Kyujung Van

Seoul National University, Sŏul, Seoul, South Korea

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Publications (50)115.27 Total impact

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    ABSTRACT: Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL) for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr) 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both Chrs. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.
    Frontiers in Plant Science 06/2013; 4:176. DOI:10.3389/fpls.2013.00176 · 3.64 Impact Factor
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    ABSTRACT: Phomopsis seed decay (PSD), primarily caused by Phomopsis longicolla, is a major contributor to poor soybean seed quality and significant yield loss, particularly in early maturing soybean genotypes. However, it is not yet known whether PSD resistance is associated with early maturity. This study was conducted to identify quantitative trait loci (QTLs) for resistance to PSD and days to maturity using a recombinant inbred line (RIL) population derived from a cross between the PSD-resistant Taekwangkong and the PSD-susceptible SS2-2. Based on a genetic linkage map incorporating 117 simple sequence repeat markers, QTL analysis revealed two and three QTLs conferring PSD resistance and days to maturity, respectively, in the RIL population. Two QTLs (PSD-6-1 and PSD-10-2) for PSD resistance were identified in the intervals of Satt100-Satt460 and Sat_038-Satt243 on chromosomes 6 and 10, respectively. Two QTLs explained phenotypic variances in PSD resistance of 46.3 and 14.1 %, respectively. At the PSD-6-1 QTL, the PSD-resistant cultivar Taekwangkong contributed the allele with negative effect decreasing the infection rate of PSD and this QTL does not overlap with any previously reported loci for PSD resistance in other soybean genotypes. Among the three QTLs for days to maturity, two (Mat-6-2 and Mat-10-3) were located at positions similar to the PSD-resistance QTLs. The identification of the QTLs linked to both PSD resistance and days to maturity indicates a biological correlation between these two traits. The newly identified QTL for resistance to PSD associated with days to maturity in Taekwangkong will help improve soybean resistance to P. longicolla.
    Theoretical and Applied Genetics 05/2013; DOI:10.1007/s00122-013-2115-8 · 3.51 Impact Factor
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    ABSTRACT: Mungbean [Vigna radiata (L.) Wilczek], a self-pollinated diploid plant with 2n = 22 chromosomes, is an important legume crop with a high-quality amino acid profile. Sequence variation at the whole-genome level was examined by comparing two mungbean cultivars, Sunhwanokdu and Gyeonggijaerae 5, using Illumina HiSeq sequencing data. More than 40 billion bp from both mungbean cultivars were sequenced to a depth of 72×. After de novo assembly of Sunhwanokdu contigs by ABySS 1.3.2 (N50 = 9,958 bp), those longer than 10 kb were aligned with Gyeonggijaerae 5 reads using the Burrows-Wheeler Aligner. SAMTools was used for retrieving single nucleotide polymorphisms (SNPs) between Sunhwanokdu and Gyeonggijaerae 5, defining the lowest and highest depths as 5 and 100, respectively, and the sequence quality as 100. Of the 305,504 single-base changes identified, 40,503 SNPs were considered heterozygous in Gyeonggijaerae 5. Among the remaining 265,001 SNPs, 65.9 % (174,579 cases) were transitions and 34.1 % (90,422 cases) were transversions. For SNP validation, a total of 42 SNPs were chosen among Sunhwanokdu contigs longer than 10 kb and sharing at least 80 % sequence identity with common bean expressed sequence tags as determined with est2genome. Using seven mungbean cultivars from various origins in addition to Sunhwanokdu and Gyeonggijaerae 5, most of the SNPs identified by bioinformatics tools were confirmed by Sanger sequencing. These genome-wide SNP markers could enrich the current molecular resources and might be of value for the construction of a mungbean genetic map and the investigation of genetic diversity.
    Theoretical and Applied Genetics 05/2013; DOI:10.1007/s00122-013-2114-9 · 3.51 Impact Factor
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    ABSTRACT: Soybeans are an important crop known to harbour a complex of Diaporthe and Phomopsis species. This complex has been reported to be involved in several soybean diseases, including Phomopsis seed decay. In this study, two species of Diaporthe/Phomopsis fungi from soybean plants were identified by morphological and molecular characterizations. Koch's postulates were confirmed by pathogenicity tests on hypocotyls of soybean seedlings. Phomopsis longicolla was found to be the most common and virulent pathogen to soybeans in Korea. Phomopsis sp., which was considered as a new soybean pathogen, might have been introduced from other plants given that similar strains of Phomopsis sp. have infected fruit trees in China, Japan and Portugal and vegetable plants in the United States.
    Journal of Phytopathology 02/2013; 161(2). DOI:10.1111/jph.12034 · 0.92 Impact Factor
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    ABSTRACT: By exploiting next-generation sequencing (NGS) technologies, many species including economically important crops, have been subjected to whole-genome sequencing by de novo assembly and resequencing. Now, sequencing technologies have evolved from genome sequencing projects using massive parallel sequencing technologies such as NGS to NGS of single DNA molecules (next–NGS). This NGS technology provides us with better opportunities for studying crop genomics and other post-genomics (transcriptomics, proteomics, metabolomics) more closely. Via the discovery of molecular markers generated by NGS and other analyses, we can also explore genetic diversity and crop evolution by full genome sequencing of crop species and many accessions within crop species. The increasing availability of high-throughput technology and the reduction of costs of these technologies have moved genomics from the sequencing of a few model species to sequencing any crop that is important for food security. In this paper, we introduce whole-genome sequencing technology and the status of crop genome sequencing, and we discuss the applications of NGS to crop improvement.
    SABRAO journal of breeding and genetics 01/2013; 45:84-99. · 0.23 Impact Factor
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    ABSTRACT: The availability of next generation sequencing instruments has made large-scale and genome-wide sequence analysis more feasible in a wild variety of species with large complex genomes, especially crops. This report suggested an approach for characterizing large complex genomes of less-studied/orphan crops. Degenerate oligonucleotide primed PCR (DOP-PCR) is a useful tool for the survey of genomes in less-studied/orphan crops, as prior sequence information is not necessary. Here, four different degenerate primers were redesigned from previously described DOP-PCR primers. The degeneracy of these primers was increased with the addition of two more ‘Ns’. The amplified DOP-PCR products from Sinpaldalkong 2, a soybean genotype, were applied to GS-FLX and the reads from Sinpaldalkong 2 were mapped against Williams 82 as a reference (http://www.phytozome.net/soybean.php), using the Burrows-Wheeler Aligner (http://bio-bwa.sourceforge.net/). These results suggest the identification of 4 single nucleotide polymorphisms between Sinpaldalkong 2 and Williams 82 and recent duplication of the soybean genome. The sequenced reads were subsequently assembled into contigs by Newbler under default conditions. A total of 29 Sinpaldalkong 2 contigs exhibited 95% similarity and < E-100 when mega-blasted with Williams 82 reference sequences. These contigs were mapped to the soybean chromosomes and positioned as clusters within each chromosome. Most of the contigs also showed similarity with the Arabidopsis RNase H domain-containing protein, suggesting a potential way to study retrotransposons in less-studied/orphan crops. Using these modified DOP-PCR primers and GS-FLX, it is possible to obtain insight into the large complex genomes of less-studied/orphan crops.
    Genes & genomics 10/2012; 34(5). DOI:10.1007/s13258-011-0238-3 · 0.57 Impact Factor
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    ABSTRACT: BACKGROUND: R genes are a key component of genetic interactions between plant and biotrophic bacteria and they regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-binding site and leucine-rich (NBS-LRR) domain. Some NBS-LRR genes in the soybean genome have also been reported to function in disease resistance. Here, we show the correlation between the number of NBS-LRR genes and the number of disease resistance quantitative trait locus (QTL) on each chromosome of soybean. We also surveyed the functional redundancy of disease resistance on recently duplicated regions known to harbor NBS-LRR genes. Moreover, we analyzed NBS-LRR gene expression in the bacterial leaf pustule (BLP)-induced soybean transcriptome. RESULTS: A total of 319 genes were determined to be putative NBS-LRR genes in the soybean genome and the number of NBS-LRR genes on each chromosome was highly correlated with the number of disease resistance QTL on each chromosome. In addition, the recently duplicated regions contained duplicated NBS-LRR genes and duplicated disease resistance QTL. These recently duplicated regions possessed either an uneven or even number of NBS-LRR genes for each pair of regions. By supporting the disease resistance functions of the NBS-LRR genes in BLP-induced transcriptome, significant differences in the expression of NBS-LRR genes between resistant near isogenic line (NIL) and susceptible NIL supports the disease resistance function of NBS-LRR genes induced by BLP. CONCLUSIONS: The correlation between the number of NBS-LRR genes and disease resistance QTL for each chromosome and for each recently duplicated region indicates that NBS-LRR genes have a disease resistance function in soybean. In addition, NBS-LRR gene expression was significantly different in the BLP-resistant NIL compared to the BLP-susceptible NIL. Moreover, the recently duplicated regions, which have each undergone a different duplication history with respect to the NBS-LRR gene content, showed putative functional diversification of the genes based on different QTL information on the duplicated regions. We concluded that NBS-LRR genes in soybean confer disease resistance in a direct and indirect way and also presented evolutional models of these genes. Therefore, NBS-LRR genes could be used to develop markers for resistance against diverse diseases in order to develop an elite cultivar with marker assisted breeding.
    BMC Plant Biology 08/2012; 12(1):139. DOI:10.1186/1471-2229-12-139 · 3.94 Impact Factor
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    ABSTRACT: Phomopsis seed decay (PSD), primarily caused by Phomopsis longicolla, is one of the most important seed-borne diseases and causes serious seed yield loss in soybean. This study was performed to evaluate reactions to P. longicolla in Korean soybean major elite cultivars, which were mainly used for parents of genetic mapping populations. The natural incidence of P. longicolla and other seed-borne fungi was determined in the fields at three different locations in South Korea during 2009–2010. The significant differences in sensitivity to seed-borne diseases were shown among cultivars. Taekwangkong exhibited the greatest resistance to P. longicolla with average incidence of 0.33% and other seed-borne fungi with average incidence of 6.17%. Moreover, Taekwangkong was free of P. longicolla infection both in Milyang and in Daegu. To confirm the effective resistance source, the Korean virulent strain of P. longicolla, SSLP-3, was inoculated artificially on soybean of R4–R7 growth stage in the greenhouse. Taekwangkong exhibited a higher level of resistance to P. longicolla with significantly lower incidence (8.67%) than any other Korean elite cultivars (78.0–99.33%) and the previously reported resistant PI genotypes (35.0–55.67%). Further verification of resistance in Taekwangkong to P. longicolla by testing germination vigor of healthy seeds in vitro showed a higher germination rate than those of the susceptible cultivars. It could be suggested that Taekwangkong is a newly identified resistance source and the better source of resistance to P. longicolla to develop breeding populations for exploiting resistance gene(s) in further studies.
    06/2012; 15(2). DOI:10.1007/s12892-012-0029-7
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    ABSTRACT: Since the genome sequences of wild species may provide key information about the genetic elements involved in speciation and domestication, the undomesticated soybean (Glycine soja Sieb. and Zucc.), a wild relative of the current cultivated soybean (G. max), was sequenced. In contrast to the current hypothesis of soybean domestication, which holds that the current cultivated soybean was domesticated from G. soja, our previous work has suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. In this review, many structural genomic differences between the two genomes are described and a total of 705 genes are identified as structural variations (SVs) between G. max and G. soja. After protein families database of alignments and hidden Markov models IDs and gene ontology terms were assigned, many interesting genes are discussed in detail using four domestication related traits, such as flowering time, transcriptional factors, carbon metabolism and disease resistance. Soybean domestication history is explored by studying these SVs in genes. Analysis of SVs in genes at the population-level may clarify the domestication history of soybean.
    Breeding Science 01/2012; 61(5):445-52. DOI:10.1270/jsbbs.61.445 · 1.34 Impact Factor
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    ABSTRACT: The general approach to discovering single nucleotide polymorphisms (SNPs) requires locus-specific PCR amplification. To enhance the efficiency of SNP discovery in soybean, we used in silico analysis prior to re-sequencing as it is both rapid and inexpensive. In silico analysis was performed to detect putative SNPs in expressed sequence tag (EST) contigs assembled using publicly available ESTs from 18 different soybean genotypes. SNP validation by direct sequencing of six soybean cultivars and a wild soybean genotype was performed with PCR primers designed from EST contigs aligned with at least 5 out of 18 soybean genotypes. The efficiency of SNP discovery among the confirmation genotypes was 81.2%. Furthermore, the efficiency of SNP discovery between Pureunkong and Jinpumkong 2 genotypes was 47.4%, a great improvement on our previous finding based on direct sequencing (22.3%). Using SNPs between Pureunkong and Jinpumkong 2 in EST contigs, which were linked to target traits, we were able to genotype 90 recombinant inbred lines by high-resolution melting (HRM) analysis. These SNPs were mapped onto the expected locations near quantitative trait loci for water-logging tolerance and seed pectin concentration. Thus, our protocol for HRM analysis can be applied successfully not only to genetic diversity studies, but also to marker-assisted selection (MAS). Our study suggests that a combination of in silico analysis and HRM can reduce the cost and labor involved in developing SNP markers and genotyping SNPs. The markers developed in this study can also easily be applied to MAS if the markers are associated with the target traits. KeywordsIn silico SNP analysis–Marker-assisted selection–Re-sequencing–SNP discovery–SNP genotyping–Soybean
    Molecular Breeding 01/2012; 29(1):221-233. DOI:10.1007/s11032-010-9541-y · 2.28 Impact Factor
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    ABSTRACT: Bacterial leaf pustule (BLP) disease is caused by Xanthomonas axonopodis pv. glycines (Xag). To investigate the plant basal defence mechanisms induced in response to Xag, differential gene expression in near-isogenic lines (NILs) of BLP-susceptible and BLP-resistant soybean was analysed by RNA-Seq. Of a total of 46 367 genes that were mapped to soybean genome reference sequences, 1978 and 783 genes were found to be up- and down-regulated, respectively, in the BLP-resistant NIL relative to the BLP-susceptible NIL at 0, 6, and 12h after inoculation (hai). Clustering analysis revealed that these genes could be grouped into 10 clusters with different expression patterns. Functional annotation based on gene ontology (GO) categories was carried out. Among the putative soybean defence response genes identified (GO:0006952), 134 exhibited significant differences in expression between the BLP-resistant and -susceptible NILs. In particular, pathogen-associated molecular pattern (PAMP) and damage-associated molecular pattern (DAMP) receptors and the genes induced by these receptors were highly expressed at 0 hai in the BLP-resistant NIL. Additionally, pathogenesis-related (PR)-1 and -14 were highly expressed at 0 hai, and PR-3, -6, and -12 were highly expressed at 12 hai. There were also significant differences in the expression of the core JA-signalling components MYC2 and JASMONATE ZIM-motif. These results indicate that powerful basal defence mechanisms involved in the recognition of PAMPs or DAMPs and a high level of accumulation of defence-related gene products may contribute to BLP resistance in soybean.
    DNA Research 11/2011; 18(6):483-97. DOI:10.1093/dnares/dsr033 · 4.98 Impact Factor
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    ABSTRACT: Soybean lipoxygenase genes comprise a multi-gene family, with the seed lipoxygenase isozymes LOX1, LOX2, and LOX3 present in soybean seeds. Among these, the LOX2 isozyme is primarily responsible for the "beany" flavor of most soybean seeds. The variety, Jinpumkong 2, having null alleles (lx1, lx2, and lx3) lacks the three seed lipoxygenases; so, sequence variations between the lipoxygenase-2 genes of Pureunkong (Lx2) and Jinpumkong 2 (lx2) cultivars were examined. One indel, four single nucleotide polymorphisms (SNPs), a 175-bp fragment in the 5'-flanking sequence, and a missense mutation within the coding region were found in Jinpumkong 2. The distribution of the sequence variations was investigated among 90 recombinant inbred lines (RILs) derived from a cross of Pureunkong × Jinpumkong 2 and in 480 germplasm accessions with various origins and maturity groups. Evidence for a genetic bottleneck was observed: the 175-bp fragment was rare in Glycine max, but present in the majority of the G. soja accessions. Furthermore, the 175-bp fragment was not detected in the 5' upstream region of the Lx2 gene on chromosome (Chr) 13 in Williams 82; instead, a similar 175-bp fragment was positioned in the homeologous region on Chr 15. The findings indicated that the novel fragment identified was originally present in the Lx2 region prior to the recent genome duplication in soybean, but became rare in the G. max gene pool. The missense mutation of the conserved histidine residue of the lx2 allele was developed into a single nucleotide-amplified polymorphism (SNAP) marker. The missense mutation showed a perfect correlation with the LOX2-lacking phenotype, so the SNAP marker is expected to facilitate breeding of soybean cultivars which lack the LOX2 isozyme.
    Theoretical and Applied Genetics 11/2011; 124(4):613-22. DOI:10.1007/s00122-011-1733-2 · 3.51 Impact Factor
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    ABSTRACT: Acclimation of Chlamydomonas reinhardtii (hereafter, Chlamydomonas) to low or limiting CO(2) or inorganic carbon (C(i)) has been studied fairly extensively with regard to the mechanisms underlying the inducible C(i) acquisition systems and the signal transduction pathway involved in recognizing and responding to decreased C(i) availability. Investigation of low C(i )acclimation responses typically is performed with non-synchronous cultures grown in continuous light to avoid any effects of the cell division cycle (CDC) confounding interpretation of acclimation responses. However, little is known about whether acclimation to low C(i) might affect the distribution of cells among the various stages of the CDC. To investigate the effects of a limiting-C(i) challenge on the CDC of Chlamydomonas, flow cytometry was used to monitor the distribution of cells among the CDC stages in both synchronous and non-synchronous cultures during acclimation to low or limiting C(i). When faced with C(i) limitation, non-synchronous cultures of Chlamydomonas undergo transient synchronization as those cells past the Commitment point of the CDC undergo division, while the remainder of the cells pause their growth in early G-phase, with the result that the cells all accumulate in early G-phase, appearing transiently synchronized until acclimated sufficiently to the decreased C(i) for growth to resume. This perturbation of the CDC by a limiting-C(i) challenge has important implications for the interpretation of gene expression and other responses apparently induced by low or limiting C(i).
    Photosynthesis Research 09/2011; 109(1-3):161-8. DOI:10.1007/s11120-010-9618-9 · 3.19 Impact Factor
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    ABSTRACT: Alpha prime (α’) subunit of β-conglycinin and Gy4 subunit of glycinin are two important subunits of soybean storage protein which have negative effects on food processing, total amino acid content, and hypersensitivity reactions. It has been possible to reduce or remove some of these problems from soybean by screening or developing mutant lines. The objective of this study was to establish a simple, cheap DNA marker for Gy4 and α’ subunit for use in non-seed destructive, marker-assisted selection (MAS) that can identify these two mutants at the same time in a unique PCR reaction. To achieve this objective, we identified eight of Gy4 mutants from diverse soybean accessions from the USDA Soybean Germplasm Collection and described a multiplex PCR based co-dominant DNA marker for Gy4 subunit of glycinin. Then we crossed one of these Gy4 mutants with Keburi (α’ mutant) for development of double mutant variety and established a multiplex PCR based, co-dominant DNA marker for screening Gy4 and α’ mutants. Thus, using this newly developed marker to identify Gy4 and α’ mutants in breeding programs we could save our time, labor, and resources. Keywordsα’ subunit–Co-dominant marker–Double mutant– Gy4 –Multiplexing PCR–Soybean
    Genes & genomics 08/2011; 33(4):383-390. DOI:10.1007/s13258-010-0158-7 · 0.57 Impact Factor
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    ABSTRACT: The cultivated soybean [Glycine max (L.) Merr.] is widely considered to descend from the wild soybean (G. soja Sieb. & Zucc.). This study was designed to evaluate the genetic variability and differentiation between G. soja and G. max, and to detect signatures of the selection that may have occurred during the domestication process from G. soja to G. max. A total of 192 G. soja accessions and 104 G. max accessions were genotyped using eight selected simple sequence repeat (SSR) markers assigned to three SSR groups. Four SSRs in group A were not located near any known QTL. Three SSRs in group B were associated with seed protein content, and an SSR in group C was associated with resistance to Sclerotinia stem rot. The number of alleles per locus and the level of genetic variability in G. soja were higher than those in G. max. A total of 122 out of 125 alleles were present in G. soja, but only 59 alleles were detected in G. max. The average gene diversity was 0.74 in G. soja and 0.64 in G. max. Four SSRs near QTLs of agronomic importance showed strong genetic differentiation and shift change in high frequency alleles in groups B and C between G. soja and G. max, revealing selection signatures that may reflect the domestication events and recent selective breeding. With reduced diversity in G. max, some undomesticated genes from G. soja should be prime candidates for introgression to increase the pool of diversity in G. max. KeywordsDomestication–Gene diversity– Glycine max – Glycine soja –Selection signature
    Genes & genomics 08/2011; 33(4):391-397. DOI:10.1007/s13258-010-0159-6 · 0.57 Impact Factor
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    ABSTRACT: Plant genetic resources (PGR) include cultivars, landraces, wild species closely related to cultivated varieties, breeder's elite lines and mutants. The loss of genetic diversity caused by the practice of agriculture and the availability of genetic information has resulted in a great effort dedicated to the collection of PGR. Prior to the advent of molecular profiling, accessions in germplasm collections were examined based on morphology. The development of molecular techniques now allows a more accurate analysis of large collections. Next-generation sequencing (NGS) with de novo assembly and resequencing has already provided a substantial amount of information, which warrants the coordination of existing databases and their integration into genebanks. Thus, the integration and coordination of genomic data into genebanks is very important and requires an international effort. From the determination of phenotypic traits to the application of NGS to whole genomes, every aspect of genomics will have a great impact not only on PGR conservation, but also on plant breeding programmes.
    Plant Genetic Resources 06/2011; 9(02):155 - 158. DOI:10.1017/S1479262111000098 · 1.06 Impact Factor
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    ABSTRACT: Since the genetic control of flowering time is very important in photoperiod-sensitive soybean (Glycine max (L.) Merr.), genes affecting flowering under different environment conditions have been identified and described. The objectives were to identify quantitative trait loci (QTLs) for flowering time in different latitudinal and climatic regions, and to understand how chromosomal rearrangement and genome organization contribute to flowering time in soybean. Recombinant inbred lines from a cross between late-flowering 'Jinpumkong 2' and early-flowering 'SS2-2' were used to evaluate the phenotypic data for days to flowering (DF) collected from Kamphaeng Saen, Thailand (14°01'N), Suwon, Korea (37°15'N), and Longjing, China (42°46'N). A weakly positive phenotypic correlation (r = 0.36) was found between DF in Korea and Thailand; however, a strong correlation (r = 0.74) was shown between Korea and China. After 178 simple sequence repeat (SSR) markers were placed on a genetic map spanning 2,551.7 cM, four independent DF QTLs were identified on different chromosomes (Chrs). Among them, three QTLs on Chrs 9, 13 and 16 were either Thailand- or Korea-specific. The DF QTL on Chr 6 was identified in both Korea and China, suggesting it is less environment-sensitive. Comparative analysis of four DF QTL regions revealed a syntenic relationship between two QTLs on Chrs 6 and 13. All five duplicated gene pairs clustered in the homeologous genomic regions were found to be involved in the flowering. Identification and comparative analysis of multiple DF QTLs from different environments will facilitate the significant improvement in soybean breeding programs with respect to control of flowering time.
    Theoretical and Applied Genetics 06/2011; 123(4):545-53. DOI:10.1007/s00122-011-1606-8 · 3.51 Impact Factor
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    ABSTRACT: Two soybean recombinant inbred line populations, Jinpumkong 2 × SS2-2 (J × S) and Iksannamulkong × SS2-2 (I x S) showed population-specific quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) and these were closely correlated within population. In the present study, we identified QTLs for six yield-related traits with simple sequence repeat markers, and biological correlations between flowering traits and yield-related traits. The yield-related traits included plant height (PH), node numbers of main stem (NNMS), pod numbers per plant (PNPP), seed numbers per pod (SNPP), 100-seed weight (SW), and seed yield per plant (SYPP). Eighteen QTLs for six yield-related traits were detected on nine chromosomes (Chrs), containing four QTLs for PH, two for NNMS, two for PNPP, three for SNPP, five for SW, and two for SYPP. Two highly significant QTLs for PH and NNMS were identified on Chr 6 (LG C2) in both populations where the major flowering gene, E1, and two DF and DM QTLs were located. One other PNPP QTL was also located on this region, explaining 12.9% of phenotypic variation. Other QTLs for yield-related traits showed population-specificity. Two significant SYPP QTLs potentially related with QTLs for SNPP and PNPP were found on the same loci of Chrs 8 (Satt390) and 10 (Sat_108). Also, highly significant positive phenotypic correlations (P < 0.01) were found between DF with PH, NNMS, PNPP, and SYPP in both populations, while flowering was negatively correlated with SNPP and SW in the J × S (P < 0.05) and I × S (P < 0.01) populations. Similar results were also shown between DM and yield-related traits, except for one SW. These QTLs identified may be useful for marker-assisted selection by soybean breeders. Key wordsdays to flowering–days to maturity–quantitative trait loci–simple sequence repeat marker–soybean–yield-related trait
    03/2011; 14(1):65-70. DOI:10.1007/s12892-010-0115-7
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    ABSTRACT: One of the most notable contrasts between the photorespiratory pathway of higher plants and that of many of the green algae including Chlamydomonas reinhardtii lies in the enzymes that serve for oxidation of glycolate to glyoxylate. The gene disrupted by insertional mutagenesis in a high-CO2-requiring mutant, HCR89, of C. reinhardtii was determined to encode glycolate dehydrogenase (EC 1.1.99.14), which serves as the counterpart of glycolate oxidase (EC 1.1.3.15) in classical higher plant photorespiration. Neither glycolate nor D-lactate oxidation from the membrane fraction of HCR89 was detected. Excretion of over-accumulated glycolate into media due to the absence of glycolate dehydrogenase activity was observed for HCR89 under both high- and low-CO2 conditions. Chlamydomonas glycolate dehydrogenase, CrGDH, with a molecular mass of 118 851 Da, comprises a relatively hydrophobic N-terminal region, a FAD-containing domain homologous to the D subunit of the glycolate oxidase complex from Escherischia coli, and an iron–sulfur cluster containing domain homologous to the C subunit of anaerobic glycerol-3-phosphate dehydrogenase complex from Escherichia coli. The second Cys residue in the second iron–sulfur cluster motif of CrGDH is replaced by Asp, as CxxDxxCxxxCP, indicating the second iron–sulfur cluster coordinates most likely 3Fe–4S instead of 4Fe–4S. The membrane association of the glycolate dehydrogenase activity agrees with three predicted transmembrane regions on the iron–sulfur domain.Key words: algae, Chlamydomonas, CO2, glycolate, lactate, mitochondria, photorespiration, photosynthesis.
    Canadian Journal of Botany 02/2011; 83(7):820-833. DOI:10.1139/b05-067 · 1.40 Impact Factor
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    ABSTRACT: Flowering is an important stage in plant development and crucial for adaptation of plant species to different environments. Two soybean mapping populations were used to identify quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) by genotyping simple sequence repeat (SSR) markers. Single-factor analysis of variance detected association of phenotypic data with SSR markers in each population. DF QTLs were identified on four chromosomes (chrs.); two QTLs located on chrs. 2 and 13 with Satt041 and Satt206 in the Jinpumkong 2 × SS2-2 population and other two DF QTLs were detected on chrs. 6 and 19 with Satt100 and Satt373 in the Iksannamulkong × SS2-2 population. The major QTLs associated with Satt100 explained 30.3% of maximum phenotypic variation. Especially, all DF QTLs included QTLs for DM, except Satt206 on chr. 13. Moreover, two additional DM QTLs were mapped on chrs. 10 and 11 with Satt243 and Satt359, respectively. DF QTL on chr. 2 with Satt041 was the newly identified QTL only in the Jinpumkong 2 × SS2-2 population and explained 10.3% of the phenotypic variation. The single locus of Satt100 on chr. 6 and Satt373 on chr. 19 were located on soybean genomic regions of the known flowering gene loci E1 and E3, respectively. These population-specific QTLs (Satt100 and Satt373) are the major QTLs for flowering time, putatively, they may be related to maturity QTLs with large effect. Additionally, these QTLs are valuable for marker-assisted approaches and could be widely adopted by soybean breeders. Key wordsdays to flowering–days to maturity–population-specific–quantitative trait loci (QTLs)–soybean
    12/2010; 13(4):213-218. DOI:10.1007/s12892-010-0100-1

Publication Stats

536 Citations
115.27 Total Impact Points

Institutions

  • 2003–2013
    • Seoul National University
      • • Research Institute for Agriculture and Life Science
      • • Department of Plant Science
      Sŏul, Seoul, South Korea
  • 2008
    • National Institute of Crop Science
      Sŏngnam, Gyeonggi-do, South Korea
  • 1999–2001
    • Iowa State University
      • Department of Genetics, Development and Cell Biology
      Ames, Iowa, United States