Blood types in pigs are divided into two types, A and O type. It is important to select and breed O-type pigs that have no hematologic rejection, because the blood type of the donor is an important factor causing immune rejection in xenotransplantation. Therefore, the gene that determines the blood type is GGTA1(glycoprotein, alpha-1,3-galactosyltransferase 1), which generally belongs to the ABO blood group. This study was carried out to develop a simple and accurate method by analyzing the structure of GGTA1 gene which determines blood type. A primer was designed to allow easy identification of the blood type of the target in the first and second deletion regions of intron 7 to distinguish between the A and O genotypes. That is, for the purpose of identifying the blood type using length difference after the PCR, the forward and reverse primers were designed in the highly conservative region. As a result, a pair of primers were prepared and PCR amplification was performed to distinguish three types of genotypes, AA, AO, and OO, using the length difference by electrophoresis. Using the above primers, the parents and their offspring were compared with each other to confirm the correct genetic pattern. And, in four pig breeds, the genes were amplified and the genotype could be correctly identified. In this study, we could diagnose the blood type of AA, AO, OO genotype of pigs by using primer of INDEL region. Especially, since it is possible to diagnose the genotype by the length difference, it is possible to diagnose it quickly and accurately from the gene amplification to the genotype reading

This study was carried out to examine a molecular marker system for parentage test in Jeju Black cattle (JBC). Based on the preliminarily studies, we finally selected for construction of a novel genetic marker system for molecular traceability, identity test, breed certification, and parentage test in JBC and its related industrial populations. The genetic marker system had eight MS markers, five indel markers, and two single nucleotide polymorphisms (SNPs; g.G299T and g.del310G) within MC1R gene which is critical to verify the breed specific genotypes for coat color of JBC differing from those of exotic black cattle breeds such as Holstein and Angus. The results showed lower level of a combined non-exclusion probability for second parent (NE-P2) of 4.1202×10-4 than those previously recommended by International Society of Animal Genetics (ISAG) of 5.000×10-4 for parentage, and a combined non-exclusion probability for sib identity (NE-SI) of 2.679×10-5. Parentage analysis has been successfully identified the JBC offspring in the indigenous population and cattle farms used the certified AI semens for production using the JBC-derived offspring for commercial beef. This combined molecular marker system will be helpful to supply genetic information for parentage test and traceability and to develop the molecular breeding system for improvement of animal productivity in JBC population.

본 연구에서는 국내 콩 유전체의 변이밀집영역(dVB)에서 유 래한 27개 InDel 마커를 신품종 20개에 적용하여 품종판별용 마커로서 범용성을 검증하고 신품종의 구별성과 국내 품종의 유전적 다양성을 확인하였다. 20개 신품종과 MyCrops에 포함된 기존 149개 품종과의 유사도는 평균 61.3%이고, 최저 25.9%에서 최대 96.3%의 유사도로 완전 일치(100%)되는 바코드는 없어 20개 신품종의 유전적 구별성을 모두 확인할 수 있었다. 유연관계를 분석한 결과에서는 신품종을 포함한 국내 169품종이 4개의 유전집단으로 구분되었으며 풋콩 및 단기성 콩의 80%가 I-2 소그룹, 나물콩의 65.9%가 II-2 소그룹에 주로 속한 반면, 장류 및 두부콩은 I-1 (44.4%), I-2 (26.4%), II-2 (23.6%) 소그룹에 고르게 분포하였다. 20개 신품종에 대한 계보도는 나물콩 주요 계보와 장류 및 두부콩으로 크게 두 그룹으로 나누어지며 유연 관계분석을 뒷받침하였다. 품종판별을 위한 최소 마커를 선발 하기 위해 PIC가 높은 공통마커와 품종별 특이마커를 선발하는 2단계 과정을 통해 품종에 따라 7~9개의 최소 마커로 신품종의 진위를 판별할 수 있었다. 이처럼 콩 변이밀집영역에서 유래된 27개 InDel 마커와 이를 이용한 신품종 바코드 정보의 지속적인 업데이트는 수입산에 대한 국산 품종의 보호와 육성가의 권리 증진에 기여하며, 더불어 육종과정 중 신규 유전변이를 도입하고 목표형질을 선발하는 등 육종 효율을 개선하는데도 도움이 될 것으로 기대한다.

Background : Jujube (Zizyphus jujuba. Mill) is a broad-leaved shrub belonging to the family Seagull. Its origin is India and its height is about 5 m. The flowers are gathered in two to three in May-June, with five petals and yellowish green. Leaves are alternate, egg-shaped or long egg-shaped, with clearly visible three veins. The fruit, called jujube, is an elliptical nucleus with the seed wrapped in a solid nucleus. It is 2.5 - 3.5 ㎝ in length, green at first, ripened in brown or reddish brown in September-October. Jujube uses the bud mutation to breed and spreads through grafting. Therefore, there is little difference in phenotype between cultivars. However, because of the lack of research on jujube molecular biology, there is no standard to distinguish the variety at the DNA level. In order to overcome such difficulties and to create a research foundation of jujube, we have developed molecular markers from jujube. Methods and Results : We collected 12 jujube varieties include Bogjo and extracted DNA using CTAB method. The DNA was diluted to 10 ng/㎕ and kept at -20℃. We designed the primer sets using CLC Main Workbench based on DNA InDel regions between the varieties. PCR and electrophoresis were performed to confirm the polymorphism. We designed 26 primer sets from 23 InDel regions. Eighteen of 26 primer sets amplified the amplicon from the primer screening. Eight primer sets were selected for polymorphism assays. All primer sets showed polymorphism. The domesticated cultivars were divided into two groups and the Japanese and Chinese varieties were separated. Conclusion : The InDel markers developed in this study could be good tools to differentiate the jujube cultivars cultivated in Korea.

Background : Angelica species are representative medicinal plants and it has been used in traditional medicinal methods, especially, in the traditional Asian medicine. The Angelica species used in conventional medicine varies by country according to specific regulations, i.e. A. gigas Nakai in Korea, A. sinensis Diels in China, and A. acutiloba Kitagawa in Japan. Because of the similarity between the names among Angelica, they can be confused in the market. Methods and Results : In this study, twenty-four chloroplast insertion or deletion (cpInDel) markers were developed from chloroplast DNA of A. gigas Nakai and tested for the classification of Angelica species. Primer sets were designed from flanking sequences of the discovered InDel loci from chloroplast DNA of A. gigas Nakai using CLC Main Workbench with the following parameters : primer length = 18 - 26 bp (Opt. 23 bp); GC% = 50 - 70% (Opt. 60%); Ta = 55 - 62℃ (Opt. 58℃); product size range = 120 - 300 bp. Polymorphism and genotype analysis of 13 Angelica species were performed using the developed cpInDel markers. Conclusion : The 24 cpInDel markers developed in this study could be used for genetic diversity analysis and classification of Angelica species.

Knowledge of the chromosomal constitution of the ancestors of modern soybean will complement plant breeding efforts to improve agronomic and economic characteristics of soybean. Variation block (VB)-based comparison using genome-wide insertion/deletion (InDel) markers was used on a diverse panel of 147 soybean cultivars to assess the impact of chromosomal changes during modern breeding. There were identical variation patterns of the examined InDels consistently appearing in the genome parts arising from parental varieties, indicating that soybean chromosomes in descendants should be all determined by genetic reshuffling of VBs inherited from parental chromosomes. Structure analysis of the accessions through the 202 InDels separated the accessions into four subgroups. Gene introgression revealed by the structure analysis agreed with the fact that a limited number of landraces and elite varieties were introduced and used as donors for breeding soybean cultivars in pedigree analysis. Especially, VBs became more reshuffled over time as a result of the breeding process, which resulted in using breeding parents with new VB-types for improving the end-use value of soybean. Therefore, their clustering using the 202 VB-specific InDels is strongly influenced by the difference in breeding ancestors among the subgroups. This indicates that the 202 InDel markers are very useful for genetic study by analyzing the reshuffling patterns of the parental genomes in the descendant.

Background : Angelica gigas is a monocarpic perennial plant. A. gigas, also called DangGui or Korean Angelica, is a major medicinal herb used in Asian countries such as Korea, Japan and China. In Korea, we are using the roots of A. gigas. but, Chinese using Angelica sinensis and Japanese using Angelica acutiloba with the same name 'DangGui'. The biggest problem in the use of A. gigas is the confusion with A. acutiloba or A. sinensis. This confusion can cause an medical accident or lack of pharmacological ingredients. In this study, we developed chloroplast InDel markers that can distinguish A. gigas, A. acutiloba or A. sinensis. Methods and Results : We collected 14 Angelica plant samples including A. gigas, A. acutiloba and A. sinensis and extrated DNA using CTAB method. The DNA was diluted to 10 ng/㎕ and kept -20℃. We designed the primer sets using CLC Main Workbench based on chloroplast DNA InDel region of between A. gigas and A. acutiloba. PCR were performed on the 14 Angelica plant samples including A. gigas, A. acutiloba and A. sinensis (5 repeats each). Electrophoresis was performed using fragment analyzer automated CE system. We designed 6 InDel primer sets and the primer sets amplified the amplicons effectively. Three of the 6 primer sets showed polymorphism. Conclusion : We could distinguish A. gigas, A. acutiloba, and A. sinensis using 2 newly developed InDel markers.

Cultivated tomato (Solanum lycopersicum L.) is an economically important vegetable and has a narrow genetic base due to intensive human selection through domestication and breeding. The low level of genetic variation between cultivated tomatoes has made it difficult to develop molecular markers for elite breeding lines. Recently, genome-wide 145,695 InDels were identified from in silico analysis of two tomato genome sequences, Heinz 1706 (S. lycoperiscum) and LA1589 (S. pimpnellifolium). Of these, 2,272 InDels were validated and 717 InDels showed polymorphism in cultivated tomatoes. In the present study, we selected 48 out of 717 InDels based on PIC value (> 0.3) and size (> 10 bp) to develop a DNA database for commercial tomato cultivars. We also used an additional set of 28 InDels that have been previously reported. These markers were distributed across 11 chromosomes with an average of 6.6 markers. A total of 48 F1 hybrid cultivars were collected from 20 seed companies and a subset of eight cultivars were used to test polymorphism of the InDel markers. The 37 InDel markers were polymorphic in these cultivars and were used to genotype additional 40 cultivars. Genetic distances and relationships between cultivars were assessed using the InDel genotypes of 48 cultivars. This analysis revealed that the InDel markers detected genetic variations to identify 46 cultivars. Our results demonstrate that the InDel markers will be a useful resource to construct a DNA database for tomato cultivars and to protect tomato breeder’s rights via variety identification.

Currently, the type of short insertions and deletions (InDels) polymorphisms are increasingly focused in genomic research. InDels have been known as a source of genetic markers that are widely spread across the genome. Genetic relationship among Korean pear cultivars compared with their parents was also identified that they are closely related P. pyrifolia, P. ussuriensis and/or hybrids between two species. Lack of genetic resources including molecular markers has made it difficult to study pears severely. Recently developed next generation sequencing (NGS) platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The main goal of this study was to develop polymorphic InDel markers in ‘Whangkeumbae’ and ‘Minibae’, which were chosen as the representative cultivars of P. pyrifolia and P. ussuriensis × pyrifolia in each among Korean pears using genomic sequences generated by NGS technology. In this study, more than 18.6 Gbp and 15.8 Gbp sequences were obtained from NGS of ‘Whangkeumbae’ and ‘Minibae’, respectively. ‘Whangkeumbae’ contained 197,210 InDels and 197,272 InDels in ‘Minibae’. In InDels validations between ‘Whangkeumbae’ and ‘Minibae’, the number of polymorphic InDels were 149,338 and non-polymorphic InDels were 122,572. For InDel primer set designing, 11,308 of primers were designed from polymorphic InDels and 10,919 of InDel primers were recommended. The study shows that the utility of NGS technology to design amount of efficient InDels and the developed InDel primers will be used for genetic mapping, breeding by marker assisted selection (MAS) and QTL mapping of Korea native pear as well as further genetic studies.

Sequence diversity was accumulated through evolution and breeding process. A set of 595 PCR-based novel insertion/deletion (InDel) markers was designed in order to widen the genetic basis for national rice breeding programs. The markers were generated by analyzing of 40 Korean cultivars and published genome sequences of rice(Oryza sativa L. spp japonica). We selected 112 markers spread across all rice chromosomes among the 595 InDel markers, and they showed polymorphic between rice cultivars, which are 284 Korean japonica and Tongil varieties. Due to their simplicity in design and robustness in genotyping, these InDel markers have been routinely used in quantitative trait loci (QTL) mapping studies and marker assisted selection programs for rice. Moreover, the PCR amplification type of InDel markers was converged to digital code, 0 or 1 and then finally represented as one- and two dimensional bar-code system, which could easily differentiate genetically highly homologous japonica rice cultivars. The developed InDel markers uniquely discriminated among each of the Korean cultivars. Therefore, the systems we developed may be valuable tools in discrimination from cultivars

Bitter buckwheat, also called tartari buckwheat (F. tartaricum), contains large amount of rutin and it has antioxidant activity compared to common buckwheat. But after harvesting and processing, the discrimination of two species through visual inspection was almost impossible. Therefore we developed InDel markers to identify common and tartari buckwheat content based on the chloroplast genome sequence. We conducted complete full chloroplast genome sequence of tartari buckwheat and compared with common buckwheat chloroplast genome sequence (NC010776). Based on the mVISTA alignment, we found eight big InDel (above 50bp) regions. Among the InDel, 6 regions are intergenic region and two are genic region in ycf1. We designed InDel specific primers and applied to PCR with buckwheat genomic DNA to check the discrimination of two species. These InDel specific primers also applied to buckwheat germplasm, 75 tartari and 21 common buckwheat. Among the primers, 5 markers could be successfully amplified in all germplasm species specific amplicon. And we can detect 10pg/ul of DNA and processed food such as tea and noodle. These results could improve the QC (Quality control) of tartari buckwheat food