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http://dx.doi.org/10.7740/kjcs.2015.60.2.224

Distribution of Genetic Variants in Korean Soybeans  

Song, Kitae (Department of Life Science, Dongguk Univ.-Seoul)
Kim, Jeong Hoon (Department of Life Science, Dongguk Univ.-Seoul)
Yoon, Gi Yong (Department of Life Science, Dongguk Univ.-Seoul)
Kim, Hyo Chul (Department of Life Science, Dongguk Univ.-Seoul)
Shin, Seungho (Department of Life Science, Dongguk Univ.-Seoul)
Yim, Won Cheol (Department of Life Science, Dongguk Univ.-Seoul)
Kim, Kyung-Hee (Department of Life Science, Dongguk Univ.-Seoul)
Lee, Byung-Moo (Department of Life Science, Dongguk Univ.-Seoul)
Publication Information
KOREAN JOURNAL OF CROP SCIENCE / v.60, no.2, 2015 , pp. 224-230 More about this Journal
Abstract
Next generation sequencing technologies provide opportunities to reveal the genetic variants and differentially expressedgenes. The genetic variants are closely relevance to understanding of genes and phenotypic differences related to agronomic characteristics among cultivars. In this study, we conducted RNA-seq using two Korean soybean accessions, including Daewon and Hwangkeum, by using next generation sequencing against Williams 82 genome as reference. A number of variants such assingle nucleotide variants (SNV), multiple nucleotide variants (MNV), insertion/deletion (InDel) and replacement, was 34,411 and 55,544 in Daewon and Hwangkeum, respectively. Among these variants, 9,611 nonsynonymous variants were detected within 4,290 genes in Daewon and 13,225 non-synonymous variants were located on 5,672 genes in Hwangkeum. The distribution of nonsynonymous variants and expression values of genes can serve as invaluable resource for genotyping and study of traits within genes for soybean improvements.
Keywords
soybean; genetic variants; RNA-seq;
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1 Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408(6814) : 796-815.   DOI   ScienceOn
2 Chung, W.-H., N. Jeong, J. Kim, W. K. Lee, Y. -G. Lee, S.-H. Lee, W. Yoon, J.-H. Kim, I.-Y. Choi, H.-K. Choi, J.-K. Moon, N. Kim, and S.-C. Jeong. 2014. Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes. DNA Res. 21(2) : 153-167.   DOI
3 Clark, R. M., G. Schweikert, C. Toomajian, S. Ossowski, G. Zeller, P. Shinn, N. Warthmann, T. T. Hu, G. Fu, D. A. Hinds, H. Chen, K. A. Frazer, D. H. Huson, B. Scholkopf, M. Nordborg, G. Ratsch, J. R. Ecker, and D. Weigel. 2007. Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana. Science. 317(5836) : 338-342.   DOI
4 Haun, W. J., D. L. Hyten, W. W. Xu, D. J. Gerhardt, T. J. Albert, T. Richmond, J. A. Jeddeloh, G. Jia, N. M. Springer, C. P. Vance, and R. M. Stupar. 2011. The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol. 155(2) : 645-655.   DOI
5 Hufford, M. B., X. Xu, J. van Heerwaarden, T. Pyhäjärvi, J.-M. Chia, R. A. Cartwright, R. J. Elshire, J. C. Glaubitz, K. E. Guill, S. M. Kaeppler, J. Lai, P. L. Morrell, L. M. Shannon, C. Song, N. M. Springer, R. A. Swanson-Wagner, P. Tiffin, J. Wang, G. Zhang, J. Doebley, M. D. McMullen, D. Ware, E. S. Buckler, S. Yang, and J. Ross-Ibarra. 2012. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44(7) : 808-811.   DOI
6 Hyten, D. L., Q. Song, Y. Zhu, I.-Y. Choi, R. L. Nelson, J. M. Costa, J. E. Specht, R. C. Shoemaker, and P. B. Cregan. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. U.S.A. 103(45) : 16666-16671.   DOI
7 International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature. 436(11) : 793-800.   DOI
8 Kim, M. Y., S. Lee, K. Van, T.-H. Kim, S.-C. Jeong, I.-Y. Choi, D.-S. Kim, Y.-S. Lee, D. Park, J. Ma, W.-Y. Kim, B.-C. Kim, S. Park, K.-A. Lee, D. H. Kim, K. H. Kim, J. H. Shin, Y. E. Jang, K. D. Kim, W. X. Liu, T. Chaisan, Y. J. Kang, Y.-H. Lee, K.-H. Kim, J.-K. Moon, J. Schmutz, S. A. Jackson, J. Bhak, and S.-H. Lee. 2010. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Natl. Acad. Sci. U.S.A. 107(51) : 22032-22037.   DOI
9 Lam, H.-M., X. Xu, X. Liu, W. Chen, G. Yang, F.-L. Wong, M.-W. Li, W. He, N. Qin, B. Wang, J. Li, M. Jian, J. Wang, G. Shao, J. Wang, S. S.-M. Sun, and G. Zhang. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42(12) : 1053-1059.   DOI
10 Lee, W. K., N. Kim, J. Kim, J.-K. Moon, N. Jeong, I.-Y. Choi, S. C. Kim, W.-H. Chung, H. S. Kim, S.-H. Lee, and S.-C. Jeong. 2013. Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps. Theor. Appl. Genet. 126(4) : 1103-1119.   DOI
11 Lee, Y.-G., N. Jeong, J. H. Kim, K. Lee, K. H. Kim, A. Pirani, B.-K. Ha, S.-T. Kang, B.-S. Park, J.-K. Moon, N. Kim, and S.-C. Jeong. 2015. Development, validation and genetic analysis of a large soybean SNP genotyping array. Plant J. 81(4) : 625-636.   DOI
12 Li, Y., S. Zhao, J. Ma, D. Li, L. Yan, J. Li, X. Qi, X. Guo, L. Zhang, W. He, R. Chang, Q. Liang, Y. Guo, C. Ye, X. Wang, Y. Tao, R. Guan, J. Wang, Y. Liu, L. Jin, X. Zhang, Z. Liu, L. Zhang, J. Chen, K. Wang, R. Nielsen, R. Li, P. Chen, W. Li, J. C. Reif, M. Purugganan, J. Wang, M. Zhang, J. Wang, and L. Qiu. 2013. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics. 14 : 579.   DOI
13 McHale, L. K., W. J. Haun, W. W. Xu, P. B. Bhaskar, J. E. Anderson, D. L. Hyten, D. J. Gerhardt, J. A. Jeddeloh, and R. M. Stupar. 2012. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 159(4) : 1295-1308.   DOI
14 McNally, K. L., K. L. Childs, R. Bohnert, R. M. Davidson, K. Zhao, V. J. Ulat, G. Zeller, R. M. Clark, D. R. Hoen, T. E. Bureau, R. Stokowski, D. G. Ballinger, K. A. Frazer, D. R. Cox, B. Padhukasahasram, C. D. Bustamante, D. Weigel, D. J. Mackill, R. M. Bruskiewich, G. Rätsch, C. R. Buell, H. Leung, and J. E. Leach. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. U.S.A. 106(30) : 12273-12278.   DOI   ScienceOn
15 Nelson, J. C., S. Wang, Y. Wu, X. Li, G. Antony, F. F. White, and J. Yu. 2011. Single-nucleotide polymorphism discovery by highthroughput sequencing in sorghum. BMC Genomics. 12 : 352.   DOI
16 Subbaiyan, G. K., D. L. E. Waters, S. K. Katiyar, A. R. Sadananda, S. Vaddadi, and R. J. Henry. 2012. Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by wholegenome sequencing. Plant Biotechnol. J. 10(6) : 623-634.   DOI
17 Pinson, S. R. M. and J. N. Rutger. 1993. Heterozygous diploid plants regenerated from anther culture of F1 rice plants. In Vitro Cell. Dev. Biol. Plant. 29(4) : 174-179.   DOI
18 Schmutz, J., S. B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D. L. Hyten, Q. Song, J. J. Thelen, J. Cheng, D. Xu, U. Hellsten, G. D. May, Y. Yu, T. Sakurai, T. Umezawa, M. K. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, B. Abernathy, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X.-C. Zhang, K. Shinozaki, H. T. Nguyen, R. A. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R. C. Shoemaker, and S. A. Jackson. 2010. Genome sequence of the palaeopolyploid soybean. Nature. 463(7278) : 178-183.   DOI
19 Song, Q., D. L. Hyten, G. Jia, C. V. Quigley, E. W. Fickus, R. L. Nelson, and P. B. Cregan. 2013. Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean. Plos One. 8(1) : e54985.   DOI
20 Van, K., E.-Y. Hwang, M. Y. Kim, H. J. Park, S.-H. Lee, and P. B. Cregan. 2005. Discovery of SNPs in Soybean Genotypes Frequently Used as the Parents of Mapping Populations in the United States and Korea. J. Hered. 96(5) : 529-535.   DOI
21 Wu, X., C. Ren, T. Joshi, T. Vuong, D. Xu, and H. T. Nguyen. 2010. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 11 : 469.   DOI
22 Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli, D. R. Grimm, S. M. Hyatt, E. W. Fickus, N. D. Young, and P. B. Cregan. 2003. Single-nucleotide polymorphisms in soybean. Genetics. 163(3) : 1123-1134.
23 Zou, X., C. Shi, R. S. Austin, D. Merico, S. Munholland, F. Marsolais, A. Navabi, W. L. Crosby, K. P. Pauls, K. Yu, and Y. Cui. 2014. Genome-wide single nucleotide polymorphism and Insertion-Deletion discovery through next-generation sequencing of reduced representation libraries in common bean. Mol. Breeding. 33(4) : 769-778.   DOI