Jang-Ho Hahn

The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice

The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

BackgroundBrassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics.ResultsWe assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago.ConclusionsThis work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.

Characterization and Mapping of a Shattering Mutant in Rice That Corresponds to a Block of Domestication Genes

Easy shattering reduces yield due to grain loss during harvest in cereals. Shattering is also a hindrance in breeding programs that use wild accessions because the shattering habit is often linked to desirable traits. We characterized a shattering mutant line of rice, Hsh, which was derived from a nonshattering japonica variety, Hwacheong, by N-methyl-N-nitrosourea (MNU) treatment. The breaking tensile strength (BTS) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering of rice varieties at 5, 10, 15, 20, 25, 30, 35, and 40 days after heading (DAH). The BTS of Hwacheong did not decrease with increasing DAH, maintaining a level of 180–240 gf, while that of Hsh decreased greatly during 10–20 DAH and finally stabilized at 50 gf. Optical microscopy revealed that Hsh had a well-developed abscission layer similar to the wild rice Oryza nivara (accession IRGC105706), while Hwacheong did not produce an abscission layer, indicating that the shattering of Hsh was caused by differentiation of the abscission layer. On the basis of the BTS value and morphology of the abscission layer of F1 plants and segregation data in F2 populations, it was concluded that the easy shattering of Hsh was controlled by the single recessive gene sh-h. The gene sh-h was determined to be located on rice chromosome 7 by bulked segregant analysis. Using 14 SSR markers on rice chromosome 7, the gene sh-h was mapped between the flanking markers RM8262 and RM7161 at distances of 1.6 and 2.0 cM, respectively. An SSR marker Rc17 cosegregated with the gene sh-h. The locus sh-h for shattering was tightly linked to the Rc locus conferring red pericarp, as well as a QTL qSDs-7-1 for seed dormancy, implying that this region might represent a domestication block in the evolutionary pathway of rice.

SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing

BackgroundAnther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).ResultsA total of 1,165 × 106 raw reads were generated with over 58× coverage that detected 1,154,063 DNA polymorphisms between the Korean rice accessions and Nipponbare. We observed that in Hwayeong and its progenies, 0.64 SNP was found per one kb of Nipponbare genome, while Dongjin, bred by a conventional breeding method, had a lower number of SNPs (0.45 SNP/kb). Among 1,154,063 DNA polymorphisms, 29,269 non-synonymous SNPs located on 30,013 genes and these genes were functionally classified based on gene ontology (GO). We also analyzed line-specific SNPs which were estimated 1 ~ 3% of the total SNPs. The frequency of non-synonymous SNPs in each accession ranged from 26 SNPs in Hwayeong to 214 SNPs in HY-04.ConclusionsThe genetic difference we detected between the progenies derived from anther culture and their mother cultivar is due to somaclonal variation during tissue culture process, such as karyotype change, chromosome rearrangement, gene amplification and deletion, transposable element, and DNA methylation. Detection of genome-wide DNA polymorphisms by high-throughput sequencer enabled to identify sequence diversity derived from anther culturing and genomic locations of heritable traits. Furthermore, it will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.

A database for allergenic proteins and tools for allergenicity prediction.

The AllergenPro database has developed a web-based system that will provide information about allergen in microbes, animals and plants. The database has three major parts and functions:(i) database list; (ii) allergen search; and (iii) allergenicity prediction. The database contains 2,434 allergens related information readily available in the database such as on allergens in rice microbes (712 records), animals (617 records) and plants (1,105 records). Furthermore, this database provides bioinformatics tools for allergenicity prediction. Users can search for specific allergens by various methods and can run tools for allergenicity prediction using three different methods. Availability The database is available for free at http://www.niab.go.kr/nabic/

Identification and characterization of flowering repressor-related genes in Chinese cabbage

In this study, we used a five-step process to identify those genes most likely involved in flowering repression in the Chinese cabbage (Brassica rapa). We tested 6,275 candidate genes with 300K microarrays, which included specific gene expression profiles of FLOWERING LOCUS C (FLC) mutants and normal cultivars during five cold vernalization stages. From that, we identified 289 transcription factor genes and 59 pathway network genes associated with floweringrelated metabolism. Then we compared the 348 genes to 1,287 genes from Gene Ontology and Clusters of Orthologous Groups analyses, which use similar orthologs to categorize conserved genes. Those analyses revealed 10 hypothetical genes for B. rapa, which we verified by reverse transcription-polymerase chain reaction. The final selected genes most likely play regulatory roles in either B. rapa flowering time control or flowering repression during vernalization. While these final genes require further characterization and validation, our study illustrates the usefulness of a multi-layered screening method after initially identifying genes from microarrays.

An integrated database for the enhanced identification of silkworm gene resources.

The National Academy of Agricultural Science (NAAS) has developed a web-based database to provide characterization information in silkworm. The silkworm database has four major function menus: variety searching, characterization viewing, general information and photo gallery. It provides 321 silkworm varieties characterization information for six different regions namely, Korean, Japanese, Chinese, European, Tropical and nonclassified group. Additionally, the database provides 1,132 photo images regarding life cycle of various silkworm varieties. A specific characterization information table provides accession number, variety, strain and larval marking, blood color, cocoon color, cocoon shape, egg colors, remarks and image table provides photos which consist of shape and color in the different stages of larval, egg and cocoon stages. Availability The database is available for free at http://www.naas.go.kr/silkworm/english/

The integrated web service and genome database for agricultural plants with biotechnology information

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage.

Analysis of germinating seed stage expressed sequence tags in Oryza sativa L.

Abstract Seed germination is the important stage to ex-press many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mech-anisms, we were analyzed the rice cDNA clones ( Oryza sativa cultivar Ilpum ) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,668 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as com-monly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages.For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively.

Structural analysis of expressed sequence tags inimmature seed of Oryza sativa L.

Abstract Rice (Oryza sativa) is the most important staple crop in Korea. With its small genome size of 389Mb, rice is a model plant for genome research. We analyzed expressed sequence tag (EST) clones from immature seeds of rice (cv. Ilpum) at 20 days after heading. The 25,668 EST clones were clustered by using SeqMan program and 7,509 clones were selected as unique clones. We compared the 7,509 unique genes with KOME database including the 32,127 FL-cDNA in rice. Finally, 4,990 clones were homologous and 2,519 clones non-homologous to FL-cDNA clones. In addition, we mapped the 7,509 cDNA clones by using TIGR rice pseudomolecule version 5. Ultimately, 7,347 clones were matched to be significant clones related to the TIGR rice pseudomolecules, but 162 clones were unmapped. For the clustering of orthologous group genes, we further analyzed the 7,509 EST clones from immature seeds using NCBI clusters of orthologous groups database. Among the clones, 4,968 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 799 (14.89%), 1,536 (28.3%), 1,148 (21.2%) and 1,936 (35.7%) clones to the previous four categories, respectively.