Background : The advancement of next-generation sequencing technology dramatically reduces the cost for sequencing and it contributes to create a new research environment that utilizes large amount of genome sequences to answer many biological questions. With this new research trend, reference genome sequences of several major crops have been released to the research community and utilized in various researches in agriculture. Coupled with molecular breeding technology, NGS based genome research will possibly allow selecting a new plant material possessing useful traits in early stage and efficiently developing a superior cultivar. Methods and Results : The objectives of this research are to collecting various genetic variations (SNPs, indels and TE mediated variations) in major and minor crops, to develop molecular markers using NGS based genomic data (resequencing, GBS, transcriptome), and to develop a visualization tools to enhance the utility of the NGS data. Currently major analysis pipelines have been developed to detect SNPs, indel and polymophic SSRs using whole genome and transcriptome data, and a pipeline for identification of MITE insertion polymorphism is under development. In addition to that, for orphan crop, we also implemented an efficient and robust method to assemble a complete chloroplast, mitochondria and 45S rDNA using low coverage whole genome data in order to develop an inter- and intra-specific molecular barcode markers. Conclusion : NGS provide a new level of researches in many crop plants. Large amount of genomic information provides an opportunity to understand domestication and genetic variations, and to develop a better crop for future.

Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops including Brassica oleracea. Therefore, it is important to identify resistance gene for CR disease and apply it to breeding of Brassica crops. In this study, we applied genotyping-by-sequencing (GBS) technique to construct high resolution genetic map and mapping of clubroot resistance (CR) genes. A total of 18,187 GBS markers were identified between two parent lines resistant and susceptible to the disease, of which 4,103 markers were genotyped in all 78 F2 plants generated from crossing of both parent lines. The markers were clustered into nine linkage groups spanning 879.9 cM, generating high resolution genetic map enough to refine reported reference genome of cabbage. In addition, through QTL analysis using 78 F2:3 progenies and mapping based on the genetic map, two and single major QTLs were identified for resistance of race 2 and race 9 of P. brassicae, respectively. These QTLs did not show collinearity with CR loci found in Chinese cabbage (Brassica rapa) but roughly overlapped with CR loci identified in cabbage for resistance to race 4. Taken together, genetic map and QTLs obtained in this study will provide valuable information to improve reference genome and clubroot resistance in cabbage.

Next generation sequencing (NGS) technologies provide a fast and easy way to understand the plant genomes, transcriptomes, regulatory elements and their interactions. About a decade ago, rice was the only crop that whole genome sequence information was publicly available but today many agricultural crops including maize, soybean, tomato, potato, cotton have been sequenced and many more will be available. Moreover newly developed method such as Genotyping-By-Sequencing (GBS) allows efficiently collecting sequence information from hundreds of individuals in population to identify genetic variations, detect quantitative trait loci (QTLs) and develop molecular markers. Coupled with high-throughput phenotyping, the accumulated genomic information will be effectively utilized in crop improvement by genomics-assisted breeding, genome-wide association mapping (GWAS) and genomic selection (GS). Rice is one of the important staple crops providing daily nutrition to more than a half of the world population. The genus Oryza consists of 23 species including two domesticated rice and it has been classified into 10 distinct genome types, represented by six diploids (A, B, C, E, F, and G) and four allotetraploids (BBCC, CCDD, HHJJ, and HHKK). It shows wide ranges of phenotypic variations to biotic and abiotic stress thus is considered a genetic reservoir of unique allelic variation for rice improvement. International collaborative efforts have been focused on generating the Oryza genomics resources including reference genome, transcriptome, smallRNAs, methylome and resequencing of many accessions to collect genetic variations and better understand the 15 MY evolution of Oryza. The Oryza genomic resources will be a backbone to layer various omics data to catalogue more genetic variations within and between Oryza species and the untapped genetic diversities existing in wild Oryza species will be finally translated to crop improvement.