In this talk, I will describe recent advances in the field of metazoan comparative genomics and regeneration, the insights into the marine animal genomic and annelid regeneration. The scientific questions arising from the ability of certain species, but not others, to massively regenerate their bodies are among the most fascinating and challenging confronting modern cell and developmental biologists today. The tremendous implications of this research area for human medicine and tissue engineering are obvious. Yet many other animals exhibit robust regenerative capabilities, including "lower" vertebrates such as amphibians, and invertebrates such as echinoderms, flatworms and annelids. In the extreme case, some species can reproduce vegetative indefinitely. Such animals must contain the operational equivalent of immortal, totipotent somatic stem cells. From invertebrates to the higher vertebrates, their metabolic pathway, developmental regulatory genes, and intercellular signaling pathways are evolutionary conserved. With these, study on regeneration is an ingenious, powerful model system for studying the post-embryonic development, innate immunity mechanisms, and primordial germ cells (PGCs).

Although decapod crustaceans are one of the most important fisheries resources with high market value, we still have only limited knowledge about their basic physiology related to growth, development, and reproduction. This is mainly due to the lack of tools to manipulate genetic information leading the phenotype changes. Recently physiological study for decapod crustaceans changed dramatically by both the development of next-generation sequencing (NGS) technology and RNA interference (RNAi). Significant decrease in the cost for reading genome or transcriptome allowed the even single lab can manage the omics-level study about the non-model system, decapod crustaceans. As genomic and transcriptomic data increased, we are able to screen novel genes in decapod crustaceans related to growth and development. As another useful tool, gene silencing through RNAi is gaining momentum for decapod crustaceans. RNAi has proven instrumental in a growing number of crustacean species, revealing the functionality of novel crustacean genes. Major research topics in decapod crustaceans include immune response, reproduction, development, homeostasis, molting and growth, and environmental stress. In addition to any changes in phenotype, tanscriptomic analysis induced by the specific gene knockdown by RNAi extended our knowledge of physiological responses of novel crustacean genes. Those new techniques extend our knowledge about crustacean physiology providing the basis for increasing productivity of decapod crustaceans.

Radish is one of the most widely consumed vegetable crops in Korea. Root is the major part of radish supplied to the market, thus the size, shape, and quality of radish roots are main targets of breeding programs. Despite of the importance of this crop, the molecular breeding of radish is still in the rudimentary stage. In Golden Seed Project, we aim to establish the molecular breeding program of radish using genome-wide approaches. To this end, we selected inbred lines that have distinctive root traits such as yield, shape, disease resistance, and texture. Single nucleotide variation (SNV) among these lines will be identified based on the low coverage genome sequencing data. These SNVs can be used for finding genomic regions associated with root traits from segregating mapping populations which are also in the middle of development. Korean radish roots are harvested after being grown for only nine weeks. During that period, root biomass reaches to more than two kilograms. While investigating the root growth of radish inbred lines, we found that cytokinin contributes as a key growth regulator that promotes radial growth of radish roots. A difference in growth rates of two distinctive inbred lines was explained by the difference in response to cytokinin. Genes responsive to cytokinin are highly enriched in the cambium, the meristematic cell population that drives radial growth. For comprehensive understanding of genes that affect yields of radish roots, we turned to developing a tissue specific transcriptome data using laser capture microdissection. We expect that the compendium of genomics-based data will help establishing molecular breeding of radish at a fast track.

Comparative analysis is a typically useful tool for translating genomic information from one species to another. However, currently available softwares are relatively difficult to directly use for researchers that are not familiar with use of bioinformatic tools. Therefore, we intended to develop a new platforms and/or interface through which one can use in more comfortable way, based on the concept of interactive comparative analysis. Towards this direction, we, firstly, constructed relational database to store the information on abiotic stress genes identified from multiple plant species using various resources, such as the TAIR (http://www.arabidopsis.org), gene expression profiles and relevant literatures, and linked with comparative analysis interface. For purposes of comparative analysis and identification of synteny blocks, cross-species orthologous genes were determined using a combination of tBlastX and BlastP homology searches. We adapted and developed a Circos-like format to present resulting comparative maps. Users can readily choose analysis parameters, for example individual genes and specific chromosomes for chosen species, in the pane of analysis DB, which is useful feature to avoid complexity of comparative genomic analysis. This DB-associated comparative analysis tool, developed in this study, will be able to provide customer-friendly interface for comparative analysis and extend its utility across a broader range of plant genomes.

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for screening target loci with agricultural traits. We propose the variation block method, a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing short-read DNA sequences of the cultivar to a reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are named as variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybeans and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for recombination block-level comparison of crop genomes. We expect that this method holds the prospect of developing crop genomics by bringing genomics technology to the field of crop breeding.

Genetic resources play a great role in crop breeding because of containing a broad array of useful genes. Currently, the harder are rice breeders trying to develop new rice cultivars with the improved traits, they are more often handicapped by the limited availability of germplasm resources. Thus, a desirable core or heuristic (HS) set of germplasm with maximum genetic diversity can be usefully exploited to breakthrough the present and future challenges of the rice breeding. As such we previously developed the rice HS sets of 166 diverse accessions out of a total 24,368 rice germplasms. Here, we report a large-scale analysis of the patterns of genome-wide genetic variations accumulated in the HS as well as Korean rice over the time. We characterized a total of about 11.8 millions of single nucleotide polymorphisms (SNPs) across the rice genome from resequencing a total of 295 rice genomes including 137 HS and 158 KB rice sets, with an average of approximately 10x depth and > 90% coverage. Using about 460,000 high-quality SNPs (HQSNPs), we specified the population structure, confirming our HS set covers all the rice sub-populations. We further traced the relative nucleotide variabilities of HQSNPs and found the level of the diversity was dynamically changing across the KB genome, which reveals the selection history of KB lines in the past and present. In addition, the results of our genome wide association study (GWAS) suggests that our HS can be also a good reservoir of valuable alleles, pinpointing those alleles underlying the important rice agronomical traits. Overall, the resequencing of our HS set re-illuminates the past, present of the germplasm utilization, which will support the Korean rice breeding in the future.

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for screening target loci with agricultural traits and for developing designed cultivars. We propose the molecular breeding platform based on the variation block (VB) method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybeans and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. In addition, we identified recombination hot spots of soybean genome in 614 recombinant inbred lines (RILs) using VB-specific indel markers. We expect that this platform facilitate the development of designed cultivars by introducing precise target loci into plant genomes.

Although much effort has been made to find agronomically important loci in the soybean plant, extensive linkage disequilibrium and genome duplication have limited efficient genome-wide linkage analyses that can identify important regulatory genes. In this respect, recombination block-based analysis of cultivated plant genomes is a potential critical step for molecular breeding and target locus screening. We propose a new three-step method of detecting recombination blocks and comparative genomics of bred cultivars. It utilizes typical reshuffling features of their genomes, which have been generated by the recombination processes of breeding ancestral genomes. To begin with, mutations were detected by comparing genomes to a reference genome. Next, sequence blocks were examined for likenesses and difference with respect to the reference genome. The boundaries between the blocks were taken as recombination sites. All recombination sites found in the cultivar set were used to split the genomes, and the resulting sequence fragments were named as core recombination blocks (CRBs). Finally, the genomes were compared at the CRB level, instead of at the sequence level. In the genomes of the five Korean soybean cultivars used, the CRB-based comparative genomics method produced long and distinct CRBs that are as large as 22.9 Mb. We also demonstrated efficiency in detecting functionally useful target loci by using indel markers, each of which represents a CRB. We further showed that the CRB method is generally applicable to both monocot and dicot crops, by analyzing publicly available genomes of 31 soybeans and 23 rice accessions.

In the past half century, production of major food crops in the world has kept pace with the population increase. The yields of major cereals such as maize, rice and wheat have been more than doubled in most parts of the world and even tripled in certain countries. However, food production is facing even greater challenges in the next half century because of high demands in both quantity and quality, and ever increasing pressures on resources and environments. At the same time, advances in genomics, biotechnology and genetic studies have brought about unprecedented opportunities for crop genetic improvement. Rice is a major food crop feeding approximately half of the world’s population, and has provided a model system for cereal research. In my presentation, I will describe the demands for increased production for future needs, address the main issues that we have encountered as challenges, present current progress in rice functional genomics research, and provide prospect on how the advance in research can be translated into technologies and activities for rice genetic improvement.

The plant cell wall is an extracellular matrix, which can be viewed as a multifunctional subcellular compartment involving many fields of research: growth and development, plant-pathogen interactions, stress, cell-to-cell signaling, metabolic processes, biomaterials and biofuels, and many others. Given its importance, much of the research effort has been directed toward investigating the plant cell walls containing plant cell wall proteins, which are essential constituents of plant cell walls and play essential roles in many biological processes, and yet there is still not a distinct repertoire of the plant cell wall proteins. Several functional screen procedures including a yeast secretion trap, an Agrobacterium-mediated transient expression assay and a subcellular localization study, have been recently optimised to confirm secretion and localization of an ever-growing list of plant cell wall proteins. These functional screen approaches collectively provide a powerful suite of means to identify and characterize a dynamic and complex plant cell wall proteome. Thus, the potential outcomes of plant cell wall functional genomics will enable plant breeding programs to develop new strategies for improvement of crop quality.

In recent years, genomic resources and information have accumulated at an ever increasing pace, in many plant species, through whole genome sequencing, large scale analysis of transcriptomes, DNA markers and functional studies of individual genes. Well-characterized species within key plant taxa, co-called "model systems", have played a pivotal role in nucleating the accumulation of genomic information and databases, thereby providing the basis for comparative genomic studies. In addition, recent advances to "Next Generation" sequencing technologies have propelled a new wave of genomics, enabling rapid, low cost analysis of numerous genomes, and the accumulation of genetic diversity data for large numbers of accessions within individual species. The resulting wealth of genomic information provides an opportunity to discern evolutionary processes that have impacted genome structure and the function of genes, using the tools of comparative analysis. Comparative genomics provides a platform to translate information from model species to crops, and to relate knowledge of genome function among crop species. Ultimately, the resulting knowledge will accelerate the development of more efficient breeding strategies through the identification of trait-associated orthologous genes and next generation functional gene-based markers.