The chloroplast (cp) is an organelle with its own genome that encodes a number of cp-specific components. Resequencing technology via next-generation sequencing has recently been successfully applied to cp genome characterization. The field of cp characterization is rapidly growing due to its wide versatility and two complete chloroplast (cp) genome sequences of Capsicum species have been reported. We herein report the complete chloroplast genome sequence of Capsicum baccatum var. baccatum, a wild Capsicum species. The total length of the chloroplast genome is 157,145 bp with 37.7% overall GC content. One pair of inverted repeats, 25,910 bp in length, was separated by a small single-copy region (17,974 bp) and large single-copy region (87,351 bp). This region contains 86 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eleven genes contain one or two introns. Pair-wise alignments of cp genome were performed for genome-wide comparison. Analysis revealed a total of 134 simple sequence repeat (SSR) motif and 282 insertions or deletions variants in the C. baccatum var. baccatum cp genome.

In order to assess the genetic diversity, phylogenetic relationships and population structure of Korean rice landraces, 76 accessions were estimated using agronomical traits and SSR markers. Among 11 agronomical traits, amylose content (AC) was the trait with the largest variance with values ranged from 4.9 to 28.39 %, while grain length (GL) was the lowest variance ranged from 4.4 to 5.9 cm. In the result of PCA, the first PC with Eigen value of 217.5 explained 60.3% of the total variance. Culm length (CL) was the variable with the largest positive loadings. Growth period (GP) was the positive variances, while AC was the negative variance. The second PC with Eigen value of 80.6 explained an additional 22.4% of the total variance. Growth period (GP) was variable with highest positive loading. Amylose content (AC) was variable with high positive, while CL was the negative variance. The 49 SSR markers produced a total of 473 alleles with an average of 9.6 alleles. The polymorphism information content (PIC) was in the range 0.11 to 0.93. The observed heterozygosity ranged from 0.12 to 0.39, with an average of 0.61. 76 rice accessions showed two subpoplations and three groups based on SSR markers. Group I and Gropu II appertained Pop-2 and Pop-1 subpopulation, respectively. They showed similar agronomical traits. Group III consisted 7 rice accessions predominantly appertained to Pop-1. These results provide insight into the characters of Korean rice landraces and help to improve our knowledge of rice breeding

Among the diverse crops, rice (Oryza sativa L.) has been domesticated as a staple carbohydrate sources mainly in Asia region, and RDA Genebank at the National Agrobiodiversity Center (NAAS) has conserved about 37 thousand rice accessions accordingly. Seed dormancy, one of domesticated traits, prevents pre-harvest sprouting (PHS) which causes degradation of grain quality in cereal crop. In previous study, we surveyed the variation of seed germinability of diverse 200 rice germplasm and detected the three distinguished groups besides admixed types; the first group (G-1) revealed high germinability at harvesting time, and the second group (G-2) and third group (G-3) acquired high germnability subsequent to after-ripening and dormancy breaking process, respectively. To reduce environmental effects on detected variation of germinability, we selected representative 14 accessions which have similar heading date of each group and measured the degree of PHS using freshly harvested panicles. Variation of PHS showed similar tendency of germinability group; generally, high PHS for G-1, low PHS for G-2 and no PHS for G-3. To resolve genetic and physiological factors concerning on PHS and seed dormancy, we checked the change and variation of ABA known for critical regulator for seed dormancy, and high PHS accessions interestingly revealed high ABA content in 10 DAF. Based on these study, we plan to analyze genetic factors affecting the degree of seed germinability and PHS.

Flavonoids and total polyphenols are important secondary plant metabolites, as they play a role in reducing the oxidative stress caused by ROS In this study, we investigated for flavonoid contents, total polyphenol contents, and antioxidant activities in 27 accessions from 10 Vicia species. Among 27 vicia accessions, NAC17 (V. monantha) and NAC14 (V. hyrcanica) had the highest total flavonoid (1.42 ± 0.09 mg/g) and total polyphenol (124.2 ± 0.5 μg/GAE mg) contents, respectively. In four flavonoids, naringenin showed the highest concentrations in Vicia species. The DPPH and ABTS were the range from 0.2 (NAC24, V. sativa subsp. nigra) to 18.5 (NAC13, V. faba) μg/ASC mg and 19.1 (NAC7, V. cracca) to 253.4 (NAC13, V. faba) μg/Trolox mg, respectively. Among the 10 Vicia species, V. monantha and V. hyrcanica had the highest flavonoid (1.31 ± 0.09 mg/g) and total polyphenol (116.5 ± 2.0 μg/GAE mg) contents, respectively. The highest antioxidant activity was detected in V. faba. These results will expand the flavonoid database and provide information on Vicia species valuable for development of functional foods or feed-additives resources.

DNA barcoding is the use of short DNA sequences of the genome for large scale species identification. The Consortium for the Barcode of Life (CBOL) plant-working group recommended the 2-locus combination as the standard plant barcode. The evolutions of the chloroplast regions combine with nuclear gens are sufficiently rapid to allow discrimination between closely related species. We evaluated the efficacy of the proposed plant barcoding loci matK along with ITS2 for barcoding Vigna species. To assess the discrimination ability of barcoding loci to resolve Vigna species, we sampled 52 of the taxonomically best known groups in the genus. Topologies of the phylogenetic trees based on ITS2 and matK analyses were similar but a few accessions were placed into distant phylogenetic groups. Neither ITS2 nor matK analyses were able to discriminate some closely related Vigna species alone. Thus, we used concatenated data to increase the resolving power of ITS2 and used matK as an additional tool for phylogenetic analysis in Vigna because characterization of the nucleotide sequences of matK region was easier to recover and more cost-effective than those of the ITS region.

Potato virus Y (PVY) and potato leafroll virus (PLRV) are among the most damaging potato viruses and prevalent in most potato growing areas. In this study, cryopreservation was used to eradicate PVY and PLRV using two cryogenic methods. Potato shoot tips proliferated in vitro were cryopreserved through droplet-vitrification and encapsulation-vitrification using plant vitrification solution 2 (PVS2; 30% glycerol + 15% dimethyl sulfoxide + 15.0% ethylene glycol + 13.7% sucrose) and modified PVS2. Both cryogenic procedures produced similar rates of survival and regrowth, which were lower than those from shoot tip culture alone. The health status of plantlets regenerated from shoot tip culture alone and cryopreservation was checked by reverse transcription-polymerase chain reaction. The frequency of virus-free plants regenerated directly from highly proliferating shoot tips reached 42.3% and 48.6% for PVY and PLRV, respectively. In comparison, the frequency of PVY and PLRV eradication after cryopreservation was 91.3~99.7% following shoot-tip culture. The highest cryopreserved shoot tip regeneration rate was observed when shoot tips were 1.0~1.5 mm in length, but virus eradication rates were very similar (96.4~99.7%), regardless of shoot tip size. This efficient cryotherapy protocol developed to eliminate viruses can also be used to prepare potato material for safe long-term preservation and the production of virus-free plants.

Soybean (Glycine max L.) is crucial legume crop as source of high quality vegetable protein and oil, and Korea is regarded as a part of center of soybean origin. To expand the information of conserved genetic diversity, we analyzed the genetic variability of soybean collection mainly introduced Korean accessions using 75 microsatellite markers. A total of 1,503 alleles with an average value of 20.0 alleles were detected among 644 accessions. Korean collection revealed average allele number of 13.4 while Chinese, Japanese and Southeast Asian accessions showed 9.0, 5.4 and 6.5 mean alleles, respectively. Especially, Korean accessions showed more number of private allele per locus as 3.4 contrary to other geographical groups. The mean expected heterozygosity and polymorphic information content was 0.654 and 0.616, respectively, and expected heterozygosity values were not significantly distinguished according to the geographical groups. The phylogenetic dendrogram and deduced population structure based on DNA profiles of 75 SSR loci showed Korean accessions formed distinct gene pool against Chinese accessions, and could be divided into five subpopulations. Korean soybean accessions have specific genetic diversity and might be serve the valuable alleles for bio-industry as a part of the center of soybean origin.

인삼 개갑종자의 초저온보존 효과 및 최적조건을 구명하기 위하여 건조 조건과 수분함량 및 액체질소 보존 전 동결처리와 보존 후 해동처리에 따른 초저온보존 효과를 조사하였다. 건조처리는 25℃ air flow 챔버(RH 10～12%)와 15℃ 건조실(RH 22～25%)을 이용하여 실시하였고 보존 전 동결은 –24℃에서 30일간 처리하였으며 보존 후 해동은 4℃에서 24시간, 40℃에서 2분 처리구를 각각 비교하였다. 그 결과 15℃에서 종자수분 8-12%로 건조된 종자가 보존 전 처리 없이 액체질소에 보존된 후 40℃에서 해동되었을 때 발아율이 가장 높은 것으로 나타났다. 그러나 종자수분이 2.2% 이하일 때 건조가 지속되면 발아율은 감소하는 것으로 나타났으며, 4% 이하에 이르면 보존 전후 처리효과는 나타나지 않는 것으로 조사되었다. 반면 25℃에서 건조된 종자는 상대적으로 높은 발아율을 유지하였다. 건조 및 초저온보존에 의한 인삼 개갑 종자의 유근 및 자엽 생장율을 조사한 결과, GA배지 치상 10일 후 무처리한 대조구에서 첫 유근이 출현하였으며 3주 후에는 자엽발달이 시작되었다. 30일째에는 자엽생장율이 유근발달과 함께 유의하게 증가하는 것으로 나타났다. 치상 30일까지 초저온보존에 의한 생장율은 같은 양상을 보이면서 대조구보다 현저히 낮게 나타났으나 40일째에는 양상은 같았으나 회복율이 대조구보다 증가세를 보였다. 또한 보존 전 동결처리 없었던 종자는 동결처리한 종자보다 모든 처리구에서 높은 유근 및 자엽 생장율을 보였다.

The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, also extending to the temperate regions of South America and tropical. However, utilization of SSR markers have not been investigated extensively in Vicia species as compared to other crop species. Here, we have assessed the potential for transferability (cross-species amplification) of cDNA microsatellites markers developed from common vetch (Vicia sativa subsp. sativa). In total, 226 alleles were detected in 36 microsatellite loci. The number of alleles per marker ranged from one to 20, with an average of 6.3. The gene diversity and polymorphism information content value averaged 0.540 and 0.503, with a range of 0–0.85 and 0–0.84 respectively. For transferability of the SSRs, amplification was carried out with selected from two to 8 accessions of 22 different Vicia species. For individual species, the successful amplification rate ranged from 32.6% in V. ervilia to 81.9% in V. sativa subsp. nigra, with average of 48.8%. As the rate of successful amplification of microsatellite markers generally correlates with genetic distance, these SSR markers are potentially useful in the analysis of genetic relationships between or within Vicia species.

Foxtail millet (Setaria italica L.) is the second most widely cultivated species of millet, especially in East Asia and is a tractable experimental model crop for studying functional genomics of millets. However, insufficient researches had been conducted about the foxtail millet germplasm and is significantly impeding its genetic improvement. We attempted to develop EST-derived-SSR (eSSR) markers and utilize them in genetic comparison of germplasm and transferability. A total of 66,027 foxtail millet EST sequences and 42,754 genomic sequence were deduced transcriptom. Approximately 42,000 single tone contigs were generated using DNAstar 5.0 software for redundancy minimization. Nearly 33% of the 14,012 unigenes contained SSRs, but primers were designed for a total of 314 microsatellites concentrating with more than 24 bp of repeats. A total of 314 primers were successfully designed with more than 24 bp of repeats. From these microsatellites, 56 primer pairs were showed polymorphism with over than 15 bp differences among 96 accessions collected from different countries. Polymorphic information content (PIC) value ranged from 0.020 to 0.700 with an average of 0.381 indicating moderate level of informativeness within these EST-SSRs markers. The EST-SSR markers developed in this study will serve as a useful source for genetic studies, such as genetic variability, transferability, association mapping, and molecular breeding

Rice (Oryza sativa L.) is important crop as a staple carbohydrate sources and was regarded as domesticated in Asia region. The seed dormancy is one of the domesticated traits, and this character allows that plants survive in various environment. The degree of dormancy have been targeted for controling in breeding program while weak dormancy cause pre-harvest sprouting contrary to the nonuniform seed germination by strong dormancy. In this study, we surveyed the variation of germiability in diverse rice genetic resources including japonica and indica ecotype. Overall, the degree of seed dormancy of rice germplasm was distinguished into four groups and admixed types; first group(G-1) included accessions revealing high germiability, the accessions of second group(G-2) acquired the high germiability by after-ripening process, third group(G-3)’s accessions showed high germiability after dormancy breaking process and the accessions of last group(G-4) maintained the low germiability in spite of the dormancy breaking process. Among the 51 japonica accessions G-1, G-2, G-3 and G-4 included 15, 15, 11 and 10 accessions, respectively, and among 40 indica accessions, G-1, G-2, G-3 and G-4 groups included 15, 15, 9 and 1 accessions, respectively. Based on these primary test, we plan to detail examine the seed germiability and survey the genetic factors affecting the degree of germiability in representative accessions of each group

Eggplant (Solanum melongena L.) is an excellent source of vitamin A and C as well as flavonoid compounds, which are important antioxidant components that may reduce the risk of diseases. In this study, we investigated ABTS, DPPH activity and flavonoid contents in eggplant leaves and fruits to identify genetic resources with high antioxidant capacity for use in food or as feed additives. A total of 102 eggplant accessions were classified into four groups by latitude of their origins: 0°~15° N (8 accessions), 15°~30° N (19 accessions), 30°~45° N (34 accessions), and 45°~60° N (41 accessions). The accessions originated from 45°~60°N showed the highest flavonoid contents (AVG. = 15.4 μg mg-1) followed by accessions originated from 30°~45° N (AVG. = 13.0 μg mg-1), 15°~30°N (AVG. = 11.0 μg mg-1) and 0°~15°N (AVG. = 9.5 μg mg-1). Same pattern was also found in ABTS and DPPH antioxidant activities. High ABTS, DPPH activity and flavonoid contents were found in the early-flowering accessions. All flavonoids of the greenish violet leaves were significantly higher than those in green leaves. The flavonoid concentration in eggplant leaves with an average of 15.6 μg mg-1 increased from 10- to 20-fold as compared with their fruit (AVG.=0.9 μg mg-1). In conclusion, eggplant leaves represent a potential source of natural antioxidants due to their very high flavonoid contents.

Rice blast (Magnaporthe oryza B.) is one of the most widespread and devastating diseases of rice. Screening of valuable genetic resources harboring resistance genes is one of the most efficient approaches against blast disease. Because the bioassay to rice blast in the field shows high variations, this study has performed to provide DNA profiles in the accessions of diverse countries using major blast resistant genes linked markers, identified and mapped in different genotypes of rice. Because durable resistance to blast is controlled by a combination of major resistance genes, we surveyed the distribution of blast resistant genes in the 1,500 accessions using major 12 blast resistance genes linked markers. These resistant genes found that the frequency distribution of Pi-39 (66.9%), Pik-m (41.9%), Pit (40.5%), Pii (21%), Pib (19.3%), Pi-d(t)2 (12.7%), but Pita, Pita/Pita-2, Pik, Piz-t, Pi5 genes were identified in less than 10% frequency. Most of accessions contain from 1 to 4 different resistant genes. Pi39 and Pik-m genes amplified in the 69.1% and 51.7% among 356 Korean accessions, Pi39 (79.6%) and Pib (55.8%) in 113 China, Pit (80.6%) and Pib (32%) in 103 Philippines, respectively. In this study, we evaluated the blast resistance degree and the information about the distribution of rice blast resistant genes in rice germplasm. This study will help to develop effective strategies for managing rice blast disease in rice germplasm.

농촌진흥청 농업유전자원센터에 보존되고 있는 우리나라 재래종 벼 유전자원 중 선발된 394품종의 미질과 관련된 특 성을 분석하고 상호관계에 대한 결과는 다음과 같다. 1. 단백질 함량은 5.2~9.9%까지 다양한 분포를 보였고, Mg함량은 12.7 mg에서 37.7 mg까지의 넓은 범위의 분포를 보였으며, K함량 또한 60.0 mg에서 125.9 mg 까지의 넓은 범위의 분포를 나타냈고, 차진정도의 지 표로 사용되는 Mg/K 비율은 일품벼보다 높게 분포하 였다. 2. 쌀의 차진정도를 결정하는 주된 인자이며 미질을 나타 내는 척도의 하나인 아밀로스 함량은 현재 우리나라 밥쌀용 수도 장려품종들이 대체로 18～20% 수준에 있는데 비하여 재래종 유전자원에서 메벼의 범위가 12.4～28.9%였고 18～20% 범위에 있는 품종은 144 품종이었다. 3. KOH에 의한 알카리붕괴도는 0.0~7.0까지 분포하였는 데 일품벼의 6.4와 유사한 품종이 95품종이었다. 4. Toyo 식미계를 이용한 식미 검정에서 현재 양식미 품 종으로 평가받고 있는 일품벼와 유사한 품종이 16품 종이고, 우리나라 사람들이 양식미로 선호하는 호화온 도가 낮고 Toyo 식미치가 높은 품종은 IT 173444번, 008530번, IT 006554번이 대표적 이었다.

Rice genetic resources are composed of various species and ecotypes, and each accession reveals different genetic and phenotypic characters. For the managenment of diverse rice genetic resources, seed integrity is important factor in that the individuals of one accession in self-pollinating crop might be homogeneous. To elevate the management efficiency of rice germplasm contrary to the phenotypic distinction, we focused on applicable microsatellite markers because this markers are widly used for genetic evaluation in diverse genetic resources with a character of high reproducibility and polymorphism. In this regard, we selected microsatellite markers based on genotypes; diversity set including 150 accessions using 249 SSR markers. As SSR loci with high PIC(polymorphism information content) values usually revealed multi bands in one accession, proper genotyping were difficult in these loci. Therefor, we checked the band clarity in addition to PIC values and chose 12 and 6 SSR markers finally. All accessions of rice diversity set were distinguished with the first marker set comprising 12 SSR markers, and only 3 combinations of tested accessions(0.03%, 3/11,175) showed same genotype with second marker set comprising 6 SSR markers. The tested 142 Korean bred varieties revealed 0.19%(19/10,011 combinations) and 0.69%(69/10,011 combinations) genotypic identity using first and second marker set, respectively. These newly selected markers might be useful for the analysis of genetic homogeneity and relationship in rice genetic resources.

The objective of this study was to analyze the genetic diversity using SSR marker and investigate the fatty acid composition of perilla (P. frutescens var. frutescens) germplasm. Genetic diversity among 95 accessions, which consisted of 29 weedy types and 66 landrace accessions, was evaluated based on 12 SSR markers carrying 91 alleles. The mean values of observed (HO) and expected heterozygosities (HE) were 0.574 and 0.640, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped into two distinct groups, which were the landrace, moderate and weedy type, genetic distance (GD) value was 0.609. The physicochemical traits about crude oil contents and fatty acid compositions were analyzed using GC. Among tested germplasm, the total average oil contents (%) showed a range from 28.57 to 49.67 %. Five fatty acids and their contents in the crude oils are as follows: α-linolenic acid (41.12%-51.81%), linoleic acid (15.38%-16.43%), oleic acid (18.93%-27.28%), stearic acid (2.56%-4.01%), and palmitic acid (7.38%-10.77%). The average oil content of wild types was lower than landrace, and the oil content of middle genotype accessions was higher than other germplasm, but no significant variation between landrace and wild types was shown. Nevertheless, IT117174, landrace of Korea, was highest in crude oil content (47.11%) and linolenic acid composition (64.58%) among the used germplasm. These traits of the selected accessions will be helped for new functional plant breeding in perilla crop.

The genus Rubus belongs to the Rosaceae family and is comprised of 600-800 species distributed worldwide. Understanding the genetic relationships and genetic structure in Rubus species is important for enabling efficient management, conservation, characterization and utilization of the species. However, as a minor crop, genetic research foundation was limited to explore genetic diversity and relationships in Rubus species. The present study shows the results of application SSR markers that were developed from SSR-enriched libraries of the one Rubus species (Rubus coreanus Mique.) in our previous study. We used 34 polymorphic microsatellite markers to analysis of genetic diversity within the Rubus species, including redraspberry, blackraspberry, blackberry and mountainberry. All the 34 SSR primers pairs produced 483 polymorphic and reproducible amplification fragments. The largest number of alleles per primer pair was confirmed at GB-RC-167, GB-RC-100, GB-RC-076 and GB-RC-245, which contained 26, 25, 23 and 21, respectively. An average value of polymorphic information contents (PIC) were 0.74 with a range of 0.36 to 0.92. Population structure and phylogenetic analyses showed that all Rubus species formed three largely distinct clusters, which were confirmed by principal coordinate analysis (PCoA). We obtained the results that the developed SSR markers showed a substantial degree of genetic diversity in the various Rubus species distributed in Korea.

Soybean (Glycine max, 2n = 2x = 40) is broadly distributed throughout East and South East Asia, and important crop as a source of protein, oil, food and animal feed. In order to better understand the morphological differentiation of soybean germplasm collected from China, Japan, Korea, Philippines, America, we analyzed the morphological variabilities among 629 soybeans with 11 morphological traits, such as growth type, leaflet, flower color, trichome, seed coat color, color inside seed etc. and measured the fatty acid composition. The result of the principal coordinates analysis (PCoA) based on the 11 morphological traits revealed diversity among all accessions. The PCoA separated the accessions into two main groups, each group with distinctive features. Among tested germplasm, the contents of five fatty acids were as follows: linolenic acid (2.8%－16.23%), linoleic acid (27.4%－56.6%), oleic acid (9.2%－35.0%), stearic acid (2.9%－8.8%), and palmitic acid (8.7%－17.1%). The fatty acid composition has not shown significant variation among all accessions. IT 22268 was the highest linolenic acid composition (16.2%), while IT 154687 was the lowest (2.8%). Forty three of 629 accessions showed the arachidic acid (0.5%-3.6%), which is the saturated fatty acid with a 20 carbon chain and is as a minor constituent of peanut oil (1.1%-1.7%). This result of this characterization served as reliable resources for detailed description and new functional plant breeding of soybean varieties.

During the last decade, considerable progress has been made to understand the molecular mechanisms of M. grisea infection in rice plants and 10 rice blast R genes have been identified and characterized via map-based cloning methods. In case of rice germplasm, the genetic backgrounds of each germplasm accessions are not uniform and the evaluation for pathogenicity is difficult. To solve these problems, we applied the single resistance gene markers to rice germplasm accessions. A molecular survey was conducted to identify the presence of major blast resistance (R) gene in 363 accessions of Korea landrace rice germplasm. The results revealed that the resistance gene Pik-p (100%), Pib (98%), Pi-d(t)2 (98%) and Piz (76%) were widely observed in tested rice germplasm, but Pita-2, Pik and Pi39 gene were identified in less than 10 accessions. Most of landrace contain the four or five different resistant genes, but these results was not consist of field nursery screening. 13 accessions were shown the blast resistance in field nursery screening and Pik-p, Pib, Pi-d(t)2 and Piz genes were observed in these accessions. The evaluation results of blast resistance genes in rice germplasm will help in breeding of multi disease resistant varieties.