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Kim JM, Lee JW, Seo JS, Ha BK, Kwon SJ. Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis. Plants (Basel) 2024; 13:584. [PMID: 38475431 DOI: 10.3390/plants13050584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jeong Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
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Kang BH, Chowdhury S, Kang SH, Shin SY, Lee WH, Lee HS, Ha BK. Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation. Plants (Basel) 2024; 13:254. [PMID: 38256807 PMCID: PMC10818854 DOI: 10.3390/plants13020254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.
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Affiliation(s)
- Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
| | - Se-Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seo-Young Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Won-Ho Lee
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyeon-Seok Lee
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
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Kim JM, Seo JS, Lee JW, Lyu JI, Ryu J, Eom SH, Ha BK, Kwon SJ. QTL mapping reveals key factors related to the isoflavone contents and agronomic traits of soybean (Glycine max). BMC Plant Biol 2023; 23:517. [PMID: 37880577 PMCID: PMC10601131 DOI: 10.1186/s12870-023-04519-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Soybean is a valuable source of edible protein and oil, as well as secondary metabolites that can be used in food products, cosmetics, and medicines. However, because soybean isoflavone content is a quantitative trait influenced by polygenes and environmental interactions, its genetic basis remains unclear. RESULTS This study was conducted to identify causal quantitative trait loci (QTLs) associated with soybean isoflavone contents. A mutant-based F2 population (190 individuals) was created by crossing the Korean cultivar Hwanggeum with low isoflavone contents (1,558 µg g-1) and the soybean mutant DB-088 with high isoflavone contents (6,393 µg g-1). A linkage map (3,049 cM) with an average chromosome length of 152 cM was constructed using the 180K AXIOM® SoyaSNP array. Thirteen QTLs related to agronomic traits were mapped to chromosomes 2, 3, 11, 13, 19, and 20, whereas 29 QTLs associated with isoflavone contents were mapped to chromosomes 1, 3, 8, 11, 14, 15, and 17. Notably, the qMGLI11, qMGNI11, qADZI11, and qTI11, which located Gm11_9877690 to Gm11_9955924 interval on chromosome 11, contributed to the high isoflavone contents and explained 11.9% to 20.1% of the phenotypic variation. This QTL region included four candidate genes, encoding β-glucosidases 13, 14, 17-1, and 17-2. We observed significant differences in the expression levels of these genes at various seed developmental stages. Candidate genes within the causal QTLs were functionally characterized based on enriched GO terms and KEGG pathways, as well as the results of a co-expression network analysis. A correlation analysis indicated that certain agronomic traits (e.g., days to flowering, days to maturity, and plant height) are positively correlated with isoflavone content. CONCLUSIONS Herein, we reported that the major QTL associated with isoflavone contents was located in the interval from Gm11_9877690 to Gm11_9955924 (78 kb) on chromosome 11. Four β-glucosidase genes were identified that may be involved in high isoflavone contents of soybean DB-088. Thus, the mutant alleles from soybean DB-088 may be useful for marker-assisted selection in developing soybean lines with high isoflavone contents and superior agronomic traits.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jae Il Lyu
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Seok Hyun Eom
- Department of Smart Farm Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
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Kim K, Jun TH, Ha BK, Wang S, Sun H. New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits. BMC Bioinformatics 2023; 24:381. [PMID: 37817069 PMCID: PMC10563219 DOI: 10.1186/s12859-023-05505-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to detect weak genetic associations missed by single-trait analyses. Many statistical methods were developed to identify pleiotropic variants with most of them being limited to quantitative traits when pleiotropic effects on both quantitative and qualitative traits have been observed. This is a statistically challenging problem because there does not exist an appropriate multivariate distribution to model both quantitative and qualitative data together. Alternatively, meta-analysis methods can be applied, which basically integrate summary statistics of individual variants associated with either a quantitative or a qualitative trait without accounting for correlations among genetic variants. RESULTS We propose a new statistical selection method based on a unified selection score quantifying how a genetic variant, i.e., a pleiotropic variant associates with both quantitative and qualitative traits. In our extensive simulation studies where various types of pleiotropic effects on both quantitative and qualitative traits were considered, we demonstrated that the proposed method outperforms the existing meta-analysis methods in terms of true positive selection. We also applied the proposed method to a peanut dataset with 6 quantitative and 2 qualitative traits, and a cowpea dataset with 2 quantitative and 6 qualitative traits. We were able to detect some potentially pleiotropic variants missed by the existing methods in both analyses. CONCLUSIONS The proposed method is able to locate pleiotropic variants associated with both quantitative and qualitative traits. It has been implemented into an R package 'UNISS', which can be downloaded from http://github.com/statpng/uniss.
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Affiliation(s)
- Kipoong Kim
- Department of Statistic, Pusan National University, 46241, Busan, Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, 50463, Miryang, Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, 61186, Gwangju, Korea
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, 10032, USA
| | - Hokeun Sun
- Department of Statistic, Pusan National University, 46241, Busan, Korea.
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Moon CY, Kang BH, Kim WJ, Chowdhury S, Kang S, Lee JD, Kwon SJ, Kim HY, Lee HS, Ha BK. Morpho-physiological and genetic characteristics of a salt-tolerant mutant line in soybean (Glycine max L.). Theor Appl Genet 2023; 136:166. [PMID: 37393202 DOI: 10.1007/s00122-023-04408-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023]
Abstract
KEY MESSAGE One major quantitative trait loci and candidate gene for salt tolerance were identified on chromosome 3 from a new soybean mutant derived from gamma-ray irradiation, which will provide a new genetic resource for improving soybean salt tolerance. Soil salinity is a worldwide problem that reduces crop yields, but the development of salt-tolerant crops can help overcome this challenge. This study was conducted with the purpose of evaluating the morpho-physiological and genetic characteristics of a new salt-tolerant mutant KA-1285 developed using gamma-ray irradiation in soybean (Glycine max L.). The morphological and physiological responses of KA-1285 were compared with salt-sensitive and salt-tolerant genotypes after treatment with 150 mM NaCl for two weeks. In addition, a major salt tolerance quantitative trait locus (QTL) was identified on chromosome 3 in this study using the Daepung X KA-1285 169 F2:3 population, and a specific deletion was identified in Glyma03g171600 (Wm82.a2.v1) near the QTL region based on re-sequencing analysis. A kompetitive allele-specific PCR (KASP) marker was developed based on the deletion of Glyma03g171600 which distinguished the wild-type and mutant alleles. Through the analysis of gene expression patterns, it was confirmed that Glyma03g171700 (Wm82.a2.v1) is a major gene that controls salt tolerance functions in Glyma03g32900 (Wm82.a1.v1). These results suggest that the gamma-ray-induced mutant KA-1285 has the potential to be employed for the development of a salt-tolerant cultivar and provide useful information for genetic research related to salt tolerance in soybeans.
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Affiliation(s)
- Chang Yeok Moon
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Byeong Hee Kang
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Woon Ji Kim
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
| | - Sehee Kang
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Han-Yong Kim
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea
| | - Hyeon-Seok Lee
- National Institute of Crop Science, RDA, Wanju, 55365, Republic of Korea.
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnnam National University, Gwangju, 61186, Republic of Korea.
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Kim WJ, Kang BH, Kang S, Shin S, Chowdhury S, Jeong SC, Choi MS, Park SK, Moon JK, Ryu J, Ha BK. A Genome-Wide Association Study of Protein, Oil, and Amino Acid Content in Wild Soybean ( Glycine soja). Plants (Basel) 2023; 12:1665. [PMID: 37111888 PMCID: PMC10143452 DOI: 10.3390/plants12081665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
Soybean (Glycine max L.) is a globally important source of plant proteins, oils, and amino acids for both humans and livestock. Wild soybean (Glycine soja Sieb. and Zucc.), the ancestor of cultivated soybean, could be a useful genetic source for increasing these components in soybean crops. In this study, 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom® Soya SNP array were investigated using an association analysis. Protein and oil content exhibited a highly significant negative correlation, while the 17 amino acids exhibited a highly significant positive correlation with each other. A genome-wide association study (GWAS) was conducted on the protein, oil, and amino acid content using the 203 wild soybean accessions. A total of 44 significant SNPs were associated with protein, oil, and amino acid content. Glyma.11g015500 and Glyma.20g050300, which contained SNPs detected from the GWAS, were selected as novel candidate genes for the protein and oil content, respectively. In addition, Glyma.01g053200 and Glyma.03g239700 were selected as novel candidate genes for nine of the amino acids (Ala, Asp, Glu, Gly, Leu, Lys, Pro, Ser, and Thr). The identification of the SNP markers related to protein, oil, and amino acid content reported in the present study is expected to help improve the quality of selective breeding programs for soybeans.
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Affiliation(s)
- Woon Ji Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Republic of Korea; (W.J.K.); (J.R.)
| | - Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.K.); (S.S.); (S.C.)
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sehee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.K.); (S.S.); (S.C.)
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seoyoung Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.K.); (S.S.); (S.C.)
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.K.); (S.S.); (S.C.)
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea;
| | - Man-Soo Choi
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea; (M.-S.C.); (S.-K.P.); (J.-K.M.)
| | - Soo-Kwon Park
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea; (M.-S.C.); (S.-K.P.); (J.-K.M.)
| | - Jung-Kyung Moon
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea; (M.-S.C.); (S.-K.P.); (J.-K.M.)
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Republic of Korea; (W.J.K.); (J.R.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.K.); (S.S.); (S.C.)
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
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Jo H, Ha BK, Park SK, Jeong SC, Lee JD, Moon JK. Genetic Diversity of Korean Wild Soybean Core Collections and Genome-Wide Association Study for Days to Flowering. Plants (Basel) 2023; 12:1305. [PMID: 36986992 PMCID: PMC10058364 DOI: 10.3390/plants12061305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The utilization of wild soybean germplasms in breeding programs increases genetic diversity, and they contain the rare alleles of traits of interest. Understanding the genetic diversity of wild germplasms is essential for determining effective strategies that can improve the economic traits of soybeans. Undesirable traits make it challenging to cultivate wild soybeans. This study aimed to construct a core subset of 1467 wild soybean accessions of the total population and analyze their genetic diversity to understand their genetic variations. Genome-wild association studies were conducted to detect the genetic loci underlying the time to flowering for a core subset collection, and they revealed the allelic variation in E genes for predicting maturity using the available resequencing data of wild soybean. Based on principal component and cluster analyses, 408 wild soybean accessions in the core collection covered the total population and were explained by 3 clusters representing the collection regions, namely, Korea, China, and Japan. Most of the wild soybean collections in this study had the E1e2E3 genotype according to association mapping and a resequencing analysis. Korean wild soybean core collections can provide helpful genetic resources to identify new flowering and maturity genes near the E gene loci and genetic materials for developing new cultivars, facilitating the introgression of genes of interest from wild soybean.
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Affiliation(s)
- Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Upland-Field Machinery Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Republic of Korea
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Kim WJ, Kang BH, Moon CY, Kang S, Shin S, Chowdhury S, Choi MS, Park SK, Moon JK, Ha BK. Quantitative Trait Loci (QTL) Analysis of Seed Protein and Oil Content in Wild Soybean ( Glycine soja). Int J Mol Sci 2023; 24:ijms24044077. [PMID: 36835486 PMCID: PMC9959443 DOI: 10.3390/ijms24044077] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Soybean seeds consist of approximately 40% protein and 20% oil, making them one of the world's most important cultivated legumes. However, the levels of these compounds are negatively correlated with each other and regulated by quantitative trait loci (QTL) that are controlled by several genes. In this study, a total of 190 F2 and 90 BC1F2 plants derived from a cross of Daepung (Glycine max) with GWS-1887 (G. soja, a source of high protein), were used for the QTL analysis of protein and oil content. In the F2:3 populations, the average protein and oil content was 45.52% and 11.59%, respectively. A QTL associated with protein levels was detected at Gm20_29512680 on chr. 20 with a likelihood of odds (LOD) of 9.57 and an R2 of 17.2%. A QTL associated with oil levels was also detected at Gm15_3621773 on chr. 15 (LOD: 5.80; R2: 12.2%). In the BC1F2:3 populations, the average protein and oil content was 44.25% and 12.14%, respectively. A QTL associated with both protein and oil content was detected at Gm20_27578013 on chr. 20 (LOD: 3.77 and 3.06; R2 15.8% and 10.7%, respectively). The crossover to the protein content of BC1F3:4 population was identified by SNP marker Gm20_32603292. Based on these results, two genes, Glyma.20g088000 (S-adenosyl-l-methionine-dependent methyltransferases) and Glyma.20g088400 (oxidoreductase, 2-oxoglutarate-Fe(II) oxygenase family protein), in which the amino acid sequence had changed and a stop codon was generated due to an InDel in the exon region, were identified.
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Affiliation(s)
- Woon Ji Kim
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chang Yeok Moon
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sehee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seoyoung Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Soo Choi
- National Institute of Crop Science, Rural Development Administration (RDA), Wanju 55365, Republic of Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration (RDA), Wanju 55365, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration (RDA), Wanju 55365, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Republic of Korea
- Correspondence: ; Tel.: +82-62-530-2055
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Kim JM, Lyu JI, Kim DG, Hung NN, Seo JS, Ahn JW, Lim YJ, Eom SH, Ha BK, Kwon SJ. Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding. Front Plant Sci 2022; 13:968466. [PMID: 36061785 PMCID: PMC9433930 DOI: 10.3389/fpls.2022.968466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of >0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (GmGSTT1), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of GmGSTT1 and two other core genes (IFS1 and IFS2) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jae Il Lyu
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan, South Korea
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Nguyen Ngoc Hung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin, South Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin, South Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
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Kim SH, Subramanian P, Hahn BS, Ha BK. High-Throughput Phenotypic Characterization and Diversity Analysis of Soybean Roots (Glycine max L.). Plants 2022; 11:plants11152017. [PMID: 35956495 PMCID: PMC9370148 DOI: 10.3390/plants11152017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/21/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Soybean (Glycine max L.) is a crop native to Northeast Asia, including China, Korea, and Japan, but currently cultivated all over the world. The National Agrobiodiversity Center in Korea at the Rural Development Administration (RDA) conserves approximately 26,000 accessions and conducts characterizations of its accessions, to accumulate new information. Roots are essential organs of a plant, providing mechanical support, as well as aiding water and nutrient acquisition. Currently, not much information is available in international gene banks regarding root characterization. We studied the root phenotype of 374 soybean accessions, using a high-throughput method. Eight root morphological traits (RMT) were studied and we observed that the surface area (SA), number of forks (NF), and number of tips (NT) had a positive correlation with total length (LENGTH), and that link average length (LAL) and other traits all had a negative correlation. Additionally, the correlation between seed traits (height, width, and 100-seed weight) and root traits was confirmed for the first time in this experiment. The germplasms were divided into three clusters by k-means clustering, and orthogonal projections to latent structures discriminant analysis (OPLS-DA) was used to compare clusters. The most distinctive characteristics between clusters were total lateral average length (LAD) and total lateral average length (DIAM). Cluster 3 had the highest LENGTH, SA, NF, and NF, whereas cluster 1 had the smallest LENGTH, SA, and NF. We selected the top 10 accessions for each RMT, and IT208321, IT216313, and IT216137 were nominated as the best germplasms. These accessions can be recommended to breeders as materials for breeding programs. This is a preliminary report on the characterization of the root phenotype at an international gene bank and will open up the possibility of improving the available information on accessions in gene banks worldwide.
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Affiliation(s)
- Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Korea;
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (S.-H.K.); (B.-S.H.); (B.-K.H.)
| | - Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Korea;
- PG & Research Department of Biotechnology and Microbiology, National College (Autonomous), Tiruchirapalli 620001, Tamilnadu, India
| | - Bum-Soo Hahn
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Korea;
- Correspondence: (S.-H.K.); (B.-S.H.); (B.-K.H.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (S.-H.K.); (B.-S.H.); (B.-K.H.)
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11
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Kim JM, Lyu JI, Kim DG, Hung NN, Ryu J, Kim JB, Ahn JW, Ha BK, Kwon SJ. Analysis of genetic diversity and relationships of Perilla frutescens using novel EST-SSR markers derived from transcriptome between wild-type and mutant Perilla. Mol Biol Rep 2021; 48:6387-6400. [PMID: 34426904 DOI: 10.1007/s11033-021-06639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/10/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Perilla frutescens (Lamiaceae) is distributed in East Asia and is classified into var. frutescens and crispa. P. frutescens is multipurpose crop for human health because of a variety of secondary metabolites such as phenolic compound and essential oil. However, a lack of genetic information has hindered the development and utilization of Perilla genotypes. METHODS AND RESULTS This study was performed to develop expressed sequence tag-simple sequence repeat (EST-SSR) markers from P. frutescens var. crispa (wild type) and Antisperill (a mutant cultivar) and used them to assess the genetic diversity of, and relationships among, 94 P. frutescens genotypes. We obtained 65 Gb of sequence data comprising 632,970 transcripts by de novo RNA-sequencing. Of the 14,780 common SSRs, 102 polymorphic EST-SSRs were selected using in silico polymerase chain reaction (PCR). Overall, successful amplification from 58 EST-SSRs markers revealed remarkable genetic diversity and relationships among 94 P. frutescens genotypes. In total, 268 alleles were identified, with an average of 4.62 alleles per locus (range 2-11 alleles/locus). The average polymorphism information content (PIC) value was 0.50 (range 0.04-0.86). In phylogenetic and population structure analyses, the genotypes formed two major groups: Group I (var. crispa) and Group II (var. frutescens). CONCLUSION This results suggest that 58 novel EST-SSR markers derived from wild-type cultivar (var. crispa) and its mutant cultivar (Antisperill) have potential uses for population genetics and recombinant inbred line mapping analyses, which will provide comprehensive insights into the genetic diversity and relationship of P. frutescens.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea.,Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea.,Department of Life-Resources, Graduate School, Sunchon National University, Suncheon, 57922, Korea
| | - Nguyen Ngoc Hung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea.,Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea.
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea.
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Kim KS, Kim JM, Jung J, Shin I, Park S, Lee JS, Jeong SC, Lee JD, Jung JK, Ha BK, Kang S. Fine-mapping and candidate gene analysis for the foxglove aphid resistance gene Raso2 from wild soybean PI 366121. Theor Appl Genet 2021; 134:2687-2698. [PMID: 33974087 DOI: 10.1007/s00122-021-03853-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE The foxglove aphid resistance gene Raso2 from PI 366121 was fine-mapped to 77 Kb region, and one candidate gene was identified. The foxglove aphid (FA: Aulacorthum solani Kaltenbach) is an important insect pest that causes serious yield losses in soybean. The FA resistance gene Raso2 from wild soybean PI 366121 was previously mapped to a 13 cM interval on soybean chromosome 7. However, fine-mapping of Raso2 was needed to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to fine-map Raso2 from PI 366121 using Axiom® 180 K SoyaSNP array, to confirm the resistance and inheritance of Raso2 in a different background, and to identify candidate gene(s). The 105 F4:8 recombinant inbred lines were used to fine-map the gene and to test antibiosis and antixenosis of Raso2 to FA. These efforts resulted in the mapping of Raso2 on 1 cM interval which corresponds to 77 Kb containing eight annotated genes based on the Williams 82 reference genome assembly (Wm82.a2.v1). Interestingly, all nonsynonymous substitutions were in Glyma.07g077700 which encodes the disease resistance protein containing LRR domain and expression of the gene in PI 366121 was significantly higher than that in Williams 82. In addition, distinct SNPs within Glyma.07g077700 that can distinguish PI 366121 and diverse FA-susceptible soybeans were identified. We also confirmed that Raso2 presented the resistance to FA and the Mendelian inheritance for single dominant gene in a different background. The results of this study would provide fundamental information on MAS for development of FA-resistant cultivars as well as functional study and cloning of the candidate gene in soybean.
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Affiliation(s)
- Ki-Seung Kim
- Deparment of Innovative Technology, FarmHannong, Ltd., Nonsan, 33010, Korea
| | - Ji-Min Kim
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Jiyeong Jung
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Ilseob Shin
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Sumin Park
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
- Business Incubation Center, Sae Han Agricultural Technology Research Station, Hwaseong, 18330, Korea
| | - Ju Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Jin Kyo Jung
- Rural Development Administration, National Institute of Crop Science, Suwon, 16613, Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju, 61186, Korea
| | - Sungtaeg Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea.
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Choi YM, Yoon H, Shin MJ, Lee Y, Hur OS, Lee BC, Ha BK, Wang X, Desta KT. Metabolite Contents and Antioxidant Activities of Soybean ( Glycine max (L.) Merrill) Seeds of Different Seed Coat Colors. Antioxidants (Basel) 2021; 10:1210. [PMID: 34439461 PMCID: PMC8388989 DOI: 10.3390/antiox10081210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
Seed coat color is one of the main agronomical traits that determine the chemical quality of soybean seeds and has been used as a parameter during cultivar development. In this study, seeds of yellow (n = 10), greenish-yellow (n = 5), and light-yellow (n = 4) soybean accessions were evaluated for their contents of total protein, total oil, total phenolic (TPC), and five prominent fatty acids including palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LLA), relative to a control cultivar, and the effect of seed coat color on each was investigated. Antioxidant activity was also evaluated using 1,1-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, Trolox equivalent antioxidant capacity (TEAC), and ferric reducing antioxidant power (FRAP). The results showed significant variations of metabolite contents and antioxidant activities between the soybeans. The average TPC, DPPH-radical scavenging activity, and FRAP were each in the order of greenish-yellow > yellow > light-yellow soybeans. In contrast, light-yellow soybeans contained a high level of OA and low levels of SA, LA, and LLA, each except LA differing significantly from yellow and greenish-yellow soybeans (p < 0.05). Our findings suggest that greenish-yellow and light-yellow soybeans could be good sources of antioxidants and high-quality soybean oil, respectively.
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Affiliation(s)
- Yu-Mi Choi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
| | - Hyemyeong Yoon
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
| | - Yoonjung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
| | - On Sook Hur
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;
| | - Bo-Keun Ha
- Division of Plant Biotechnology, Chonnam National University, Gwangju 61186, Korea;
| | - Xiaohan Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
| | - Kebede Taye Desta
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (Y.-M.C.); (H.Y.); (M.-J.S.); (Y.L.); (O.S.H.); (X.W.)
- Department of Applied Chemistry, Adama Science and Technology University, Adama 1888, Ethiopia
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Jo H, Kim M, Cho H, Ha BK, Kang S, Song JT, Lee JD. Identification of a Potential Gene for Elevating ω-3 Concentration and Its Efficiency for Improving the ω-6/ω-3 Ratio in Soybean. J Agric Food Chem 2021; 69:3836-3847. [PMID: 33770440 DOI: 10.1021/acs.jafc.0c05830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This present study was to identify a novel candidate gene that contributes to the elevated α-linolenic acid (ALA, ω-3) concentration in PE2166 from mutagenesis of Pungsannamul. Major loci qALA5_1 and qALA5_2 were detected on chromosome 5 of soybean through quantitative trait loci mapping analyses of recombinant inbred lines. With next-generation sequencing of parental lines and Pungsannamul and recombinant analyses, a potential gene, Glyma.05g221500 (HD), controlling elevated ALA concentration was identified. HD is a homeodomain-like transcriptional regulator that may regulate the expression level of microsomal ω-3 fatty acid desaturase (FAD3) genes responsible for the conversion of linoleic acid into ALA in the fatty acid biosynthetic pathway. In addition, we hypothesized that a combination of mutant alleles, HD, and either of microsomal delta-12 fatty acid desaturase 2-1 (FAD2-1) could reduce the ω-6/ω-3 ratio. In populations where HD, FAD2-1A, and FAD2-1B genes were segregated, a combination of a hd allele from PE2166 and either of the variant FAD2-1 alleles was sufficient to reduce the ω-6/ω-3 ratio in seeds.
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Affiliation(s)
- Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Minsu Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeontae Cho
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sungtaeg Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan 16890, Republic of Korea
| | - Jong Tae Song
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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Kang R, Seo E, Park A, Kim WJ, Kang BH, Lee JH, Kim SH, Kang SY, Ha BK. A Comparison of the Transcriptomes of Cowpeas in Response to Two Different Ionizing Radiations. Plants (Basel) 2021; 10:567. [PMID: 33802840 PMCID: PMC8002818 DOI: 10.3390/plants10030567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022]
Abstract
In this study, gene expression changes in cowpea plants irradiated by two different types of radiation: proton-beams and gamma-rays were investigated. Seeds of the Okdang cultivar were exposed to 100, 200, and 300 Gy of gamma-rays and proton-beams. In transcriptome analysis, the 32, 75, and 69 differentially expressed genes (DEGs) at each dose of gamma-ray irradiation compared with that of the control were identified. A total of eight genes were commonly up-regulated for all gamma-ray doses. However, there were no down-regulated genes. In contrast, 168, 434, and 387 DEGs were identified for each dose of proton-beam irradiation compared with that of the control. A total of 61 DEGs were commonly up-regulated for all proton-beam doses. As a result of GO and KEGG analysis, the ranks of functional categories according to the number of DEGs were not the same in both treatments and were more diverse in terms of pathways in the proton-beam treatments than gamma-ray treatments. The number of genes related to defense, photosynthesis, reactive oxygen species (ROS), plant hormones, and transcription factors (TF) that were up-/down-regulated was higher in the proton beam treatment than that in gamma ray treatment. Proton-beam treatment had a distinct mutation spectrum and gene expression pattern compared to that of gamma-ray treatment. These results provide important information on the mechanism for gene regulation in response to two ionizing radiations in cowpeas.
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Affiliation(s)
- Ryulyi Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea; (R.K.); (E.S.); (A.P.); (W.J.K.); (B.H.K.)
| | - Eunju Seo
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea; (R.K.); (E.S.); (A.P.); (W.J.K.); (B.H.K.)
| | - Aron Park
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea; (R.K.); (E.S.); (A.P.); (W.J.K.); (B.H.K.)
| | - Woon Ji Kim
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea; (R.K.); (E.S.); (A.P.); (W.J.K.); (B.H.K.)
| | - Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea; (R.K.); (E.S.); (A.P.); (W.J.K.); (B.H.K.)
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Korea
| | | | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea;
| | - Si-Yong Kang
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea; (R.K.); (E.S.); (A.P.); (W.J.K.); (B.H.K.)
- BK21 FOUR Center for IT-Bio Convergence System Agriculture, Chonnam National University, Gwangju 61186, Korea
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Zou K, Kim KS, Kim K, Kang D, Park YH, Sun H, Ha BK, Ha J, Jun TH. Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut ( Arachis hypogaea L.). Genes (Basel) 2020; 12:E2. [PMID: 33375051 PMCID: PMC7822046 DOI: 10.3390/genes12010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022] Open
Abstract
Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.
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Affiliation(s)
- Kunyan Zou
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
| | | | - Kipoong Kim
- Department of Statistics, Pusan National University, Busan 46241, Korea; (K.K.); (H.S.)
| | - Dongwoo Kang
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
| | - Yu-Hyeon Park
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
| | - Hokeun Sun
- Department of Statistics, Pusan National University, Busan 46241, Korea; (K.K.); (H.S.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea;
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea;
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea; (K.Z.); (D.K.); (Y.-H.P.)
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
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Seo E, Kim K, Jun TH, Choi J, Kim SH, Muñoz-Amatriaín M, Sun H, Ha BK. Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. Plants (Basel) 2020; 9:plants9091190. [PMID: 32932572 PMCID: PMC7569878 DOI: 10.3390/plants9091190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.
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Affiliation(s)
- Eunju Seo
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea;
| | - Kipoong Kim
- Department of Statistics, Pusan National University, Busan 46241, Korea;
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Busan 46241, Korea;
| | - Jinsil Choi
- Jeollanamdo Agricultural Research and Extension Services, Naju 58213, Korea;
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea;
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA;
| | - Hokeun Sun
- Department of Statistics, Pusan National University, Busan 46241, Korea;
- Correspondence: (H.S.); (B.-K.H.); Tel.: +92-51-510-2257 (H.S.); +82-62-530-2055 (B.-K.H.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea;
- Correspondence: (H.S.); (B.-K.H.); Tel.: +92-51-510-2257 (H.S.); +82-62-530-2055 (B.-K.H.)
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Redekar NR, Glover NM, Biyashev RM, Ha BK, Raboy V, Maroof MAS. Genetic interactions regulating seed phytate and oligosaccharides in soybean (Glycine max L.). PLoS One 2020; 15:e0235120. [PMID: 32584851 PMCID: PMC7316244 DOI: 10.1371/journal.pone.0235120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022] Open
Abstract
Two low-phytate soybean (Glycine max (L.) Merr.) mutant lines- V99-5089 (mips mutation on chromosome 11) and CX-1834 (mrp-l and mrp-n mutations on chromosomes 19 and 3, respectively) have proven to be valuable resources for breeding of low-phytate, high-sucrose, and low-raffinosaccharide soybeans, traits that are highly desirable from a nutritional and environmental standpoint. A recombinant inbred population derived from the cross CX1834 x V99-5089 provides an opportunity to study the effect of different combinations of these three mutations on soybean phytate and oligosaccharides levels. Of the 173 recombinant inbred lines tested, 163 lines were homozygous for various combinations of MIPS and two MRP loci alleles. These individuals were grouped into eight genotypic classes based on the combination of SNP alleles at the three mutant loci. The two genotypic classes that were homozygous mrp-l/mrp-n and either homozygous wild-type or mutant at the mips locus (MIPS/mrp-l/mrp-n or mips/mrp-l/mrp-n) displayed relatively similar ~55% reductions in seed phytate, 6.94 mg g -1 and 6.70 mg g-1 respectively, as compared with 15.2 mg g-1 in the wild-type MIPS/MRP-L/MRP-N seed. Therefore, in the presence of the double mutant mrp-l/mrp-n, the mips mutation did not cause a substantially greater decrease in seed phytate level. However, the nutritionally-desirable high-sucrose/low-stachyose/low-raffinose seed phenotype originally observed in soybeans homozygous for the mips allele was reversed in the presence of mrp-l/mrp-n mutations: homozygous mips/mrp-l/mrp-n seed displayed low-sucrose (7.70%), high-stachyose (4.18%), and the highest observed raffinose (0.94%) contents per gram of dry seed. Perhaps the block in phytic acid transport from its cytoplasmic synthesis site to its storage site, conditioned by mrp-l/mrp-n, alters myo-inositol flux in mips seeds in a way that restores to wild-type levels the mips conditioned reductions in raffinosaccharides. Overall this study determined the combinatorial effects of three low phytic acid causing mutations on regulation of seed phytate and oligosaccharides in soybean.
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Affiliation(s)
- Neelam R. Redekar
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Natasha M. Glover
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Ruslan M. Biyashev
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Bo-Keun Ha
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Victor Raboy
- National Small Grains Germplasm Center, USDA-ARS, Aberdeen, Idaho, United States of America
| | - M. A. Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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Kim S, Jeong YJ, Park SH, Park SC, Lee SB, Lee J, Kim SW, Ha BK, Kim HS, Kim H, Ryu YB, Jeong JC, Kim CY. The Synergistic Effect of Co-Treatment of Methyl Jasmonate and Cyclodextrins on Pterocarpan Production in Sophora flavescens Cell Cultures. Int J Mol Sci 2020; 21:ijms21113944. [PMID: 32486319 PMCID: PMC7313034 DOI: 10.3390/ijms21113944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 12/02/2022] Open
Abstract
Pterocarpans are derivatives of isoflavonoids, found in many species of the family Fabaceae. Sophora flavescens Aiton is a promising traditional Asian medicinal plant. Plant cell suspension cultures represent an excellent source for the production of valuable secondary metabolites. Herein, we found that methyl jasmonate (MJ) elicited the activation of pterocarpan biosynthetic genes in cell suspension cultures of S. flavescens and enhanced the accumulation of pterocarpans, producing mainly trifolirhizin, trifolirhizin malonate, and maackiain. MJ application stimulated the expression of structural genes (PAL, C4H, 4CL, CHS, CHR, CHI, IFS, I3’H, and IFR) of the pterocarpan biosynthetic pathway. In addition, the co-treatment of MJ and methyl-β-cyclodextrin (MeβCD) as a solubilizer exhibited a synergistic effect on the activation of the pterocarpan biosynthetic genes. The maximum level of total pterocarpan production (37.2 mg/g dry weight (DW)) was obtained on day 17 after the application of 50 μM MJ on cells. We also found that the combined treatment of cells for seven days with MJ and MeβCD synergistically induced the pterocarpan production (trifolirhizin, trifolirhizin malonate, and maackiain) in the cells (58 mg/g DW) and culture medium (222.7 mg/L). Noteworthy, the co-treatment only stimulated the elevated extracellular production of maackiain in the culture medium, indicating its extracellular secretion; however, its glycosides (trifolirhizin and trifolirhizin malonate) were not detected in any significant amounts in the culture medium. This work provides new strategies for the pterocarpan production in plant cell suspension cultures, and shows MeβCD to be an effective solubilizer for the extracellular production of maackiain in the cell cultures of S. flavescens.
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Affiliation(s)
- Soyoung Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
- Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea;
| | - Yu Jeong Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
| | - Su Hyun Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
| | - Sung-Chul Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
| | - Saet Buyl Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
| | - Jiyoung Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
| | - Bo-Keun Ha
- Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea;
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-S.K.); (H.K.)
| | - HyeRan Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-S.K.); (H.K.)
| | - Young Bae Ryu
- Functional Biomaterials Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea;
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
- Correspondence: (J.C.J.); (C.Y.K.); Tel.: +82-63-570-5001 (C.Y.K.); Fax: +82-63-570-5009 (C.Y.K.)
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (S.K.); (Y.J.J.); (S.H.P.); (S.-C.P.); (S.B.L.); (J.L.); (S.W.K.)
- Correspondence: (J.C.J.); (C.Y.K.); Tel.: +82-63-570-5001 (C.Y.K.); Fax: +82-63-570-5009 (C.Y.K.)
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Jeong N, Kim KS, Jeong S, Kim JY, Park SK, Lee JS, Jeong SC, Kang ST, Ha BK, Kim DY, Kim N, Moon JK, Choi MS. Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study. PLoS One 2019; 14:e0224074. [PMID: 31639154 PMCID: PMC6804985 DOI: 10.1371/journal.pone.0224074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022] Open
Abstract
A core collection is a subset that represents genetic diversity of the total collection. Soybean (Glycine max (L.) Merr.) is one of major food and feed crops. It is the world's most cultivated annual herbaceous legume. Constructing a core collection for soybean could play a pivotal role in conserving and utilizing its genetic variability for research and breeding programs. To construct and evaluate a Korean soybean core collection, genotypic and phenotypic data as well as population structure, were analyzed. The Korean soybean core collection consisted of 430 accessions selected from 2,872 collections based on Affymetrix Axiom® 180k SoyaSNP array data. The core collection represented 99% of genotypic diversity of the total collection. Analysis of population structure clustered the core collection into five subpopulations. Accessions from South Korea and North Korea were distributed across five subpopulations. Analysis of molecular variance indicated that only 2.01% of genetic variation could be explained by geographic origins while 16.18% of genetic variation was accounted for by subpopulations. Genome-wide association study (GWAS) for days to flowering, flower color, pubescent color, and growth habit confirmed that the core collection had the same genetic diversity for tested traits as the total collection. The Korean soybean core collection was constructed based on genotypic information of the 180k SNP data. Size and phenotypic diversity of the core collection accounted for approximately 14.9% and 18.1% of the total collection, respectively. GWAS of core and total collections successfully confirmed loci associated with tested traits. Consequently, the present study showed that the Korean soybean core collection could provide fundamental and practical material and information for both soybean genetic research and breeding programs.
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Affiliation(s)
- Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| | | | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Ju Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - Sung-Taeg Kang
- Department of Crop Science & Biotechnology, Dankook University, Cheonan, Chungcheongnam-do, Republic of Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Dool-Yi Kim
- National Institute of Crop Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Jeollabuk-do, Republic of Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
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Hong MJ, Jang YE, Kim DG, Kim JM, Lee MK, Kim JB, Eom SH, Ha BK, Lyu JI, Kwon SJ. Selection of mutants with high linolenic acid contents and characterization of fatty acid desaturase 2 and 3 genes during seed development in soybean (Glycine max). J Sci Food Agric 2019; 99:5384-5391. [PMID: 31077382 DOI: 10.1002/jsfa.9798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/14/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Soybean seeds contain 18-24% lipids, which are made up of 85% polyunsaturated fatty acids. Two of these (linoleic and linolenic acids) comprise essential fatty acids that are not synthesized in humans and animals. Linolenic acid plays a vital role in the maintenance of brain function and is a source of docosahexaenoic acid for retinal and nerve tissue, with its physiological functions being a focus of attention. RESULTS We developed mutant soybean populations via gamma irradiation of Korean cultivars Danbaek and Daepung and evaluated the linolenic acid content of 78 and 154 M9 mutant progenies. We selected the four mutant lines with the highest linolenic acid contents based on 2 years of investigation of fatty acids. The selected mutant lines had linolenic acid contents that were 33.9% to 67.7% higher than those of the original cultivars and exhibited increased fatty acid desaturase (FAD) gene expression levels during seed development. We also identified nucleotide polymorphisms of FAD genes in the four mutant lines. CONCLUSION The present study found that linolenic acid content is related to significantly increased expression levels of the FAD3C and FAD3D genes in the endoplasmic reticulum, which was uncovered by radiation mutation breeding of soybean. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Young Eun Jang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
- Department of Life-Resources, Graduate School, Sunchon National University, Sunchon, Korea
| | - Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
- Division of Plant Biotechnology, Collage of Agriculture and Life Science, Chonnam National University, Gwangju, Korea
| | - Min-Kyu Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
- Division of Plant Biotechnology, Collage of Agriculture and Life Science, Chonnam National University, Gwangju, Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, Collage of Agriculture and Life Science, Chonnam National University, Gwangju, Korea
| | - Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
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Lee MK, Lyu JI, Hong MJ, Kim DG, Kim JM, Kim JB, Eom SH, Ha BK, Kwon SJ. Utility of TRAP markers to determine indel mutation frequencies induced by gamma-ray irradiation of faba bean ( Vicia faba L.) seeds. Int J Radiat Biol 2019; 95:1160-1171. [PMID: 30964373 DOI: 10.1080/09553002.2019.1605462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Purpose: The aims were to determine the optimal gamma ray dose for faba bean (Vicia faba) and to identify genetic variation and indel mutation frequency among mutants using target region amplification polymorphism (TRAP) markers. Materials and methods: Seeds from 10 elite lines were irradiated with gamma rays (50-700 Gy), and germination, survival rate, and representative morphological traits were measured. The extent of DNA damage was investigated using comet assays, and TRAP markers were used to evaluate genetic variation, genetic diversity, and mutation frequencies. Results: Germination percentages significantly decreased at doses >100 Gy. Survival percentages and morphological traits decreased with elevation in dose. The comet assays revealed that high irradiation doses decreased head DNA levels. Phylogenetic and principal component analysis of 555 individual faba bean plants resolved eight major groups. Genetic variation between controls and mutants was limited to within groups. Mutation frequencies were associated with gamma dose in each mutant line. Conclusions: The optimal gamma dose was 100-150 Gy on the basis of survival percentage and morphological response analysis. The TRAP markers distinguished mutant lines and showed association between mutation frequency and gamma doses. This study will be useful for faba bean mutation breeding and may be applicable to other crops.
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Affiliation(s)
- Min-Kyu Lee
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea.,b Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University , Gwangju , Korea
| | - Jae Il Lyu
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea
| | - Min Jeong Hong
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea
| | - Dong-Gun Kim
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea.,c Department of Life-Resources, Graduate School, Sunchon National University , Sunchon , Korea
| | - Jung Min Kim
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea.,b Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University , Gwangju , Korea
| | - Jin-Baek Kim
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea
| | - Seok Hyun Eom
- d Department of Horticultural Biotechnology, College of Life Sciences, Kyung Hee University , Yongin , Korea
| | - Bo-Keun Ha
- b Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University , Gwangju , Korea
| | - Soon-Jae Kwon
- a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Korea
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Kim WJ, Ryu J, Im J, Kim SH, Kang SY, Lee JH, Jo SH, Ha BK. Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing. Mol Genet Genomics 2018; 293:1169-1180. [PMID: 29785615 DOI: 10.1007/s00438-018-1448-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/16/2018] [Indexed: 10/16/2022]
Abstract
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS). In total, 7453 single nucleotide polymorphisms (SNPs) were detected in the 20 M2 plants, compared with the two wild-type controls. The SNP frequency was 1/36,976 bp with proton beam irradiation at 118 Gy, and 1/32,945 bp at 239 Gy. Of these, 3569 SNPs were detected in genic regions. We observed that proton beam irradiation induced more substitutions than small insertion-deletions (INDELs). Based on the mutagenic effect of proton beam irradiation, the frequency of transition mutations was shown to be higher than that of transversions. The proton beam-induced SNPs were distributed uniformly in most of the chromosomes. Gene ontology (GO) analysis showed that there were many genes involved in protein metabolic process under biological process, intracellular membrane-bounded organelle under cellular component, and nucleic acid binding under molecular function. This study could provide valuable information for investigating the potential mechanisms of mutation, and guidance for developing soybeans cultivars using mutation breeding.
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Affiliation(s)
- Woon Ji Kim
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Jaihyunk Ryu
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 56212, Korea
| | - Juhyun Im
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Sang Hun Kim
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 56212, Korea
| | | | | | - Bo-Keun Ha
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea.
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Ryu J, Kim WJ, Im J, Kim SH, Lee KS, Jo HJ, Kim EY, Kang SY, Lee JH, Ha BK. Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Lee MK, Kim DG, Kim JM, Ryu J, Eom SH, Hong MJ, Jang YE, Ha BK, Kwon SJ. Selection of the Elite Lines with High Adaptability to Autumn Sowing of South Korea in Faba Bean. ACTA ACUST UNITED AC 2018. [DOI: 10.9787/pbb.2018.6.1.57] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kwon SJ, Kim DG, Kim JM, Kang KY, Lee MK, Hong MJ, Kim JB, Eom SH, Kang SY, Ha BK, Ryu J. Phytochemical Compounds and Antioxidant Activity in the Grain of Selected Faba Bean (Vicia faba) Genotypes. ACTA ACUST UNITED AC 2018. [DOI: 10.9787/pbb.2018.6.1.65] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee KJ, Kim DS, Kim JB, Jo SH, Kang SY, Choi HI, Ha BK. Identification of candidate genes for an early-maturing soybean mutant by genome resequencing analysis. Mol Genet Genomics 2016; 291:1561-71. [PMID: 27033554 DOI: 10.1007/s00438-016-1183-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/15/2016] [Indexed: 10/22/2022]
Abstract
Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In this study, we performed whole genome resequencing by Illumina HiSeq to identify changes in flowering genes using an early-flowering phenotype of soybean mutant line Josaengserori (JS) derived from Korean landrace, Seoritae (SR), and we obtained mapped reads of 131,769,690 and 167,669,640 bp in JS and SR, respectively. From the whole genome sequencing results between JS and SR, we identified 332,821 polymorphic SNPs and 65,178 indels, respectively. Among these, 30 flowering genes were in SNPs and 25 were in indels. Among 30 flowering genes detected in SNPs, Glyma02g33040, Glyma06g22650, Glyma10g36600, Glyma13g01290, Glyma14g10530, Glyma16g01980, Glyma17g11040, Glyma18g53690, and Glyma20g29300 were non-synonymous substitutions between JS and SR. Changes in Glyma10g36600 (GI), Glya02g33040 (AGL18), Glyma17g11040 (TOC1), and Glyma14g10530 (ELF3) in JS affected the expression of GmFT2a and resulted in early flowering. These results provide insight into the regulatory pathways of flowering in soybean mutants and help to improve our knowledge of soybean mutation breeding.
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Affiliation(s)
- Kyung Jun Lee
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
- National Agrobiodiversity Center, NAAS, RDA, Jeonju, 560-500, Republic of Korea
| | - Dong Sub Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Jin-Baek Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea.
| | - Sung-Hwan Jo
- Seeders Inc., Daejeon, 305-509, Republic of Korea
| | - Si-Yong Kang
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Hong-Il Choi
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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Ryu J, Kwon SJ, Jo YD, Jin CH, Nam BM, Lee SY, Jeong SW, Im SB, Oh SC, Cho L, Ha BK, Kang SY. Comparison of Phytochemicals and Antioxidant Activity in Blackberry (Rubus fruticosus L.) Fruits of Mutant Lines at the Different Harvest Time. ACTA ACUST UNITED AC 2016. [DOI: 10.9787/pbb.2016.4.2.242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ryu J, Kwon SJ, Sung SY, Kim WJ, Kim DS, Ahn JW, Kim JB, Kim SH, Ha BK, Kang SY. Molecular cloning, characterization, and expression analysis of lignin biosynthesis genes from kenaf (Hibiscus cannabinus L.). Genes Genomics 2016. [DOI: 10.1007/s13258-015-0341-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lee YG, Jeong N, Kim JH, Lee K, Kim KH, Pirani A, Ha BK, Kang ST, Park BS, Moon JK, Kim N, Jeong SC. Development, validation and genetic analysis of a large soybean SNP genotyping array. Plant J 2015; 81:625-36. [PMID: 25641104 DOI: 10.1111/tpj.12755] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/18/2014] [Accepted: 12/18/2014] [Indexed: 05/19/2023]
Abstract
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.
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Affiliation(s)
- Yun-Gyeong Lee
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea; Department of Bioinformatics, University of Science and Technology, Daejeon, 305-806, Korea
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Kang YJ, Kim SK, Kim MY, Lestari P, Kim KH, Ha BK, Jun TH, Hwang WJ, Lee T, Lee J, Shim S, Yoon MY, Jang YE, Han KS, Taeprayoon P, Yoon N, Somta P, Tanya P, Kim KS, Gwag JG, Moon JK, Lee YH, Park BS, Bombarely A, Doyle JJ, Jackson SA, Schafleitner R, Srinives P, Varshney RK, Lee SH. Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun 2014; 5:5443. [PMID: 25384727 PMCID: PMC4241982 DOI: 10.1038/ncomms6443] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022] Open
Abstract
Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.
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Affiliation(s)
- Yang Jae Kang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Sue K. Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Moon Young Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Puji Lestari
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, IAARD, Jl. Tentara Pelajar 3A, Bogor 16111, Indonesia
| | - Kil Hyun Kim
- Upland Crop Division, National Institute of Crop Science, Rural Development Administration, Suwon 441-770, Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju 500-757, Korea
| | - Tae Hwan Jun
- Department of Plant Bioscience, College of Natural Resources & Life Science, Pusan National University, Pusan 627-706, Korea
| | - Won Joo Hwang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jayern Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Sangrea Shim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Min Young Yoon
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Young Eun Jang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kwang Soo Han
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Puntaree Taeprayoon
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Na Yoon
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Patcharin Tanya
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Kwang Soo Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jae-Gyun Gwag
- National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon 441-707, Korea
| | - Jung-Kyung Moon
- Upland Crop Division, National Institute of Crop Science, Rural Development Administration, Suwon 441-770, Korea
| | - Yeong-Ho Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Beom-Seok Park
- The Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea
| | - Aureliano Bombarely
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NewYork 14853, USA
| | - Jeffrey J. Doyle
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NewYork 14853, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA
| | - Roland Schafleitner
- Biotechnology/Molecular Breeding, AVRDC-The World Vegetable Center, 60, Yi-Min Liao, Tainan 74199, Taiwan
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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Goh EJ, Kim JB, Kim WJ, Ha BK, Kim SH, Kang SY, Seo YW, Kim DS. Physiological changes and anti-oxidative responses of Arabidopsis plants after acute and chronic γ-irradiation. Radiat Environ Biophys 2014; 53:677-93. [PMID: 25169704 DOI: 10.1007/s00411-014-0562-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 08/14/2014] [Indexed: 05/22/2023]
Abstract
To identify the effects of acute and chronic γ-irradiation in Arabidopsis plants, physiological responses and antioxidant-related gene expression were investigated. Seedlings were exposed to 200 Gy of γ-irradiation in acute manner for 1 or 24 h (A1 and A24) or in chronic manner for 1, 2, or 3 weeks (C1 W, C2 W, and C3 W). Plant height, silique number, and silique length in A1 and A24 irradiated plants were significantly reduced when compared to non-irradiated plants. Silique number decreased in response to both acute and chronic irradiation, except with the C3 W treatment, and the number of trichomes dramatically increased in A1 and C1 W. Electron spin resonance signal intensities increased in A1 and in all chronically irradiated plants, but decreased in the A24-treated plant. To investigate the effects of acute and chronic γ-irradiation on antioxidant enzymes, we examined activity of four antioxidant enzymes: catalase (CAT), peroxidase (POD), ascorbate peroxidase, and superoxide dismutase. In general, POD and CAT activities decreased in response to acute and chronic γ-irradiation. Oligonucleotide microarrays were used to investigate transcriptional changes after irradiation. Several genes related to reactive oxygen species signaling were up-regulated after acute and chronic exposure, including genes encoding heat shock factors, zinc finger proteins, NADPH oxidase, WRKY DNA-binding proteins, and calcium binding proteins. Taken together, our data indicate that the responses and activation of antioxidant systems prompted by irradiation exposure are dependent upon the γ-ray dose rate.
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Affiliation(s)
- Eun Jeong Goh
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup, Jeonbuk, 580-185, Republic of korea
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Lee KJ, Hwang JE, Velusamy V, Ha BK, Kim JB, Kim SH, Ahn JW, Kang SY, Kim DS. Selection and molecular characterization of a lipoxygenase-free soybean mutant line induced by gamma irradiation. Theor Appl Genet 2014; 127:2405-13. [PMID: 25190478 DOI: 10.1007/s00122-014-2385-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 07/15/2014] [Indexed: 05/25/2023]
Abstract
KEY MESSAGE A lipoxygenase-free soybean mutant line (H70) induced by gamma ray was selected and its detailed information about the lipoxygenase was analyzed by comparison of DNA sequence. Soybean seeds contain three lipoxygenase enzymes, which induce a beany or grassy flavor. The elimination of lipoxygenases can reduce the poor stability and off-flavors of soybean oil and protein products. In this study, we selected a soybean mutant (H70) in which the three lipoxygenases had been mutated using gamma rays. To obtain detailed information about the lipoxygenase, we investigated the sequences of the Lox1, Lox2 and Lox3 genes in H70 compared to the original cultivar, Hwanggum. Comparisons of the sequences of the Lox1 and Lox2 genes in H70 with those in a line with normal lipoxygenase (HG) showed that the mutations in these genes affected a highly conserved group of six histidine residues necessary for enzymatic activity. Lox1 in H70 contained a 74 bp deletion in exon 8, creating a stop codon that prematurely terminates translation. A single point mutation (T-A) in exon 8 of Lox2 changed histidine (H532, one of the iron-binding ligands essential for Lox2 activity) to glutamine. The mutation in the Lox3 gene in H70 was a single-point mutation in exon 6 (A-G), which changed the amino acid from histidine to arginine. This amino acid alteration in Lox3 was located in the N-terminal barrel, which might play a role in molecular recognition during catalysis and/or proteolysis. These results suggest that gene analysis based on DNA sequencing could be useful for elucidating the lipoxygenase content in soybean mutant lines. Additionally, the soybean mutant line selected in this study could be used to develop soybean cultivars with improved flavor.
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Affiliation(s)
- Kyung Jun Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, Republic of Korea,
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Ha BK, Kim HJ, Velusamy V, Vuong TD, Nguyen HT, Shannon JG, Lee JD. Identification of quantitative trait loci controlling linolenic acid concentration in PI483463 (Glycine soja). Theor Appl Genet 2014; 127:1501-12. [PMID: 24794978 DOI: 10.1007/s00122-014-2314-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 04/12/2014] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE The QTLs controlling alpha-linolenic acid concentration from wild soybean were mapped on nine soybean chromosomes with various phenotypic variations. New QTLs for alpha-linolenic acid were detected in wild soybean. Alpha-linolenic acid (ALA) is a polyunsaturated fatty acid desired in human and animal diets. Some wild soybean (Glycine soja) genotypes are high in ALA. The objective of this study was to identify quantitative trait loci (QTLs) controlling ALA concentration in a wild soybean accession, PI483463. In total, 188 recombinant inbred lines of F5:6, F5:7, and F5:8 generations derived from a cross of wild soybean PI483463 (~15 % ALA) and cultivar Hutcheson (~9 % ALA) were planted in four environments. Harvested seeds were used to measure fatty acid concentration. Single nucleotide polymorphism markers of the universal soybean linkage panel (USLP 1.0) and simple sequence repeat markers were used for molecular genotyping. Nine putative QTLs were identified that controlled ALA concentration by model-based composite interval mapping and mapped to different soybean chromosomes. The QTLs detected in four environments explained 2.4-7.9 % of the total phenotypic variation (PV). Five QTLs, qALA5_3, qALA6_1, qALA14_1, qALA15_1, and qALA17_1, located on chromosomes 5, 6, 14, 15, and 17 were identified by model-based composite interval mapping and composite interval mapping in two individual environments. Among them, qALA6_1 showed the highest contribution to the PV with 10.0-10.2 % in two environments. The total detected QTLs for additive and epistatic effects explained 52.4 % of the PV for ALA concentration. These findings will provide useful information for understanding genetic structure and marker-assisted breeding programs to increase ALA concentration in seeds derived from wild soybean PI483463.
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Affiliation(s)
- Bo-Keun Ha
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
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Hwang JE, Hwang SG, Kim SH, Lee KJ, Jang CS, Kim JB, Kim SH, Ha BK, Ahn JW, Kang SY, Kim DS. Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice. Physiol Plant 2014; 150:604-19. [PMID: 24164326 DOI: 10.1111/ppl.12121] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/01/2013] [Accepted: 10/22/2013] [Indexed: 05/24/2023]
Abstract
Ionizing radiation (IR) affects gene expression from plant genomes. To monitor the genome-wide transcriptional changes induced by three types of IR, we used the rice Affymetrix GeneChip microarray to identify genes that are up- or down-regulated by gamma rays (GAs), cosmic rays (CRs) and ion beams (IBs). The overall expression patterns in rice seedlings generated from seeds exposed to GAs and IBs were similar but differed for CRs exposure. Expression profiles of genes involved in metabolic pathways and cellular response were identified using MapMan analysis. This result revealed that IRs induced gene expression related to sucrose-starch metabolisms; sugar and starch accumulation was significantly increased in response to three types of IR in rice. In addition, we compared the genes commonly up- or down-regulated by exposure to three types of IR and identified 53 candidate radio marker genes (RMGs) that were differentially regulated by radiation exposure but not by other stresses. Among these genes, we selected six RMGs commonly applicable to different types of IR by specific coexpression networks using the algorithm for the reconstruction of accurate cellular networks (aracne) and confirmed the expression of these genes by reverse transcription-polymerase chain reaction (RT-PCR) analysis. Our results provided insight into the mechanisms of the responses to different types of IR and identified multiple marker genes to predict sensitivity to three types of IR.
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Affiliation(s)
- Jung Eun Hwang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, Republic of Korea
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Kim SH, Hwang SG, Hwang JE, Jang CS, Velusamy V, Kim JB, Kim SH, Ha BK, Kang SY, Kim DS. The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice. Physiol Plant 2013; 149:554-570. [PMID: 23617399 DOI: 10.1111/ppl.12058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/28/2013] [Accepted: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma-ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma-irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up- and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root-induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT-PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root-induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.
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Affiliation(s)
- Sun-Hee Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Sun-Goo Hwang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Jung Eun Hwang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Vijayanand Velusamy
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Bo-Keun Ha
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
| | - Dong Sub Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea
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Kim DS, Song M, Kim SH, Jang DS, Kim JB, Ha BK, Kim SH, Lee KJ, Kang SY, Jeong IY. The improvement of ginsenoside accumulation in Panax ginseng as a result of γ-irradiation. J Ginseng Res 2013; 37:332-40. [PMID: 24198659 PMCID: PMC3818960 DOI: 10.5142/jgr.2013.37.332] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 11/14/2012] [Accepted: 05/06/2013] [Indexed: 11/18/2022] Open
Abstract
In this study, gamma rays were used to irradiate embryogenic calli induced from cotyledon explants of Panax ginseng Meyer. After the embryogenic calli were irradiated, they were transferred to adventitious roots using an induction medium; next, mutated adventitious root (MAR) lines with a high frequency of adventitious root formations were selected. Two MAR lines (MAR 5-2 and MAR 5-9) from the calli treated with 50 Gy of gamma rays were cultured on an NH4NO3-free Murashige and Skoog medium with indole-3-butyric acid 3 mg/L. The expression of genes related to ginsenoside biosynthesis was analyzed using reverse transcription polymerase chain reaction with RNA prepared from native ginseng (NG), non-irradiated adventitious root (NAR) and 2 MAR lines. The expression of the squalene epoxidase and dammarenediol synthase genes was increased in the MAR 5-2 line, whereas the phytosterol synthase was increased in the MAR 5-9 line. The content and pattern of major ginsenosides (Rb1, Rb2, Rc, Rd, Re, Rf, and Rg1) were analyzed in the NG, NAR, and 2 MAR lines (MAR 5-2 and MAR 5-9) using TLC and HPLC. In the TLC analysis, the ginsenoside patterns in the NG, NAR, and 2 MAR lines were similar; in contrast, the MAR 5-9 line showed strong bands of primary ginsenosides. In the HPLC analysis, compared with the NG, one new type of ginsenoside was observed in the NAR and 2 MAR lines, and another new type of ginsenoside was observed in the 2 MAR lines irradiated with gamma rays. The ginsenoside content of the MAR 5-9 line was significantly greater in comparison to the NG.
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Affiliation(s)
- Dong Sub Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185, Korea
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Sung SY, Kim SH, Velusamy V, Lee YM, Ha BK, Kim JB, Kang SY, Kim HG, Kim DS. Comparative gene expression analysis in a highly anthocyanin pigmented mutant of colorless chrysanthemum. Mol Biol Rep 2013; 40:5177-89. [PMID: 23666061 DOI: 10.1007/s11033-013-2620-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 04/30/2013] [Indexed: 11/25/2022]
Abstract
In this study, we investigated differentially expressed genes between the original chrysanthemum cultivar 'Argus' with white flower color and its gamma-ray irradiated mutant 'ARTI-purple' with purple flower color. The expression levels of anthocyanin biosynthetic genes were not associated with anthocyanin accumulations of Argus and ARTI-purple. Expressed sequence tags (ESTs) analysis was performed to identify a novel cDNAs encoding enzymes of specific plant metabolic pathways and the biological effects of gamma-ray mutation through alterations in expression in each flower. A total of 796 unigenes were isolated from chrysanthemum ray florets. These unigenes were functionally classified using gene ontologies and tentative pathway associations were established to 99 sequences in the Kyoto encyclopedia of genes and genomes. The expressions of the isolated ESTs were screened by cDNA dot blot hybridization. Seven differentially expressed genes were identified as being involved in carbohydrate and lipid metabolic pathways and five as transcription factor or signal transduction genes. Of particular note, decreased expression of CmMYB1 was identified at the 'ARTI-purple'. The CmMYB1 shared high similarity with AtMYB4 and AtMYBL2 which is a negative regulator of anthocyanin and flavonol accumulation. Furthermore, two genes involved in lipid metabolism, enoyl-ACP reductase and [acyl-carrier-protein] S-malonyltransferase, were decreased in the 'ARTI-purple' flower. Our results suggest that the purple pigmentation of the 'ARTI-purple' is not just dependent on the expression of anthocyanin synthesis genes, and that the pigmentation may also affect other metabolic processing and the plant cell environment.
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Affiliation(s)
- Sang Yeop Sung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea.
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Kim DS, Lee KJ, Yim WC, Kim JB, Ha BK, Kim SH, Kang SY. Transcriptional network analysis of the tryptophan-accumulating rice mutant during grain filling. Mol Genet Genomics 2012; 287:699-709. [PMID: 22836167 DOI: 10.1007/s00438-012-0712-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/14/2012] [Indexed: 01/03/2023]
Abstract
In a previous study, we selected a high tryptophan (Trp)-accumulating rice (Oryza sativa L.) mutant line by in vitro mutagenesis using gamma rays. To obtain detailed information about the Trp biosynthetic pathway during the grain-filling in rice, we investigated the gene expression profiles in the wild-type (cv. Dongan) and the high-level Trp-accumulating mutant line (MRVII-33) at five different grain-filling stages using microarray analysis. The mutant line showed approximately 6.3-fold higher Trp content and 2.3-fold higher amino acids compared with the original cultivar at the final stage (stage V). The intensity of gene expression was analyzed and compared between the wild-type and mutant line at each of the five grain-filling stages using the Rice 4 × 44K oligo DNA microarray. Among the five stages, stage III showed the highest gene expression changes for both up- and down-regulated genes. Among the Trp biosynthesis-related genes, trpG showed high expression in the mutant line during stages I to IV and trpE showed higher at stage III. Gene clustering was performed based on the genes of KEGG's amino acid metabolism, and a total of 276 genes related to amino acid metabolism were placed into three clusters. The functional annotation enrichment analysis of the genes classified into the three clusters was also conducted using ClueGO. It was found that cluster 3 uniquely included biological processes related to aromatic amino acid metabolism. These results suggest that gene analysis based on microarray data is useful for elucidating the biological mechanisms of Trp accumulation in high Trp-accumulating mutants at each of the grain-filling stages.
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Affiliation(s)
- Dong Sub Kim
- Radiation Research Center for Bio-technology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, Korea.
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Lee KJ, Kim JB, Kim SH, Ha BK, Lee BM, Kang SY, Kim DS. Alteration of seed storage protein composition in soybean [Glycine max (L.) Merrill] mutant lines induced by γ-irradiation mutagenesis. J Agric Food Chem 2011; 59:12405-10. [PMID: 22077400 DOI: 10.1021/jf202809j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This study investigated the alteration of seed storage proteins in soybean mutants induced by γ-irradiation. Five soybean cultivars and four landraces were irradiated with 250 Gy of γ rays to induce variability. The seed storage protein profiles of 414 genetic fixed mutants (M(12)-M(20)) having excellent agricultural traits were analyzed by SDS-PAGE. Among the 414 mutants, 58 were identifed as lacking lipoxygenase, 89 lacking the α' subunit, 113 lacking the α subunit, and 40 with an altered β subunit. One hundred and forty-nine mutants lacked the A(3) subunit of glycinin. Fifty-four mutants showed higher trypsin inhibitor (TIA) activity, whereas 139 showed lower TIA activity compared to their original cultivars. The selected mutants with low amounts of antinutritional factors such as trypsin inhibitor, lipoxygenase, and α subunit will constitute genetic resources for improving soybean protein quality.
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Affiliation(s)
- Kyung Jun Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup 580-185, Republic of Korea
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Kendrick MD, Harris DK, Ha BK, Hyten DL, Cregan PB, Frederick RD, Boerma HR, Pedley KF. Identification of a second Asian soybean rust resistance gene in Hyuuga soybean. Phytopathology 2011; 101:535-43. [PMID: 21244223 DOI: 10.1094/phyto-09-10-0257] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
ABSTRACT Asian soybean rust (ASR) is an economically significant disease caused by the fungus Phakopsora pachyrhizi. The soybean genes Rpp3 and Rpp?(Hyuuga) confer resistance to specific isolates of the pathogen. Both genes map to chromosome 6 (Gm06) (linkage group [LG] C2). We recently identified 12 additional soybean accessions that harbor ASR resistance mapping to Gm06, within 5 centimorgans of Rpp3 and Rpp?(Hyuuga). To further characterize genotypes with resistance on Gm06, we used a set of eight P. pachyrhizi isolates collected from geographically diverse areas to inoculate plants and evaluate them for differential phenotypic responses. Three isolates elicited different responses from soybean accessions PI 462312 (Ankur) (Rpp3) and PI 506764 (Hyuuga) (Rpp?[Hyuuga]). In all, 11 of the new accessions yielded responses identical to either PI 462312 or Hyuuga and 1 of the new accessions, PI 417089B (Kuro daizu), differed from all others. Additional screening of Hyuuga-derived recombinant inbred lines indicated that Hyuuga carries two resistance genes, one at the Rpp3 locus on Gm06 and a second, unlinked ASR resistance gene mapping to Gm03 (LG-N) near Rpp5. These findings reveal a natural case of gene pyramiding for ASR resistance in Hyuuga and underscore the importance of utilizing multiple isolates of P. pachyrhizi when screening for ASR resistance.
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Affiliation(s)
- Mandy D Kendrick
- United States Department of Agriculture-Agricultureal Research Service, Ft. Detrick, MD, USA
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Monteros MJ, Ha BK, Phillips DV, Boerma HR. SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust. Theor Appl Genet 2010; 121:1023-32. [PMID: 20532750 PMCID: PMC2938421 DOI: 10.1007/s00122-010-1368-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 05/21/2010] [Indexed: 05/23/2023]
Abstract
Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean, Glycine max L. Merr., production in the USA. A novel rust resistance gene, Rpp?(Hyuuga), from the Japanese soybean cultivar Hyuuga has been identified and mapped to soybean chromosome 6 (Gm06). Our objectives were to fine-map the Rpp?(Hyuuga) gene and develop a high-throughput single nucleotide polymorphism (SNP) assay to detect this ASR resistance gene. The integration of recombination events from two different soybean populations and the ASR reaction data indicates that the Rpp?(Hyuuga) locus is located in a region of approximately 371 kb between STS70887 and STS70923 on chromosome Gm06. A set of 32 ancestral genotypes which is predicted to contain 95% of the alleles present in current elite North American breeding populations and the sources of the previously reported ASR resistance genes (Rpp1, Rpp2, Rpp3, Rpp4, Rpp5, and rpp5) were genotyped with five SNP markers. We developed a SimpleProbe assay based on melting curve analysis for SNP06-44058 which is tighly linked to the Rpp?(Hyuuga) gene. This SNP assay can differentiate plants/lines that are homozygous/homogeneous or heterozygous/heterogeneous for the resistant and susceptible alleles at the Rpp?(Hyuuga) locus.
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Affiliation(s)
- Maria J Monteros
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
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Abstract
In the adult cerebellum, corticotropin releasing factor (CRF), that is localized in climbing fibers, mossy fibers, and a fine varicose plexus along the Purkinje cell layer, modulates the responsiveness of Purkinje cells to excitatory amino acids. During development, CRF has been detected in the primitive cerebellar anlage as early as embryonic day (E)10, and is continuously expressed throughout embryonic and postnatal cerebellar ontogeny. To investigate a possible trophic role for CRF during cerebellar development, cerebellar culture studies using E18 mouse embryos were carried out. In our culture paradigm, that used serum-free defined medium to suppress cell proliferation, CRF induced proliferation of cells in a dose-dependent manner in a range of concentrations between 0.1-10 microM. The proliferating cells were identified as astrocytes based on their expression of vimentin and GFAP. BrdU incorporation studies supported the proposed mitogenic effect of CRF on developing astrocytes. The mitogenic effects of CRF seemed to be primarily on immature astrocytes determined by their differential expression of vimentin and GFAP. Astrocytes at more advanced stages of development, as determined by the extent of process outgrowth and GFAP expression, incorporated less BrdU compared to immature astrocytes. CRF receptors were localized in astrocytes, and the proliferation of astrocytes induced by CRF was inhibited by astressin, a competitive CRF receptor antagonist. In conclusion, CRF induces proliferation of astrocytes derived from the developing cerebellum, that suggests a gliotrophic role for CRF during cerebellar development.
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Affiliation(s)
- B K Ha
- Department of Neuroscience, Ohio State University, Columbus, Ohio 43210, USA
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Abstract
Interleukin-6 (IL-6) type cytokines show functional redundancy in the immune, hematopoietic, and nervous system, which is believed to result from sharing of the signal transducing receptor gp130. IL-6 type cytokines and their binding receptors have been localized in the adult cerebellum. However, the cellular localization and developmental regulation of gp130 in the cerebellum have not been determined. In the present study the expression pattern of gp130 in the developing and adult mouse cerebellum was investigated. At embryonic day (E)15 and E17, gp130 immunoreactivity is present primarily in fiber bundles that course from the brainstem to the cerebellum. At postnatal day (P)0, gp130 immunoreactivity first appears in the Purkinje cell layer, external granule cell layer, and cerebellar nuclei. As Purkinje cells differentiate, gp130 immunoreactivity progressively extends from the cell body along their developing dendritic arbor. All Purkinje cells show intense gp130 immunoreactivity in their cell bodies by P7. In contrast the gp130 immunoreactivity detected in fiber bundles at E15 and E17 is downregulated postnatally, and cannot be detected after P7. Granule cells show gp130 immunoreactivity at P0 in the external granule cell layer and subsequently in the internal granule cell layer. Astrocytes in the white matter express gp130 at P0, and show intense gp130 immunoreactivity between P7 and P14. As the cerebellum matures gp130 immunoreactivity in the white matter decreases. The present description of the differential spatial and temporal distribution of gp130 provides an initial step in defining specific cellular populations that are potential targets of IL-6 type cytokines during cerebellar ontogeny.
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Affiliation(s)
- B K Ha
- Department of Neuroscience, The Ohio State University, 4068 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA
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Lin FY, Vo AH, Phan VB, Nguyen TT, Bryla D, Tran CT, Ha BK, Dang DT, Robbins JB. The epidemiology of typhoid fever in the Dong Thap Province, Mekong Delta region of Vietnam. Am J Trop Med Hyg 2000; 62:644-8. [PMID: 11289678 DOI: 10.4269/ajtmh.2000.62.644] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A population-based surveillance for typhoid fever was conducted in three rural communes of Dong Thap Province in southern Vietnam (population 28,329) for a 12-month-period starting on December 4, 1995. Cases of typhoid fever were detected by obtaining blood for culture from residents with fever > or = 3 days. Among 658 blood cultures, 56 (8.5%) were positive for Salmonella typhi with an overall incidence of 198 per 10(5) population per year. The peak occurrence was at the end of the dry season in March and April. The attack rate was highest among 5-9 year-olds (531/10(5)/year), and lowest in > 30 year-olds (39/10(5)/year). The attack rate was 358/10(5)/year in 2-4 year-olds. The isolation of S. typhi from blood cultures was highest (17.4%) in patients with 5 to 6 days of fever. Typhoid fever is highly endemic in Vietnam and is a significant disease in both preschool and school-aged children.
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Affiliation(s)
- F Y Lin
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
In vitro receptor autoradiography was used to localize sigma 1 receptors, sigma 2 receptors, and novel haloperidol/DTG-inaccessible sites for sigma and opiate ligands in rat spleen. Sigma-1 receptors were present throughout the spleen, but were most concentrated in the T cell zones. Binding under "sigma 2 receptor-selective' conditions was 70% nonspecific, and sigma 2 receptors could not be detected. Haloperidol/DTG-inaccessible sites had a coarse, punctate distribution in the red pulp and marginal zones of the white pulp. This anatomical localization suggests types of cells and functions that should be examined for modulation by sigma receptors.
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Affiliation(s)
- S A Wolfe
- Department of Medical Microbiology and Immunology, Ohio State University College of Medicine, Columbus 43210, USA.
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Whitlock BB, Liu Y, Chang S, Saini P, Ha BK, Barrett TW, Wolfe SA. Initial characterization and autoradiographic localization of a novel sigma/opioid binding site in immune tissues. J Neuroimmunol 1996; 67:83-96. [PMID: 8765330 DOI: 10.1016/0165-5728(96)00041-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
High concentrations of novel, haloperidol- and DTG-inaccessible (+)-[3H]-3-PPP binding sites were found in human peripheral blood leukocytes rat spleen and splenocytes, but not in rat brain. Splenic sites were localized in a course punctate pattern in the marginal zones and red pulp. The pharmacology of the splenic sites was: (-)-SKF 10,047 > or = naltrexone = (-)-pentazocine > (+)-pentazocine = (-)-3-PPP = (+)-SKF 10,047 > or = (+)-3-PPP > or = dextrorphan > dextromethorphan > PCP > clorgyline. DTG, haloperidol, TCP, (-)-deprenyl and SKF 525-A did not complete. Binding activity was destroyed by heating and phospholipase C, but not by proteases or glycosidases. These sites may be involved in immunomodulation by opiate and sigma receptor agonists.
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Affiliation(s)
- B B Whitlock
- Department of Medical Microbiology and Immunology, Ohio State University College of Medicine, Columbus 43210, USA
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Menu E, Truong TX, Lafon ME, Nguyen TH, Müller-Trutwin MC, Nguyen TT, Deslandres A, Chaouat G, Duong QT, Ha BK, Fleury HJ, Barré-Sinoussi F. HIV type 1 Thai subtype E is predominant in South Vietnam. AIDS Res Hum Retroviruses 1996; 12:629-33. [PMID: 8743088 DOI: 10.1089/aid.1996.12.629] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- E Menu
- Institut Pasteur, Unité de Biologie des Rétrovirus, Paris, France
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Nguyen TT, Ha BK. [Epidemiologic trends of HIV infection in South Vietnam]. Sante 1996; 6:72-3. [PMID: 8705127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- T T Nguyen
- Institut Pasteur, Ho Chi Minh-Ville, Vi t-nam
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