In the painting process of automotive factory, color changeover cost is incurred every time the color of vehicle is changed. To solve this problem, automotive company usually uses storage space such as Selectivity Banks(SB) or Car Rescheduling Storage and carries out sequence planning so that vehicles of the same color are consecutive, which is called Car Resequencing Problem (CRP). So far, research works for CRP has focused on algorithms finding optimal or approximated optimal solutions under the condition that the number of vehicles is fixed in SB. However, these results cannot be directly applied to the actual automotive paint shops since they have continuous flows of cars into SB to be handled in a day. Therefore, in this paper, we propose an efficient cyclic scheduling method that starts the painting process using the result of Accelerated Dynamic Programming (ADP) and then reapplies the ADP to the vehicles in SB for renewing the painting schedule whenever a certain number of vehicles is painted, represented as a threshold. To show the effectiveness of the proposed method, we performed a numerical experiment by designing system configurations, based onthe actual vehicle painting process, and proposed a good threshold that can reduce overall color changeover cost.

As a first step of mapping genes conferring resistance to the brown planthopper, Nilaparvata lugens Stål, in Gayabyeo using a population derived from a cross between Gayabyeo and Taebaegbyeo, we performed the whole genome resequencing of these two Tongil-type rice varieties. The amount of raw sequence data was about 18.5X109 bp and 17.9X109 bp in Gayabyeo and Taebaegbyeo, respectively. After quality trimming and read mapping onto Nipponbare reference genome sequence, 9.3X109 bp was mapped in Gayabyeo with mapping depth of 25.0X, and 9.5X109 bp was mapped in Taebaegbyeo with mapping depth of 25.5X. Between Gayabyeo and Nipponbare, 1,585,880 SNPs were detected, while 1,416,898 SNPs were detected between Taebaegbyeo and Nipponbare. Between Gayabyeo and Taebaegbyeo, 284,501 SNPs were detected. Among the SNPs between Gayabyeo and Taebaegbyeo, 21.2% were in genic region and 78.8% were in intergenic region. In CDS region, 15,924 SNPs were detected, among which synonymous SNPs covered 47.3% and non-synonymous SNPs covered 52.7%. We designed Cleaved Amplified Polymorphic Sequences (CAPS) markers with SNPs in the restriction enzyme recognition sites, and 20 CAPS markers were tested. Of the 20 markers, 19 markers showed polymorphism and one marker showed monomorphism between Gayabyeo and Taebaegbyeo. It is expected that sufficient DNA markers for mapping genes with a population derived from a cross between Gayabyeo and Taebaegbyeo can be developed based on the results of the study.

BADH1 and BADH2 are two homology genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcription region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP P11483(T/A)ishighlycorrelatedwithsalttoleranceindex(STI)(P<10-4). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (P23036, P25390) explain 97% of aroma variation in our germplasm. It indicated that there are no overlapping functions between the two homology genes. In addition, a large LD block was detected in BADH2 region, however, no large LD blocks in a 4-Mb region of BADH1. Only BADH2 region shown significant bias Tajima’s D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (P23036) of BADH2, while both of the BADH1 alleles (SNP P11483(T/A)) did not show large extended LDblock. All these results suggested that BADH2 was identified as a domesticated gene during rice evolution, while BADH1 was not selected by human beings.

Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remain as a great challenge, it is important to establish piratical ways to manage them. A core collection, by definition, refers to a subset of entire population but preserves most of the possible genetic diversity, enhancing the efficiency for germplasm utilizations. Here we reports the whole genome resequencing of the 137 Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in Korean genebank of Rural Development Administration (RDA). We implemented the Illumna HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8x depth using Nipponbare as a reference. Comparisons of the sequences with the reference genome yield more than 15 million(M) single nucleotide polymorphisms (SNPs) and 1.3M insertion/deletion (INDELs). Phylogenetic and population analyses using 2,046,529 high quality SNPs successfully assigned each rice accessions to the relevant subgroups, suggesting those SNPs comprehensively capture evolutionary signatures accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for 4 exemplary agronomic traits from the KRIC_CORE manifest the utility of KRICE_CORE, identifying previously defined gene or novel genetic polymorphisms that potentially regulate the important phenotypes. This study provides strong evidences that the size of KRICE_CORE is small but contains such a high genetic and functional diversity across the genome. Thus those resequencing results will be useful for future breeding, functional and evolutionary studies in the post-genomic era.

Chloroplasts are plant-specific organelles, which have their own genome. Most of the plant chloroplast genomes (CP genome) are highly conserved in terms of its gene contents and genome structures, and they exist in cells with abundant copy numbers. Because of numerous copy numbers, the complete chloroplast sequence assembly pipeline with small amount of whole genome resequencing data, produced by NGS technique, was established in our laboratory. From 14 accessions of cabbage (Brassica oleracea L.) resequencing data produced by Illumina Hi-seq 2000, CP genomes were assembled and compared to each other. 18 sequence variance regions were detected, and 6 HRM(High Resolution Melting curves) markers were developed. Approximately 1 Gb of whole genome sequencing data of 10 Brassica rapa and 2 Brassica napus were also obtained from Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science. With these resequencing data, all CP genomes from these accessions were assembled. Total 27 complete CP genomes of B.oleracea, B.rapa, B.napus, and brassico-raphanus which is a novel allotetraploid species between B.rapa and Raphanus sativus, were compared in sequence level. Phylogenetic analysis based on the comparison revealed that B.rapa could be the maternal species when rapeseeds and brassico-raphanus became allotetraploid species. Additionally, CP genome of B.napus cv.M083 is closer to B.rapa accessions than the other B.napus accessions, thus B.napus could have several different origins.

As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.

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.

Rice is one of the most important crop in the world and the genome sequences of a rice cultivar, Nipponbare has been used not only for rice research, but also as the model reference genome sequences in monocotyledon species among the crops. With the development of the next generation sequencing(NGS) techniques producing high order of coverage and with the need for epigenomic analysis, the need for resequencing of the domestic rice cultivars with the reference “Nipponbare” genome sequence at the de novo level. According the simulation of Nipponbare reference genomes with Eulerian methods, the target size of maximal contig and N50 of ones of the domestic cutivar rice were estimated to be 10M and 1M, respectively. To achieve the target size, various mate-paired libraries were constructed and sequenced. With the high order of coverage obtained from domestic rice cultivar, Ilmi, with NGS technology, the effect of trimming and error correction on reads quality profiles and size distribution of contigs were analyzed. Also the computational parameters for validation of assembled contigs were analyzed. For the analysis of epigenomic methylation modification of the genome sequences, the methyl binding microarray technology was developed. The various methyl-CG binding proteins were characterized. The binding and scanning of methyl-CG domain to promoter binding microarray and their downstream genes were analyzed. Also rice mutants related to methylation were selected to understand the effect of methylation on gene expresson and its effect on phenotypes.

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.

Soybean is one of the most important crop plants used for seed protein and oil content that has undergone substantial phenotypic and physiological changes during domestication. Thanks to the advent of the next-generation sequencing platforms, genome sequences of many major crop plants including soybean and maize have been unraveled. We have resequenced the genomes of 10 cultivated soybean and 6 accessions of their wild progenitors (Glycine soja) selected from the Korean soybean germplasm to >15 × raw data coverage. We have investigated genome-wide variation patterns in soybean and obtained millions of high-quality single nucleotide polymorphisms (SNPs). Further analyses of the extracted SNPs including population structure analysis, introgressions, linkage disequilibrium, and reduction of diversity are ongoing in order to provide an unprecedented opportunity to finely resolve the domestication history of cultivated soybean. At the same time, we have conducted a comparison study between the Williams 82 soybean reference genome sequence and a genetic map. Here, I will present our current analysis status of the soybean genome resequencing data. Then, I present our recent progresses in the understanding of dynamic genetic features of soybean chromosome revealed by comparison of genetic and sequence-based physical maps in which we have used a portion of our resequencing data to substantiate putative introgression region detected during the construction of a genomewide soybean genetic map.

Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples, such as control and exposed tissue. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20x and 50x coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30x coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference EST sequence. In any NGS application, the transcriptome expression information would be more useful than complete genome information research with the lowest sequencing budget for biologists to better understand gene regulation of related genetic phenotypes with the in silico method. The study of target genes related to specific traits including disease resists is available pathway analysis through comparing RNA sequencing among the genotypes.

The application of next generation sequencing technologies allows us to discover the high levels of DNA polymorphism throughout a genome, e.g., single nucleotide polymorphisms (SNPs), and insertions and deletions (InDels). We performed whole-genome resequencing of a Korean rice cultivar (cv. Donganbyeo) and then obtained the sequences of covered 366,042,872 bp (96.63%) with average mapped read depth of 34.17 on 382,788,128 bp of the Japanese cultivar genome (cv. Nipponbare). We characterized the polymorphisms of 173,711 SNPs, 295,334 insertions and 40,642 deletions based on the comparison of both genomes. About 11.5% and 17.8% of the annotated total SNPs were presented in the regions of 1kb upstreams and genes, respectively. The annotated InDels in gene regions were similar with 15.5% insertion (4,588) and 15.9% (5,100) deletions, but not in 1kb upstream regions with 9.0% insertion (2,662) and 14.3% deletions (5,100). In addition, the Korea rice genome sequences were mapped on individual chromosome, resulted that SNPs were shown with different frequencies from each chromosome. The InDels distributions on individual chromosomes exhibited similar pattern as compared to those of SNPs. Some gene families such as NB-ARC (NB-LRR), F-box, RLK (serine/threonine protein kinase) and Zinc-finger (RING) for SNPs occurred the similar pattern with those of Arabidopsis. These results might be useful for better understanding the genome structure and genetic diversity of the Korean rice cultivars.