Korean Journal of Breeding Science (한국육종학회지)

The Korean Society of Breeding Science (한국육종학회)
권호 표지
DOI QR코드

DOI QR Code

Identification and Chromosomal Reshuffling Patterns of Soybean Cultivars Bred in Gangwon-do using 202 InDel Markers Specific to Variation Blocks

변이영역 특이 202개 InDel 마커를 이용한 강원도 육성 콩 품종의 판별 및 염색체 재조합 양상 구명

  • Sohn, Hwang-Bae (Highland Agricultural Research Institute, National Institute of Crop Science, RDA) ;
  • Song, Yun-Ho (Gangwondo Agricultural Research and Extension Services) ;
  • Kim, Su-Jeong (Highland Agricultural Research Institute, National Institute of Crop Science, RDA) ;
  • Hong, Su-Young (Highland Agricultural Research Institute, National Institute of Crop Science, RDA) ;
  • Kim, Ki-Deog (Highland Agricultural Research Institute, National Institute of Crop Science, RDA) ;
  • Koo, Bon-Cheol (Highland Agricultural Research Institute, National Institute of Crop Science, RDA) ;
  • Kim, Yul-Ho (Highland Agricultural Research Institute, National Institute of Crop Science, RDA)
  • 손황배 (농촌진흥청 국립식량과학원 고령지농업연구소) ;
  • 송윤호 (강원도농업기술원 연구개발국 작물연구과) ;
  • 김수정 (농촌진흥청 국립식량과학원 고령지농업연구소) ;
  • 홍수영 (농촌진흥청 국립식량과학원 고령지농업연구소) ;
  • 김기덕 (농촌진흥청 국립식량과학원 고령지농업연구소) ;
  • 구본철 (농촌진흥청 국립식량과학원 고령지농업연구소) ;
  • 김율호 (농촌진흥청 국립식량과학원 고령지농업연구소)
  • Received : 2018.08.23
  • Accepted : 2018.10.10
  • Published : 2018.12.01
⟨ Previous Next ⟩

Abstract

The areas of soybean (Glycine max (L.) Merrill) cultivation in Gangwon-do have increased due to the growing demand for well-being foods. The soybean barcode system is a useful tool for cultivar identification and diversity analysis, which could be used in the seed production system for soybean cultivars. We genotyped cultivars using 202 insertion and deletion (InDel) markers specific to dense variation blocks (dVBs), and examined their ability to identify cultivars and analyze diversity by comparison to the database in the soybean barcode system. The genetic homology of "Cheonga," "Gichan," "Daewang," "Haesal," and "Gangil" to the 147 accessions was lower than 81.2%, demonstrating that these barcodes have potentiality in cultivar identification. Diversity analysis of one hundred and fifty-three soybean cultivars revealed four subgroups and one admixture (major allele frequency <0.6). Among the accessions, "Heugcheong," "Hoban," and "Cheonga" were included in subgroup 1 and "Gichan," "Daewang," "Haesal," and "Gangil" in the admixture. The genetic regions of subgroups 3 and 4 in the admixture were reshuffled for early maturity and environmental tolerance, respectively, suggesting that soybean accessions with new dVB types should be developed to improve the value of soybean products to the end user. These results indicated that the two-dimensional barcodes of soybean cultivars enable not only genetic identification, but also management of genetic resources through diversity analysis.

본 연구에서는 dVB 특이적인 202개 InDel 마커를 이용하여 강원도에서 육성된 콩 품종의 바코드 데이터베이스 구축 및 유전분석을 수행하였다. 강원도에서 육성된 품종의 202개 InDel의 다형성을 기존의 147 품종과 비교한 결과 강원도 품종이 명확하게 구분되었다. 이는 식량원에서 개발된 콩 품종 인식 시스템이 강원도 품종의 보급종 체계에서 품종의 균일성과 안정성 평가에 적용 가능함을 나타낸다. 153개 품종의 유전형을 이용하여 집단구조를 분석한 결과, '흑청', '호반', '청아'는 subgroup 1으로, '기찬', '대왕', '햇살', '강일'은 admixture로 구분되었다. 강원도 재래종의 숙기를 앞당기 위하여 subgroup 3의 유전 영역이 도입되었으며, 강원도의 특이 환경 및 기후변화 대응에는 subgroup 4가 주로 이용되었음이 유전분석집단에서 확인되었다. 특히, 다양한 소비자의 욕구를 충족과 함께 지역 환경에 적응성을 높이기 위해서 신품종 육성에 유전구조가 다른 다양한 재래종(혹은 품종)의 유전 영역이 지속적으로 도입되어 admixture 집단이 증가한 것으로 판단된다. 결론적으로 강원도 품종의 바코드 데이터베이스 구축은 품종 식별 정확성과 효율성을 향상시켜 품종의 권리 보호와 함께 종자산업 경쟁력을 보다 높일 수 있을 것으로 기대된다. 향후 dVB에 연관된 양적/질적 형질에 대한 추가 연구와 함께 202개 InDel 마커를 이용하여 실험실 수준에서 교배모부본의 잠재적 가능성을 평가할 수 있기 때문에 품종 육성의 효율을 더욱 높일 수 있을 것이다.

Keywords

Acknowledgement

Supported by : 국립식량과학원

References

  1. Agarwal M, Shrivastava N, Padh H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27: 617-631. https://doi.org/10.1007/s00299-008-0507-z
  2. Choi JK, Ha KS, Byum HS, Heo NK, Jang EH, Kim SS, Lee SJ, Sa JG. 2011. A new soybean cultivar ‘Daewang' with high quality and large seed size. Korean J Breed Sci 43: 177-179.
  3. Deschamps S, Campbell MA. 2010. Utilization of nextgeneration sequencing platforms in plant genomics and genetic variant discovery. Mol Breed 25: 553-570. https://doi.org/10.1007/s11032-009-9357-9
  4. Ganal MW, Altman T, Roder MS. 2009. SNP identification in crop plants. Curr Opin Plant Biol 12: 211-217. https://doi.org/10.1016/j.pbi.2008.12.009
  5. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  6. Ha KS, Heo NK, Han TJ. 2002. A green seed soybean variety ‘Heugcheongkong' with black seed. Korean J Breed Sci 34: 80-81.
  7. Ha KS, Choi JK, Heo NK, Kim SS, Lee AS, Jang JS, Yun HT. 2013a. A new tofu and soy-paste soybean cultivar 'Hoban' with large seed and high yield. Korean J Breed Sci 45: 158-162. https://doi.org/10.9787/KJBS.2013.45.2.158
  8. Ha KS, Choi JK, Cho SH, Byun HS, Kim SW, Jang JS, Yun HT, Moon JK, Kim SJ, Park KY. 2013b. A new and soy-paste soybean cultivar, ‘Cheonga' with disease resistance, lodging tolerance and high yield. Korean J Breed Sci 45: 452-456. https://doi.org/10.9787/KJBS.2013.45.4.452
  9. Hou XH, Li LC, Peng ZY, Wei BY, Tang SJ, Ding MY, Liu JJ, Zhang FX, Zhao YD, Gu HY, Qu LJ. 2010. A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis. Plant J 63: 880-888. https://doi.org/10.1111/j.1365-313X.2010.04277.x
  10. Hwang TY, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, Hisano H, Sasamoto S, Sato S, Tabata S, Kono I, Hoshi M, Hanawa M, Yano C, Xia Z, Harada K, Kitamura K, Ishimoto M. 2009. High-density integrated linkage map based on SSR markers in soybean. DNA Res 16: 213-225. https://doi.org/10.1093/dnares/dsp010
  11. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB. 2010. Highthroughput SNP discovery and assay development in common bean. BMC Genomics 11: 475. https://doi.org/10.1186/1471-2164-11-475
  12. Inger H, Rodomiro O. 2000. In situ and ex situ assessment of morphological and fruit variation in Scandinavian sweet cherry. Sci Hortic 85: 37-39. https://doi.org/10.1016/S0304-4238(99)00123-5
  13. Kim MY, Lee S, Van K, Kim TH, Jeong SC, Chio IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YT, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH. 2010. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107: 22032-22037. https://doi.org/10.1073/pnas.1009526107
  14. Kim S, Misra A. 2007. SNP genotyping: technologies and biomedical applications. Annul Rev Biomed Eng 9: 289-320. https://doi.org/10.1146/annurev.bioeng.9.060906.152037
  15. Kim YH, Hwang TY, Seo MJ, Lee SK, Park HM, Jeong KH, Lee YY, Kim SL, Yun HT, Lee JE, Kim DW, Jung GH, Kwon YU, Kim HS. 2012. Discrimination of 110 Korean soybean cultivars by sequence tagged sites (STS)-CAPS markers. Korean J Breed Sci 44: 258-272.
  16. Kim YH, Park HM, Hwang TY, Lee SK, Choi MS, Jho S, Hwang S, Kim HM, Lee D, Kim BC, Hong CP, Cho YS, Kim H, Jeong KH, Seo MJ, Yun HT, Kim SL, Kwon YU, Kim WH, Chun HK, Lim SJ, Shin YA, Choi IK, Kim YS, Yoon HS, Lee SH, Lee S. 2014. Variation block-based genomics method for crop plants. BMC Genomics 15: 477. https://doi.org/10.1186/1471-2164-15-477
  17. Kim SH, Jung JW, Moon JK, Woo SH, Cho YG, Jong SK, Kim HS. 2006. Genetic diversity and relationship by SSR markers of Korean soybean cultivars. Korean J Crop Sci 51: 248-258.
  18. Korir NK, Han J, Shangguan L., Wang C, Kayesh E., Zhang Y, Fang J. 2013. Plant variety and cultivar identification: advances and prospects. Critical Rev in Biotech 33: 111-125. https://doi.org/10.3109/07388551.2012.675314
  19. Lee C, Choi MS, Kim HT, Yun HT, Lee B, Chung YS, Kim RW, Choi HK. 2015. Soybean [Glycine max (L.) Merrill]: Importance as a crop and pedigree reconstruction of Korean varieties. Plant Breed Biotech 3: 179-196. https://doi.org/10.9787/PBB.2015.3.3.179
  20. Lee YG, Jeong N, Kim JH, Lee K, Kim KH, Pirani A, Ha BG, Kang ST, Park BS, Moon JK, Kim N, Jeong SC. 2015. Development, validation and genetic analysis of a large soybean SNP genotyping array. The Plant J 81: 625-636. https://doi.org/10.1111/tpj.12755
  21. Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui Y, Cheng F, Wang X, Wu J. 2012. Development of INDEL markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet 126: 231-239.
  22. Li Y, Liu B, Relif JC, Liu Y, Li H, Chang R, Qiu L. 2014. Development of insertion and deletion markers based on biparental resequencing for fine mapping seed weight in soybean. The Plant Genome 7: 1-8.
  23. Moghaddam SM, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osomo JM, McClean PE. 2014. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Front Plant Sci 5: 295-300.
  24. Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G. 2013. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res 23: 749-761. https://doi.org/10.1101/gr.148718.112
  25. Mullaney JM, Mills RE, Pittard WS, Se D. 2010. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 19(R2): 131-136. https://doi.org/10.1093/hmg/ddq400
  26. Pacurar DI, Pacurar ML, Street N, Bussell JD, Pop TI, Gutierrez L, Bellini C. 2012. A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. J Exp Bot 63: 2491-2501. https://doi.org/10.1093/jxb/err422
  27. Perrier X, Jacquemoud JP. 2006. Darwin software. http://darwin.cirad.fr/darwin.
  28. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. 2000. Association mapping in structured populations. Am J Hum Genet 67: 170-181. https://doi.org/10.1086/302959
  29. Reyes-Valdes MH, Santacruz-Varela A, Martinez O, Simpson J, Hayano-Kanashiro C, Cortes-Romero C. 2013. Analysis and optimization of bulk DNA sampling with binary scoring for germplasm characterization. PLOS ONE 8: e79936. https://doi.org/10.1371/journal.pone.0079936
  30. Rogers SO, Bendich AJ. 1994. Extraction of total cellular DNA from plants, algae and fungi, pp. 1-8. In: Gelvin SB and Schilperoort RA (Eds). Plant Molecular Biology Manual. 2nd edition. Kluwer Academic Publishers. Dordrecht.
  31. Sham P, Bader JS, Craig I, Donovan M, Owen M. 2002. DNA pooling: a tool for large-scale association studies. Nat Rev Genet 3: 862-871. https://doi.org/10.1038/nrg930
  32. Sohn HB, Kim SJ, Hwang TY, Park HM, Lee YY, Markkandan K, Lee D, Lee S, Hong SY, Song YH, Koo BC, Kim YH. 2017a. Barcode system for genetic identification of soybean [Glycine max (L.) Merrill] cultivars using InDel markers specific to dense variation blocks. Front Plant Sci 8: 520.
  33. Sohn HB, Kim SJ, Hwang TY, Park HM, Lee YY, Koo BC, Kim YH. 2017b. Chromosome reshuffling patterns of Korean soybean cultivars using genome-wide 202 InDel markers. Korean J Breed Sci 49: 213-223. https://doi.org/10.9787/KJBS.2017.49.3.213
  34. Song Q, Jia G, Zhu Y, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci 50: 1950-1960. https://doi.org/10.2135/cropsci2009.10.0607
  35. Song X, Wei H, Cheng W, Yang S, Zhao Y, Li X, Luo D, Zhang H, Feng X. 2015. Development of INDEL markers for genetic mapping based on whole genome resequencing in soybean. G3 (Bethesda) 5: 2793-2799.
  36. Yamaki S, Ohyanagi H, Yamasaki M, Eiguchi M, Miyabayashi T, Kubo T, Kurata N, Nonomura KI. 2013. Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza. Breed Sci 63: 246-254. https://doi.org/10.1270/jsbbs.63.246