Background : Codonopsis lanceolata is used as a natural medicine or vegetables. It originates in East Asia such as Korea, Japan and China. C. lanceolata roots contain various chemical compounds including saponins like Panax ginseng. Although C. lanceolata are cultivated in different regions of South Korea, no variety has been developed. Therefore, it is necessary to develop discriminating methods such as molecular markers in C. lanceolata species. Methods and Results : To find simple sequence repeat (SSR) markers, we sequenced C. lanceolata genomic DNA using Illumina HiSeq 2000 System. A total of 250,455 putative SSR loci were obtained, and 26,334 non-redundant primers were designed to amplify these SSRs. Di-nucleotied repeats were the most abundant SSR reapeats, accounting for 89.53% (23,578) of primer designed SSRs. Tri-nucleotide, tetra-nucleotide and penta-nucleotide accounted for 8.44% (2,223), 1.3%, (348) 0.2% (55), respectively. Tri-, tetra-, and penta-nucleotide (total of 2,626 SSRs) were investigated in silico to identify polymorphism between individuals. Consequently, 573 SSRs showed polymorphism. Forty genomic SSR markers were tested in 16 C. lanceolata plants for determination of PCR amplification and polymorphism. From these primers, 27 (67.5%) amplified products and the average polymorphism information content (PIC) value was 0.52. Conclusion : We development 27 SSR markers from C. lanceolata using NGS, and it could be used for breeding of new varieties in the future.

Background : Astragalus membranaceus is one of the most widely used traditional medicinal herbs in Korea. Studies on the genomic of A. membranaceus resources have not been carried out so far. The present study was carried out to discriminate A. membranaceus based on genetic diversity using genomic simple sequence repeat (SSR) markers. Methods and Results : We collected 5 A. membranaceus lines: Asung, Poongsung, Am-Jecheon, Am-Sancheong, and Am-China. One hundred mg of fresh leaves were used for genomic DNA extraction using the DNeasy plant DNA isolation kit (Qiagen GmbH, Hilden, Germany). 450,449 contigs were searched for 147,766 SSR candidate loci in this study using the MicroSAtellite identification tool (MISA). We selected 949 A. membranaceus genomic SSR markers that were showed variation for the five collections in silico screening with CLC genomics workbench program. The genetic diversity of all A. membranaceus resources was analyzed using 17 SSR markers employing the DNA fragment analysis method. Based on the genetic diversity analysis, these lines were classified into four distinct groups. Conclusion : These findings could be used for further research on cultivar development using molecular breeding techniques and for conservation of the genetic diversity of A. membranaceus. Furthermore, the markers could be used for marker-assisted selection for crop breeding.

Ramie (Boehmeria nivea L.) is a hardy perennial herbaceous plant of the Urticaceae family and has been grown as a fiber crop in several countries including Korea for many centuries. Ramie leaves also have been traditionally used as a major ingredient of a type of rice cake called ‘Song-pyun’ in the Southwest area of Korea, especially Yeong-Gwang province. Despite its economic importance, the molecular genetics of ramie have not been studied in detail yet. Genetic resources of ramie were widely collected from domestic local sites by Bioenergy Crop Research Center (RDA) and Yeong-Gwang Agricultural Technology Center. For the systematic and efficient management of the genetic resources, we developed SSR (simple sequence repeat) markers of ramie. To do this, we generated microsatellite-enriched genomic DNA libraries using magnetic bead hybridization selection method. 247 non-redundant contigs containing SSR motif were generated using nucleotide sequences of 376 clones from the libraries. Primer sets were designed from the flanking sequences of the repeat motif. Finally, we selected 10 SSR markers, possibly showing polymorphism among the genetic resources. Results on the genotype analysis of the ramie genetic resources using the SSR markers will be presented.

Assessing genetic diversity, population structure, and linkage disequilibrium is important in identifying potential parental lines for breeding programs. In this study, we assessed the genetic and phenotypic variation of 174 normal maize (Zea mays) inbred lines and made association analyses with respect to nine agronomical traits, using 150 simple sequence repeats (SSR). From population structure analysis, the lines were divided into three groups. Association analysis was done with a mixed linear model and a general linear model. Twenty one marker-trait associations involving 19 SSR markers were observed using the mixed model, with a significance level of P<0.01. All of these associations, as well as 120 additional marker-trait associations involving 77 SSR markers, were observed with the general model. Two significant marker-trait associations (SMTAs) were detected at P ≤ 0.0001. In the mixed linear model, one locus was associated with water content, two loci were associated with 100-kernel weight, setted ear length, ear thickness and stem thickness; three loci were associated with ear height, four loci were associated with total kernel weight and five loci were associated with plant height. These results should prove useful to breeders in the selection of parental lines and markers.

본 연구는 국내외에서 육성 및 수집된 장미품종에 대하여 SSR 마커를 이용하여 품종식별 연구를 수행하였다. 장미 품종식별에 적합한 SSR 마커를 선정하기 위하여 112개의 SSR 마커를 12개의 주요품종을 대상으로 분석하였다. 최종 선발된 22개의 SSR 마커를 대상으로 69품종을 이용하여 분석하였을 때 대립유전자의 수는 2～10개의 분포를 나타내었으며 총 114개의 대립유전자가 분석되었다. PIC 값은 0.211～ 0.813의 범위에 속하였으며 평균값은 0.621로 나타났다. SSR 마커를 이용하여 작성된 장미 69품종의 품종간 유전적 거리는 0.41～0.87의 범위로 나타났고, 공시 품종 모두 SSR 마커의 유전자형에 의해 구분되었다. 본 연구결과는 장미 품종의 식별과 유전적 다양성 연구를 위한 기초 자료로 유용하게 활용될 수 있을 것으로 기대된다.

총 22개의 감 SSR primer set을 사용하여 주요 재배품종 17품종, 수집한 단감 변이개체 13종 등, 총 30개의 유전적 연관성을 분석하였다. 획득한 469개의 다형성 밴드를 이용하여 UPGMA 방식으로 유사도 및 집괴분석을 수행한 결과, 30개의 품종 및 수집 계통들은 크게 2개의 그룹(cluster)으로 나뉘어졌으며, 제 1 cluster는 다시 3개의 subcluster로, 제 2 cluster는 다시 2개의 subcluster를 형성하였다. 이는 수집 계통들이 기존 대조품종들과 서로 동일군으로 분포되고 있어 형태적으로 유사할 수 있고 근연되어 있지만, 유전자적 수준에서는 다른 조성을 가지고 있음을 보여준다. 평균 유사도의 값은 0.164 이였고 품종간 가장 높은 유사도 값(0.31)을 나타낸 것은 ‘차랑’과 ‘전천차랑’이였고, 가장 낮은 유사도 값(0.02)를 나타낸 것은 Ⅱ 그룹과 비교하여 Ⅰ 그룹에 속하는 ‘Rojo Brillante’였다. 본 연구에 사용된 22 SSR primer set을 통해, ‘차랑’과 ‘전천차랑’을 제외한 대조품종과 수집 계통간의 구별이 가능하여 향후 신품종 개발시 품종보호를 위한 특이적 마커로 효율적으로 사용될 수 있을 것으로 판단된다.

The SSR markers were generally used to analysis the plant genetic diversity, but it have been rarely reported in case of castor bean. We constructed the microsatellite-enriched genomic library and sequenced totally 775 clones to obtain the microsatellite sequence information of the castor bean. Among the sequenced clones, one hundred fifty clones (19.3%) were redundant and four hundred twenty (67.2%) were found to contain microsatellite sequences within the remaining 625 unique clones. A total of 237 primer pairs were designed based on the sequenced microsatellite clones information and evaluated for polymorphism in ten castor bean accessions. Twenty-eight SSR markers produced reproducible polymorphic bands and were further characterized using a diverse set of 25 castor bean accessions. The majority of unique SSRs revealed dinucleotide motives (84%) on the other hand the ratio of trinucleotide motives was 15%. A microsatellite enriched library from the Ricinus communis L. was mainly consisted of [(AG), (GA)/(CT), (TC)] and [(CTT)/(AAG)] microsatellite motifs. The length of dinucleotide SSRs ranged from 4 to 50 repeats with an average 12.4, and that of trinucleotide SSRs from 4 to 56 with an average of 7.35 repeats. These newly developed microsatellite markers will be useful for breeding system and classification of Ricinus communis L.

This study was conducted to assess genetic diversity among 16 genotypes of boxthorn (Lycium chinensis Mill.) using inter-simple sequence repeat (ISSR) markers. The 18 ISSR primers out of 100 primers showed the amplification of 101 reproducible fragments. A total of 56 DNA fragments were polymorphic with an average 3.1 polymorphic bands per primer. The polymorphic primers were divided into 16 anchored primers and 2 non-anchored primers. All of the anchored primers were di-nucleotide repeat motif, and polymorphism level was higher in the primers with poly GA and CT motif than CA and GT motif primers. Based on polymorphism, cluster analysis was conducted by the unweighted pair-group method with arithmetic average (UPGMA) methods. Sixteen boxthorn varieties and accessions were separated into 2 distinctive groups and genetic distance of cluster ranged from 0.82 to 0.97. Eighteen markers were able to distinguish every variety. Therefore, ISSR markers may be suitable for characterizing the large numbers of germplasms and fingerprinting of boxthorn varieties.

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Present study was conducted to evaluate the genetic diversity within a diverse collection of rice accessions used for Korean breeding programs. Two hundred eighty-seven rice cultivars, composed of temperate japonica, tropical japonica, indica, and Tongil-type of Korean crossing parents were evaluated by means of 15 simple sequence repeat (SSR) markers. A total of 99 alleles were detected, and the number of alleles per marker ranged from 4 to 11, with an average of 6.6 per locus. Polymorphism information content (PIC) for each of the SSR markers ranged from 0.2924 to 0.8102 with an average of 0.5785. These results, with the result that use of only 15 SSR markers made all rice cultivars examined could be uniquely distinguished, imply the efficiency of SSR markers for analysis of genetic diversity in rice. Cluster analysis was performed on similar coefficient matrics calculated from SSR markers to generate a dendogram in which two major groups corresponding to japonica (Group I) and indica and Tongil type rice (group II) with additional subclasses within both major groups. The narrowness of the Korean breeding germplasm was revealed by the fact that most of the Korean-bred and Japan-bred temperate japonica cultivars were concentrated into only 2 of the sub-group I-1 (143 cultivars) and I-2 (58 cultivars) among six sub-groups in major group of japonica. This is because of the japonica accessions used in this study was a very closely related ones because of frequent sharing of the crossing parents with similar genetic background with synergy effect of the inherited genetic difference between indica and japonica. A rice breeding strategy with the use of molecular markers was discussed for overcoming of genetic vulnerability owing to this genetic narrowness.