Korean Journal of Plant Resources (한국자원식물학회지)

The Plant Resources Society of Korea (한국자원식물학회)
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Genetic Identification and Phylogenic Analysis of New Varieties and 149 Korean Cultivars using 27 InDel Markers Selected from Dense Variation Blocks in Soybean (Glycine max (L.) Merrill)

변이밀집영역 유래 27개 InDel 마커를 이용한 콩(Glycine max (L.) Merrill) 신품종 판별 및 국내 149 품종과 유연관계 분석

  • Chun, JaeBuhm (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Jin, Mina (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Jeong, Namhee (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Cho, Chuloh (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Seo, Mi-Suk (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Choi, Man-Soo (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Kim, Dool-Yi (Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Sohn, Hwang-Bae (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration) ;
  • Kim, Yul-Ho (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration)
  • 전재범 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 진민아 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 정남희 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 조철오 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 서미숙 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 최만수 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 김둘이 (농촌진흥청 국립식량과학원 작물기초기반과) ;
  • 손황배 (국립식량과학원 고령지농업연구소) ;
  • 김율호 (국립식량과학원 고령지농업연구소)
  • Received : 2019.09.21
  • Accepted : 2019.10.10
  • Published : 2019.10.31
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Abstract

Twenty soybean cultivars developed recently were assessed using 27 insertion and deletion (InDel) markers derived from dense variation blocks (dVBs) of soybean genome. The objective of this study is to identify the distinctness and genetic relationships among a total of 169 soybean accessions including new cultivars. The genetic homology between 149 accessions in the soybean barcode system and 20 new cultivars was 61.3% on average with the range from 25.9% to 96.3%, demonstrating the versatile application of these markers for cultivars identification. The phylogenic analysis revealed four subgroups related to their usage. The 80% of cultivars for vegetable and early maturity and the 65.9% of cultivars for bean sprouts were clustered in subgroup I-2 and II-2, respectively, indicating of the limited gene pools of their crossing parents in breeding. On the other hands, the cultivars for soy sauce and tofu with considerable gene flow by genome reshuffling were distributed evenly to several subgroups, I-1 (44.4%), I-2 (26.4%) and II-2 (23.6%). We believe that the 27 InDel markers specific to dVBs can be used not only for cultivar identification and genetic diversity, but also in breeding purposes such as introduction of genetic resources and selection of breeding lines with target traits.

본 연구에서는 국내 콩 유전체의 변이밀집영역(dVB)에서 유래한 27개 InDel 마커를 신품종 20개에 적용하여 품종판별용 마커로서 범용성을 검증하고 신품종의 구별성과 국내 품종의 유전적 다양성을 확인하였다. 20개 신품종과 MyCrops에 포함된 기존 149개 품종과의 유사도는 평균 61.3%이고, 최저 25.9%에서 최대 96.3%의 유사도로 완전 일치(100%)되는 바코드는 없어 20개 신품종의 유전적 구별성을 모두 확인할 수 있었다. 유연관계를 분석한 결과에서는 신품종을 포함한 국내 169품종이 4개의 유전집단으로 구분되었으며 풋콩 및 단기성 콩의 80%가 I-2 소그룹, 나물콩의 65.9%가 II-2 소그룹에 주로 속한 반면, 장류 및 두부콩은 I-1 (44.4%), I-2 (26.4%), II-2 (23.6%) 소그룹에 고르게 분포하였다. 20개 신품종에 대한 계보도는 나물콩 주요 계보와 장류 및 두부콩으로 크게 두 그룹으로 나누어지며 유연관계분석을 뒷받침하였다. 품종판별을 위한 최소 마커를 선발하기 위해 PIC가 높은 공통마커와 품종별 특이마커를 선발하는 2단계 과정을 통해 품종에 따라 7~9개의 최소 마커로 신품종의 진위를 판별할 수 있었다. 이처럼 콩 변이밀집영역에서 유래된 27개 InDel 마커와 이를 이용한 신품종 바코드 정보의 지속적인 업데이트는 수입산에 대한 국산 품종의 보호와 육성가의 권리 증진에 기여하며, 더불어 육종과정 중 신규 유전변이를 도입하고 목표형질을 선발하는 등 육종 효율을 개선하는데도 도움이 될 것으로 기대한다.

Keywords

References

  1. Agarwal, M., N. Shrivastava and H. Padh. 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. Anderson, J.A., G.A. Churchill, J.E. Autrique, S.D. Tanksley and M.E. Sorrells. 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181-186. https://doi.org/10.1139/g93-024
  3. Heo, M.S., K. Han, J.K. Kwon and B.C. Kang. 2017. Development of SNP markers using genotyping-by-sequencing for cultivar identification in rose (Rosa hybrida). Hortic. Environ. Biote. 58:292-302. https://doi.org/10.1007/s13580-017-0268-0
  4. Hwang, T.Y., T. Sayama, M. Takahashi, Y. Takada, Y. Nakamoto, H. Funatsuki, H. Hisano, S. Sasamoto, S. Sato, S. Tabata, I. Kono, M. Hoshi, M. Hanawa, C. Yano, Z. Xia, K. Harada, K. Kitamura and M. Ishimoto. 2009. High-density integrated linkage map based on SSR markers in soybean. DNA Res. 16:213-225. https://doi.org/10.1093/dnares/dsp010
  5. Hyten, D.L., Q. Song, E.W. Fickus, C.V. Quigley, J.S. Lim, I.Y. Choi, E.Y. Hwang, M. Pastor-Corrales and P.B. Cregan. 2010. High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475-475. https://doi.org/10.1186/1471-2164-11-475
  6. Ji, H.S., E.k. Ahn, B.Y. Seo, H.J. Kang, S.B. Lee, U.J. Hyun, I.C. Choi, K.H. Kim, S.L. Kim, S.B. Lee, S.C. Suh and G.S. Lee. 2018. Detection of genes conferring resistance to the brown planthopper (BPH) in Gayabyeo through genome resequencing and development of their selection markers. Korean J. Breed. Sci. 50:104-115 (in Korean). https://doi.org/10.9787/KJBS.2018.50.2.104
  7. Kim, G.J., Y.H. Song, G.Y. Gi, S.T. Kim, J.H. Lee and T.H. Han. 2011. Application of UPOV data for the analysis of genetic variation in rose cultivars. Korean J. Hortic. Sci. 29(3):240-246.
  8. Kim, M.Y., S. Lee, K. Van, T.H. Kim, S.C. Jeong, I.Y. Chio, 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.T. 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. USA 107:22032-22037. https://doi.org/10.1073/pnas.1009526107
  9. Kim, S.H., E.Y. Nam, K.H. Cho, J.H. Jun and K.H. Chung. 2019. Development of SNP molecular marker for red-fleshed color identification of peach genetic resources. Korean J. Plant Res. 32(4):303-311 (in Korean).
  10. Kim, Y.H., H.M. Park, T.Y. Hwang, S.K. Lee, M.S. Choi, S. Jho, S. Hwang, H.M. Kim, D. Lee, B.C. Kim, C.P. Hong, Y.S. Cho, H. Kim, K.H. Jeong, M.J. Seo, H.T. Yun, S.L. Kim, Y.U. Kwon, W.H. Kim, H.K. Chun, S.J. Lim, Y.A. Shin, I.K. Choi, Y.S. Kim, H.S. Yoon, S.H. Lee and S. Lee. 2014. Variation block-based genomics method for crop plants. BMC Genomics 15:477-477. https://doi.org/10.1186/1471-2164-15-477
  11. Korir, N.K., J. Han, L. Shangguan, C. Wang, E. Kayesh, Y. Zhang and J. Fang. 2013. Plant variety and cultivar identification: advances and prospects. Crit. Rev. Biotechol. 33:111-125. https://doi.org/10.3109/07388551.2012.675314
  12. Lee, C., M.S. Choi, H.T. Kim, H.T. Yun, B. Lee, Y.S. Chung, R.W. Kim and H.K. Choi. 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
  13. Lee, E.S., J.H. Kim, J.P. Hong, D.S. Kim, M.K. Kim, Y.C. Huh, C.G. Back, J.D. Lee, and H.E. Lee. 2018. Development of HRM markers based on SNPs identified from next generation resequencing of susceptible and resistant parents to Gummy stem blight in watermelon. Korean J. Breed. Sci. 50:424-433 (in Korean). https://doi.org/10.9787/KJBS.2018.50.4.424
  14. Lee, K.J., Y.J. An, J.K. Ham, K.H. Ma, J.R. Lee, Y.H. Cho and G.A. Lee. 2017. Development of microsatellite markers and their use in genetic diversity and population analysis in Eleutherococcus senticosus. Korean J. Plant Res. 30(3):323-330. https://doi.org/10.7732/kjpr.2017.30.3.323
  15. Liu, B., Y. Wang, W. Zhai, J. Deng, H. Wang, Y. Cui, F. Cheng, X. Wang and J. Wu. 2012. Development of INDEL markers for Brassica rapa based on whole-genome re-sequencing. Theor. Appl. Genet. 126:231-239.
  16. Moghaddam, S.M., Q. Song, S. Mamidi, J. Schmutz, R. Lee, P. Cregan, J.M. Osomo and P.E. McClean. 2014. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Front. Plant Sci. 5:295-300.
  17. Mwangi, E.W., S. Marzougui, J.S. Sung, E.C. Bwalya, Y.M. Choi and M.C. Lee. 2019. Assessment of genetic diversity and population structure on Kenyan sunflower (Helianthus annus L.) breeding lines by SSR markers. Korean J. Plant Res. 32(3):244-253. https://doi.org/10.7732/KJPR.2019.32.3.244
  18. Nguyen, K.L., A. Grondin, B. Courtois and P. Gantet. 2019. Next-generation sequencing accelerates crop gene discovery. Trends Plant Sci. 24:263-274. https://doi.org/10.1016/j.tplants.2018.11.008
  19. Sohn, H.B., S.J. Kim, T.Y. Hwang, H.M. Park, Y.Y. Lee, K. Markkandan, D. Lee, S. Lee, S.Y. Hong, Y.H. Song, B.C. Koo and Y.H. Kim. 2017a. Barcode system for genetic identification of soybean [Glycine max (L.) Merrill] cultivars using InDel markers specific to dense variation blocks. Front. Plant Sci. 8:520-520.
  20. Sohn, H.B., S.J. Kim, T.Y. Hwang, H.M. Park, Y.Y. Lee, B.C. Koo and Y.H. Kim. 2017b. Chromosome reshuffling patterns of Korean soybean cultivars using genome-wide 202 InDel markers. Korean J. Breed. Sci. 49:213-223 (in Korean). https://doi.org/10.9787/KJBS.2017.49.3.213
  21. Sohn, H.B., Y.H. Song, S.J. Kim, S.Y. Hong, K.D. Kim, B.C. Koo and Y.H. Kim. 2018. Identification and chromosomal reshuffling patterns of soybean cultivars bred in Gangwon-do using 202 InDel markers specific to variation blocks. Korean J. Breed. Sci. 50:396-405 (in Korean). https://doi.org/10.9787/KJBS.2018.50.4.396
  22. Song, Q., G. Jia, Y. Zhu, D. Grant, R.T. Nelson, E.Y. Hwang, D.L. Hyten and P.B. Cregan. 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
  23. Yaqi, M. 2018. Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants. Breeding Sci. 68:62-70. https://doi.org/10.1270/jsbbs.17080