption and germination by various factors such as carotol and so on. Accordingly, mechanical hair removal process is essential before commercialization of carrot seeds. Because of this process, producers will have additional losses such as time consuming, manpower, capital and so on. Furthermore, physical damage of seeds causes irregular germination rate. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed and studies for molecular markers related to seed-hair characteristic is needed for a new breeding program. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-SMR 616 OP 659-1 line, hairy-seed phenotype CT-SMR 616 OP 677-14 line and short-hair seed phenotype CT-ATR 615 OP 666-13 line, hairy-seed phenotype CT-ATR 615 OP 671-9 were constructed, respectively. Furthermore, 1,248 ESTs in each line, total 4,992 ESTs were sequenced. As a result, 19 SNP sites and 14 SNP sites in each of 2 combinations were confirmed by analyzing these EST sequences from short-hair and hairy-seed lines. Then we designed SNP primer sets from EST sequences of SNP sites for high resolution melting (HRM) analysis. Designed HRM primers were analyzed using hairy seed phenotype CT-SMR 616 OP 1040 line and short-hair seed phenotype CT-SMR 616 OP 1024, 1025, 1026 lines. One set of HRM primers showed specific difference between the melting curves of hairy and short-hair seed phenotype lines. Based on this result, allele-specific (AS) PCR primers were designed for easier selection between hairy-seed carrot and hairless seed carrot. These results of HRM and AS-PCR are expected to be useful in breeding of hairless seed carrot cultivar as a molecular marker.

당근 종모 형질 관련 EST profiling과 이를 이용한 EST-SSR 및 SNP 마커 개발

오규동(Gyu-Dong Oh),황은미(Eun-Mi Hwang),심은조(Eun-Jo Shim),전상진(Sang-Jin Jeon),박영두(Young-Doo Park) 한국원예학회 2010 원예과학기술지 Vol.28 No.6

Carrot (Daucus carota L. var. sativa) is one of the most widely used crops in the world. Moreover it is an important crop because of its high content of β-carotene, well-known as the precursor of vitamin A carotenoid. However, seed-hair which is generated in epidermal cell of seeds inhibits absorption and germination. For that reason, carrot seeds are commercialized after mechanical hair removal process. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-ATR615 OP 666-13line and hairy seed CT-ATR615 OP-CK1-9 line were constructed and expression patterns related to generation of seed-hair were analyzed by comparison of EST sequences. Differential EST sequence results between two lines were classified into FunCat functional categories based on the results of BlastX search. Higher expression quantities belonging to metabolic category were shown on short-hair seed line than hairy-seed one. Differential expression quantities between those two lines in the protein folding and stabilization, subcellular localization categories were supposed to contribute variously on the generation of seed-hair. We confirmed 50 and 59 SSR sites, and 2 SNP sites by analyzing EST sequences in two lines; thereafter, we designed SNP and SSR primer sets from these EST sequence information as a molecular marker. These markers are thought to be used in research of molecular markers for classification of carrot family and related to various traits, as well as seed-hair characteristic.

불화합성 교잡조합에서 온도가 화주내 화분관 신장에 미치는 영향

경혜영(Hea Young Kyung),정고은(Ko Eun Jung),심은조(Eun Jo Shim),김종화(Jong Hwa Kim) 한국원예학회 2002 한국원예학회 학술발표요지 Vol.2002 No.6