Perilla is a annual herb plant of the mint family, Laminaceae and mainly cultivated in eastern Asia, i.e. Korea, China and Japan. In response to an increased interest for healthy supplement food from the public, people are focusing on the properties of perilla. The applicable parts of perilla plants are the leaves and seeds. Perilla has been cultivated as a source of unsaturated fatty acid oil. But in spite of advantage of the important nutritional traits the genome or molecular studies on perilla remains largely unknown. Sequence comparisons of chloroplast (cp) genomes or nuclear ribosomal DNA (nrDNA) are of great important to provide a evidence for taxonomic studies or species identification or understanding mechanisms that underlie the evolution of perilla species. So, we tried to study a structural analysis of perilla genome and 45s nrDNA using 9 species (3 Diploid; Perilla B-17, P. hirtella, P. setoyensis / 6 Tetraploid; YCPL 285, YCPL 170, YCPL 205-1, YCPL 181-1, YCPL 177-1, YCPL 207-1). The complete cp genome and nrDNA of 9 perilla species were determined using Illumina sequencing technology and analyzed on the variance in base level between perilla B-17 and salvia miltiorrhiza. Total chloroplast genome size of perilla B-17 as a reference was 152,589 bp in length. We also identified an slightly overlapped intergenic regions between salvia miltiorrhiza and B-17. The results above will contribute to growing of molecular or genome structure and functional genomics of perilla available in studying perilla biology. For further study, we will look for genetic diversity of perilla species.

The next-generation sequencing(NGS) technology is being used for more effective genetic mapping. In previous study, we obtained 60x coverage of sequence from Milyang23 and Gihobyeo on average comparing with Nipponbare reference genome. Also, we developed new derived cleaved amplified polymorphic sequence(dCAPS) markers based on the single nucleotide polymorphisms(SNPs) in coding region sequence(CDS) between these varieties. Totally, 1,726,798 SNPs between Milyang23 and Gihobyeo were detected. Among them, 146 SNP were selected for making dCAPS markers and located on genetic map with previously reported 219 PCR-based DNA markers. The map was applied to the detection of quantitative trait loci(QTLs) for stem internode diameters, culm length and panicle length within MGRIL population, and six QTLs with relatively high LOD score were found at three chromosomes; culm length and stem diameter including the first internode diameter, third and fourth internode diameter. This study showed that the NGS allowed the rapid discovery of a large number of SNPs for dCAPS marker. So, we tried to find out more single nucleotide polymorphisms(SNPs) which were located on the whole genome sequence, such as un-translated region(UTR), intron, Inter-region and coding region sequence(CDS) between Milyang23 and Gihobyeo varieties. And we collected phenotypic information about culm length, panicle length, four stem internode diameters and panicle number in rice MGRIL population for QTLs. Furthermore, results of QTL analysis described above will shows relevance of molecular markers in mapping genes for useful breeding.

The next-generation sequencing (NGS) technology is being used for more effective genetic mapping and genome analysis. In this study, we performed whole-genome sequencing on the genomic DNA of Milyang23 and Gihobyeo using NGS and developed new cleaved amplified polymorphic sequence (CAPS) markers based on the single nucleotide polymorphisms (SNPs) in coding sequence between these varieties. Approximately, sequences of 60x coverage of the Nipponbare reference genome on average were obtained following Illumina sequencing. Totally, 1,726,798 SNPs between Milyang23 and Gihobyeo were detected. Among them, 149 SNP were selected for CAPS markers and located on genetic map with previously reported 219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internode diameters, culm length and panicle length in rice with MGRIL population. Newly 6 QTLs were detected for culm length (CL) and stem diameter (ID) traits including the first internode diameter (I1D), third internode diameter (I3D), and fourth internode diameter (I4D). Among those QTLs, qI1D5 and qCL5 had relatively higher LOD score and explained 8.99% and 4.24% of total variation. This study showed that the NGS allowed the rapid discovery of a large number of SNPs for CAPS marker. Only very small portion of SNPs through re-sequencing were used in this study. Furthermore, the results of QTL analysis described above shows relevance of molecular markers in mapping genes for useful traits.

It is well known that Dharial (Bangladesh origin and weedy rice line) has longer seed longevity than indica and japonica rice varieties. To study the genetic basis of seed longevity of Dharial, we developed 240 BC3F7 backcross recombinant inbred lines derived from the crosses between Dharial (a donor parent) and two korea rice accessions (recurrent parents) including Ilmi and Gopum, respectively. Among these lines, we selected two introgression lines with longer seed longevity and named them Ilmi-NIL and Gopum-NIL. Also, we developed an EMS-induced mutant line from Dharial which has shortened seed longevity, and named it Dharial-EMS. We performed re-sequencing of four rice accessions that are Dharial, Dharial-EMS, Ilmi-NIL, and Gopum-NIL. A total of 706×106 raw reads were generated which provided sequence data over 46x rice genome coverage per each accession. We did genome-wide variation analysis comparing produced re-sequencing data and the re-sequencing data of Ilmi from NABIC database with the Nipponbare reference sequence. By graphical analysis of SNP distribution in rice genome of the five accessions, we could select candidate chromosomal segments introgressed from Dharial in Ilmi-NIL and Gopum-NIL. The introgressed chromosomal segments were in seven regions in Ilmi-NIL and eight regions in Gopum-NIL, and four common introgressed regions between Ilmi-NIL and Gopum-NIL were identified. 2,758 SNPs between Dharial and Dharial-EMS were found in the introgressed regions. Also, we detected 450 genes including at least one SNP among these SNPs. This result will facilitate identification of genes and development of molecular markers for improvement of seed longevity.

최근 급속하게 발달한 차세대 유전체분석기술을 기반으로 밀양23호와 기호벼의 유전체 서열을 분석하고, 새로운 CAPS 마커를 개발하였다. NGS를 통해 Nipponbare 유전체 길이의 60 배수만큼 염기서열을 결정하였고, CDS 안에서 두 품종간 특이적으로 나타나는 SNP를 CAPS 마커로 이용하였다. 새롭게 개발된 146개 CAPS 마커와 기존의 보고된 219개 마커를 통합하여 총 365개의 마커로 밀양23호/기호벼의 재조합자식 유전집단에 대해 분자 유전지도를 작성하였다. 벼의 줄기굵기와 간장 그리고 수장에 관한 QTL을 탐색한 결과, 총 19개의 유의성이 있는 QTL을 찾을 수 있었다. 이 중에 4개 줄기굵기 형질 관련 QTL과 2개 간장 형질 관련 QTL이 기존에 보고되지 않은 새로운 QTL이었다. 그 줄기굵기 QTL 중 가장 큰 LOD값을 갖는 qI1D5는 5번 염색체에서 탐색되었으며, 1절굵기 표현형 변이는 8.99%였다. 또한, 간장관련 QTL 중 가장 큰 LOD 값을 갖는 qCL5은 5번 염색체에서 탐색되었고, 이 QTL의 간장 표현형 변이는 4.24%였다. 재염기서열을 통해 밝혀진 SNP 중 소수만이 본 연구에 사용되었다. 향후 본 연구에서 밝혀진 SNP 정보를 이용한다면 더 많은 마커를 개발하여, 고밀도 유전지도 작성이 가능할 것이다. 더 나아가 MGRIL을 이용하여 농업적으로 유용한 형질에 대해 더 정확한 QTL 분석과 유용유전자의 개발이 가능하게 될 것이다.

With the rapid development of sequencing technologies, next-generation sequencing is widely utilized for molecular breeding in several crops including rice. We performed whole genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. In total, 2,448 million raw reads were generated with over 58x coverage of Nipponbare genome. We mapped the reads from each of the ten accessions onto genomic sequence of japonica rice cultivar, Nipponbare. We detected 3,144,016 SNPs, which estimated to be one per 2.2kb on average. We found SNPs in genes that have been reported to be involved in rice flowering time regulation and bacterial blight resistance among ten rice accessions. Unmapped region against Nipponbare genome occupied about 1 ~ 2% in each accession. Over 50% of the unmapped region were found in the repeat region. The minimum length of gap in all accessions were 1bp and the maximum length of gap was 45,967bp in Ilpum. We also identified 3,497 possible gene loss events within these unmapped regions. The frequency of gene loss in each chromosome ranged from 33 on chromosome 5 to 913 on chromosome 11. The genetic variations we detected among ten rice accessions will provide invaluable resources for identification of genes associated with diverse traits of agronomical importance for molecular breeding.

Progress in next-generation sequencing technologies have enabled discovery of massive amount of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDels), which are an invaluable resource to analyze genetic diversity in a population. We performed whole-genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. A total of 2,448 million raw reads was generated with 58-fold coverage and uniquely mapped to 87.5% of the Nipponbare as a reference genome. We identified 3,240,025 DNA polymorphisms including 2,867,878 SNPs, 151,845 insertions and 220,302 deletions between the Korean rice accessions and Nipponbare. We observed that in ten Korean rice accessions, the frequency of potential SNPs was estimated to be one per 2.1kb on Nipponbare (382Mb). According to annotation of DNA polymorphisms, 634,617 SNPs were found in gene region, and only 169,738 SNPs were occurred in coding region. Altogether, 86,251 non-synonymous SNPs were located on 76,891 genes. We also examined the cultivar-specific SNPs to select candidate SNPs which would have possibility of being associated with unique phenotype or agronomical trait of each cultivar. It was estimated that the portion of cultivar specific SNPs is 1~12% of the total SNPs. These DNA polymorphisms obtained from our result will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.

Advances in genome sequencing technologies have aided discovery of millions of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDels), which are an invaluable resource to analyze genetic diversity in a population. We performed whole-genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. A total of 2,447 million raw reads were generated with over 58x coverage and detected 3,240,025 DNA polymorphisms between the Korean rice accessions and Nipponbare as reference genome. We observed that in ten Korean rice accessions, the frequency of potential SNPs was estimated to be one per 2.1kb on Nipponbare (382Mb). Potential SNPs were classified into two types, homozygous SNP and heterozygous SNP, which approximately 87% of the total was homozygous SNPs from ten accessions and heterozygous SNPs accounted for 13%. According to annotation of DNA polymorphisms, 634,620 SNPs were found in gene region, and only 169,738 SNPs were occurred in coding region. Altogether, 86,251 non-synonymous SNPs were located on 76,891 genes. We also examined genes which had at least one SNP in all ten accessions. It was estimated that the total of 290 genes had one or more non-synonymous SNPs and 25 genes had only synonymous SNPs. These genes were functionally classified based on gene ontology (GO). These DNA polymorphisms obtained from our result will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.

The changes in the volatile organic compounds in plum after its electron beam irradiation and storage were determined using the simultaneous distillation extraction method and gas chromatograph-mass spectrometry. There were 44, 46, 45, 47, and 38 volatile compounds in the 0-, 0.25-, 0.5-, 0.75-, and 1 kGy irradiated samples, respectively. Also, the volatile flavor components of the plum that was stored for 30 days were identified as 48, 40, 40, 39, and 40 components. The compositions of the volatile compounds of the control and irradiated samples showed a similarity after the storage. Especially, the more important volatile flavor of the plum was identified as hexanal of the C6compounds, (E)-2-hexenal and (Z)-3-hexenal. In particular, hexanal, (E)-2-hexenal, and (Z)-3-hexen-1-ol increased in all the doses, where as hexanol and (E)-2-hexen-1-ol decreased. Among the lactone compounds, γ -hexalactone, γ-octalactone, and γ-decalactone were identified during the storage period in the raw samples. Hexanonic acid and 2-hexenoic acid were not identified during the storage of the samples, and 2-methylprrole was detected only when the storage samples were irradiated at a dose higher than 0.5kGy. Therefore, it was shown that there was no effect on the variation of the volatile organic component suntil 1 kGy in the plum was irradiated with an electron beam.