Showing papers by "Beom-Seok Park published in 2015"

Draft genome sequence of adzuki bean, Vigna angularis.

Abstract: Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.

Development, validation and genetic analysis of a large soybean SNP genotyping array

Abstract: Summary Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under-use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high-density genetic mapping and genome-wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome-wide association analyses. More than four million high-quality SNPs identified from high-depth genome re-sequencing of 16 soybean accessions and low-depth genome re-sequencing of 31 soybean accessions were used to select 180 961 SNPs for creation of the Axiom® SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170 223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions suggest that this array may be suitable for genome-wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.

Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing

Abstract: This manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population. Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of R. sativus cv. WK10039 whose genome has been sequenced onto the chromosomes, we developed a reference genetic map based on genotyping of two parents (maternal WK10039 and paternal WK10024) and 93 individuals of the F2 mapping population by whole-genome resequencing. To develop high-confidence genetic markers, ~83 Gb of parental lines and ~591 Gb of mapping population data were generated as Illumina 100 bp paired-end reads. High stringent sequence analysis of the reads mapped to the 344 Mb of genome sequence scaffolds identified a total of 16,282 SNPs and 150 PCR-based markers. Using a subset of the markers, a high-density genetic map was constructed from the analysis of 2,637 markers spanning 1,538 cM with 1,000 unique framework loci. The genetic markers integrated 295 Mb of genome sequences to the cytogenetically defined chromosome arms. Comparative analysis of the chromosome-anchored sequences with Arabidopsis thaliana and Brassica rapa revealed that the R. sativus genome has evident triplicated sub-genome blocks and the structure of gene space is highly similar to that of B. rapa. The genetic map developed in this study will serve as fundamental genomic resources for the study of R. sativus.

FISH Karyotype and GISH Meiotic Pairing Analyses of a Stable Intergeneric Hybrid xBrassicoraphanus Line BB#5

Abstract: 6 BioBreeding Institute, Ansung 456-756, Korea Abstract: xBrassicoraphanus line BB#5, a new synthetic intergeneric hybrid between Brassica rapa L. ssp. pekinensis and Raphanus sativus L. var. rafiphera induced by N-methyl-N-nitroso-urethane mutagenesis in microspore culture, shows high seed fertility and morphological uniformity. Dual-color fluorescence in situ hybridization (FISH) using 5S and 45S rDNA probes and genomic in situ hybridization (GISH) using B. rapa genomic DNA probe were carried out to analyze the chromosome composition and the meiosis pairing pattern compared to its parental lines. The somatic chromosome complement is 2n = 38, which consists of 17 metacentric and two submetacentric chromosomes with lengths of 2.18 to 5.01 µm. FISH karyotype analysis showed five and eight pairs of 5S and 45S rDNA loci. GISH meiosis pairing analysis showed that 19 complete bivalents were most frequent and accounted for 42% of the 100 pollen mother cells examined. Based on chromosome number, size, morphology, rDNA distribution, and meiosis pairing pattern, both parental genomes of B. rapa and R. sativus appear to exist in xBrassicoraphanus line BB#5, demonstrating its genome integrity. Such stable chromosome constitutions and meiotic pairing patterns in somatic and meiotic cells are very rare in natural and synthetic intergeneric hybrids. Chromosomal studies and genetic and phenotypic changes in allopolyploids are discussed.he results presented herein will be usef ul r fu rther genomic study of x Brassicoraphanus lines and their improvement as promising new breeding varieties.

Genomic Survey of the Hidden Components of the B. rapa Genome

Abstract: The sequencing of the Brassica rapa genome has enabled better understanding of its structure and evolution, and created numerous opportunities for exploration of genome function and breeding applications. Nevertheless, the currently available completed genome sequences are estimated to cover only about 60 % of the genome, while the remaining 40 % is unassembled mainly due to the highly repetitive nature of this portion of the genome. Elucidation of the nature and distribution of repeat elements in the context of the entire genome would enhance our understanding of their role in genome structure, function, and evolution. In this chapter, we review the genomic distribution, characterization and evolutionary implications of currently identified repeat elements comprising the ‘hidden’ portion of the B. rapa genome. Low-coverage whole-genome sequence (WGS) was used to survey the major genomic repeats and their proportion in the B. rapa genome. Coupling this with molecular cytogenetics, we characterized the abundance and genomic distribution of seven major repeats, namely centromeric tandem repeats 1 and 2, centromeric retrotransposons, pericentromeric retrotransposons, 5S rDNA, 45S rDNA, and subtelomeric tandem repeats. These repeats accounted for approximately 20 % of the B. rapa genome, which is much more than the <1 % covered by repeats in the currently available genome assembly. We also compared their distributions among different B. rapa accessions and in the close relative Brassica oleracea, for better understanding of the plasticity of the Brassica genomes.

Genomic Resources and Physical Mapping of the B. rapa Genome

Abstract: The genus Brassica includes the most extensively cultivated dicotyledonous vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. Among the Brassica crops, Brassica rapa has been an ideal model for genomic studies on the Brassica species. B. rapa (AA genome) has a relatively compact diploid genome (529 Mb), compared to Brassica nigra (BB genome, 632 Mb) and Brassica oleracea (CC genome, 696 Mb). There is also a large collection of cultivars and a broad array of available genomic resources including five large-insert bacterial artificial chromosome (BAC) libraries providing 53-fold genome coverage, end sequences of approximately 146,000 BAC clones, >150,000 ESTs from 33 cDNA libraries, successful shotgun sequencing of 886 euchromatic region-tiling BACs, and a BAC-based physical map. These genomic resources provided fundamental basis of the genome sequencing project and contributed to successful assembly of the whole genome sequences.