KOREAN JOURNAL OF CROP SCIENCE (한국작물학회지)

The Korean Society of Crop Science (한국작물학회)
권호 표지
DOI QR코드

DOI QR Code

Characterization of Traits Related to Grain Shape in Korean Rice Varieties

국내 육성 벼 품종 입형 관련 특성 분석

  • Lee, Chang-Min (Crop Breeding Division, National Institute of Crop Science) ;
  • Lee, Keon-Mi (Crop Breeding Division, National Institute of Crop Science) ;
  • Baek, Man-Kee (Crop Breeding Division, National Institute of Crop Science) ;
  • Kim, Woo-Jae (Crop Breeding Division, National Institute of Crop Science) ;
  • Suh, Jung-Pil (Crop Breeding Division, National Institute of Crop Science) ;
  • Jeong, Oh-Young (Crop Breeding Division, National Institute of Crop Science) ;
  • Cho, Young-Chan (Crop Breeding Division, National Institute of Crop Science) ;
  • Park, Hyun-Su (Crop Breeding Division, National Institute of Crop Science) ;
  • Kim, Suk-Man (Crop Breeding Division, National Institute of Crop Science)
  • 이창민 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 이건미 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 백만기 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 김우재 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 서정필 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 정오영 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 조영찬 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 박현수 (농촌진흥청 국립식량과학원 작물육종과) ;
  • 김석만 (농촌진흥청 국립식량과학원 작물육종과)
  • Received : 2020.05.23
  • Accepted : 2020.07.06
  • Published : 2020.09.01
Download PDF
⟨ Previous Next ⟩

Abstract

Grain size and shape are the two important components contributing to rice yield and quality. To analyze traits related to grain-shape, a total of 272 varieties derived from japonica, japonica black and Tongil-type rice accession in Korea were evaluated in this study. The traits, grain length (GL), grain width (GW), grain thickness (GT), length to width ratio (RLW), and 1000-grain weight (TGW) were measured and replicated 10 times. Genes (GW2, GS3, qGL3, qSW5, GS5, TGW6, GW7, and GW8) related to grain-shape were validated in the accessions using specific DNA marker sets. K-mean clustering of the accession based on phenotypic data revealed three groups: group 1 was classified by GW and GT and included most of japonica type, group 2 was classified by RLW and GL reached a medium size and possessed a half spindle-shaped type, and group 3 was classified by TGW, reached a long size and possessed a semi-round shape. In validation tests using the marker sets, both gw2 and tgw6 were validated in less than 1% of the tested accessions and two allelic types, qgl3 and gw8, were only verified in Tongil-type accessions. For GW8 and GW2, any different amplicons were not amplified in any japonica or Tongil-type accessions, respectively. In order to suggest the representative grain-shape gene combinations for each ecotype, the allelic combinations were evaluated by PCR analysis. Cj1 and 2 in japonica (Cj1-7), Cj_b1 and 2 in japonica-black (Cj_b1-3), and CT3 in Tongil-type (CT1-13) turned out to be the dominant combination in each ecotype, respectively. In addition, the results revealed that introgression of four genes (gw2, gs3, qSW5, and GS5) would expand the diversity of grain shape in Korean japonica varieties. The gene combinations information could be utilized practically to understand or enhance grain shape in japonica rice breeding program.

국내 육성 벼 품종의 입형 특성은 협소한 유전적 배경을 가지고 있는 것으로 알려져 있다. 본 연구는 육성품종의 입형 관련 표현형과 유전자형을 분석하여 생태형에 따른 입형 특성과 대립유전자 효과를 파악하고, 자포니카 품종에 도입된 대립유전자의 기원을 확인하고자 수행되었다. 자포니카 225, 흑미 14, 통일형 생태형 33품종 등 272품종에 대해서 현미 길이, 너비, 두께, 장폭비, 천립중의 표현형과 GW2, GS3, qGL3, qSW5, GS5, TGW6, GW7, GW8 등 8개 입형 관련 유전자형을 분석하였다. 자포니카 품종은 중단립종에 단원형, 흑미와 통일형 품종은 중립종에 중원형 입형 특성을 나타냈다. 표현형에 대한 군집분석을 통해 자포니카 품종 대부분으로 구성된 그룹 1, 흑미와 통일형 품종 위주로 구성된 그룹 2, 자포니카 품종이 포함된 그룹 3 등 세 그룹으로 나눌 수 있었다. 그룹 1은 현미 너비와 두께, 그룹 2는 장폭비와 길이, 그룹 3은 천립중에 의해 영향을 많이 받아 구분되며 그룹 1은 중단립종·단원형, 그룹 2는 중립종·중원형, 그룹 3은 장립종·단원형 입형 특성을 나타냈다. 입형 관련 대립유전자형 분석 결과 gw2 (빈도수 1.1%)와 tgw6 (0.4%) 대립유전자는 매우 드물었으며, qgl3와 gw8는 통일형 생태형에서만 존재하였고 자포니카 품종의 qSW5 유전자형은 qsw5_N이 대부분을 차지하였다. 생태형별 대립유전자 조합의 수는 자포니카 7개(Cj1-Cj7), 흑미 3개(Cj_b1-Cj_b3), 통일형 13개(CT1-CT13)로 자포니카에 비해 품종수가 적은 통일형 생태형이 더 다양하였다. 자포니카 품종의 대표 대립유전자 조합은 자포니카 Cj1, 2 (GW2-GS3_C-qGL3-qsw5_N-gs5-TGW6-gw7(GW7)-GW8)로 여기에 gw2, gs3, qSW5, GS5 대립유전자가 도입됨으로써 다양성이 확대되었다. 흑미 품종의 대표 대립유전자 조합은 Cj_b2, 3 (GW2-gs3-qGL3-qsw5_N-gs5-TGW6-gw7(GW7)-GW8)로 자포니카 대표 조합에서 GS3_C가 gs3로 치환된 조합이다. 통일형 생태형은 GW2 유전자만 다형성이 없었고 7개 유전자에서 13개 대립유전자 조합이 확인되었으며 대표조합은 CT3 (GW2-GS3_C-qgl3-qsw5_N-gs5-TGW6-GW7-gw8)이다. 우리나라 대표 품종인 '신동진'의 입형 특성은 자포니카 대립유전자 조합 Cj2에서 gs3가 도입됨으로써 중대립화되었고, gs3는 미국품종 Calrose로부터 유래한 것으로 판단된다. 국내 육성 벼 품종에 대한 입형 관련 표현형과 유전자형 분석 결과는 우리나라 벼 품종의 입형 특성을 다양화하는데 기여할 것으로 기대된다.

Keywords

References

  1. Ahn, E. K., Y. J. Won, H. M. Park, K. H. Jung, and U. J. Hyun. 2018. Feed value and yield potential of main whole-crop silage rice cultivars with harvesting time in the central plains of Korea. Korean J Crop Sci. 63 : 294-303. https://doi.org/10.7740/KJCS.2018.63.4.294
  2. Ando, I., C. Kaneda, M. Yokoo, H. Nemoto, T. Hata, K. Ise, R. Ikeda, Y. Akama, A. Nakane et al. 2004. "Sari Queen", a new aromatic rice cultivar with basmati rice grain character. Bulletin of the National Institute of Crop Science. 5 : 53-66.
  3. Calingacion, M., A. Laborte, A. Nelson, A. Resurreccion, J. C. Concepcion, V. D. Daygon, R. Mumm, R. Reinke, S. Dipti et al. 2014. Diversity of global rice markets and the science required for consumer-targeted rice breeding. PloS one. 9(1) : e85106. https://doi.org/10.1371/journal.pone.0085106
  4. de Mendiburu, F. and M. F. de Mendiburu. 2019. Package 'agricolae'. R Package Version : 1.2-8.
  5. Fan, C., Y. Xing, H. Mao, T. Lu, B. Han, C. Xu, X. Li, and Q. Zhang. 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics. 112(6) : 1164-1171. https://doi.org/10.1007/s00122-006-0218-1
  6. Fan, C., S. Yu, C. Wang, and Y. Xing. 2009. A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theoretical and Applied Genetics. 118(3) : 465-472. https://doi.org/10.1007/s00122-008-0913-1
  7. Korea Seed and Variety Service (KSVS). 2005. The guidelines of characteristics for application and registration on new varieties in rice. Anyang. Korea. pp. 8-14.
  8. Huang, R., L. Jiang, J. Zheng, T. Wang, H. Wang, Y. Huang, and Z. Hong. 2013. Genetic bases of rice grain shape: so many genes, so little known. Trends in plant science. 18(4) : 218-226. https://doi.org/10.1016/j.tplants.2012.11.001
  9. Huang, X., Y. Zhao, X. Wei, C. Li, A. Wang, Q. Zhao, W. Li, Y. Guo, L. Deng et al. 2012. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature genetics. 44(1) : 32-39. doi:10.1038/ng.1018.
  10. Ishimaru, K., N. Hirotsu, Y. Madoka, N. Murakami, N. Hara, H. Onodera, T. Kashiwagi, K. Ujiie, B.-I. Shimizu et al. 2013. Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nature genetics. 45(6) : 707-711. https://doi.org/10.1038/ng.2612
  11. Juliano, B. 1979. The chemical basis of rice grain quality In: Proceedings of the workshop on chemical aspects of rice grain quality. International Rice Research Institute. Los Banos. Phiippines. pp. 69-90.
  12. Kassambara, A. and F. Mundt. 2017. Package 'factoextra'. Extract and visualize the results of multivariate data analyses. R topics documented : 75.
  13. Kim, S. R., J. Ramos, M. Ashikari, P. S. Vrik, E. A. Torres, E. Nissila, S. L. Hechanova, R. Mauleon, and K. K. Jena. 2016. Development and validation of allele-specific SNP/indle markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L. Rice. 9 : 12. https://doi.org/10.1186/s12284-016-0084-7
  14. Lee, C. M., J. H. Park, B. K. Kim, J. H. Seo, G. E. Lee, S. Jang, and H. J. Koh. 2015. Influence of multi-gene allele combinations on grain size of rice and development of a regression equation model to predict grain parameters. Rice. 8(1) : 33. https://doi.org/10.1186/s12284-015-0066-1
  15. Li, Y., C. Fan, Y. Xing, Y. Jiang, L. Luo, L. Sun, D. Shao, C. Xu, X. Li et al. 2011. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature genetics. 43(12) : 1266-1269. https://doi.org/10.1038/ng.977
  16. Mao, H., S. Sun, J. Yao, C. Wang, S. Yu, C. Xu, X. Li, and Q. Zhang. 2010. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proceedings of the National Academy of Sciences. 107(45) : 19579-19584. https://doi.org/10.1073/pnas.1014419107
  17. Mo, Y., J.-M. Jeong, B.-K. Kim, S.-W. Kwon, and J.-U. Jeung. 2020. Utilization of Elite Korean Japonica Rice Varieties for Association Mapping of Heading Time, Culm Length, and Amylose and Protein Content. Korean Journal of Crop Science. 65(1) : 1-21. https://doi.org/10.7740/kjcs.2020.65.1.001
  18. Ngangkham, U., S. Samantaray, M. K. Yadav, A. Kumar, P. Chidambaranathan, and J. L. Katara. 2018. Effect of multiple allelic combinations of genes on regulating grain size in rice. PloS one. 13(1) : e0190684. doi:10.1371/journal.pone.0190684.
  19. Park, H. S., M. K. Baek, J. K. Nam, W. C. Shin, J. M. Jeong, G. M. Lee, S. G. Park, C. S. Kim, Y. C. Cho et al. 2017. Development and characterization of breeding materials with diverse grain size and shape in japonica rice. Korean J Breed Sci. 49(4) : 369-389. https://doi.org/10.9787/KJBS.2017.49.4.369
  20. Park, H. S., M. K. Baek, J. K. Nam, W. C. Shin, G. M. Lee, S. G. Park, C. M. Lee, C. S. Kim, and Y. C. Cho. 2018. Development and characterization of japonica rice line with long and spindle-shaped grain. Kor J Breed Sci. 50(2) : 116-130. https://doi.org/10.9787/KJBS.2018.50.2.116
  21. Qi, P., Y.-S. Lin, X.-J. Song, J.-B. Shen, W. Huang, J.-X. Shan, M.-Z. Zhu, L. Jiang, J.-P. Gao et al. 2012. The novel quantitative trait locus GL3. 1 controls rice grain size and yield by regulating Cyclin-T1; 3. Cell research. 22(12) : 1666-1680. https://doi.org/10.1038/cr.2012.151
  22. RDA. 2012. Standard of analysis and survey for agricultural research. Suwon. Korea.
  23. Revelle, W. R. 2017. psych: Procedures for Personality and Psychological Research. Software.
  24. Shomura, A., T. Izawa, K. Ebana, T. Ebitani, H. Kanegae, S. Konishi, and M. Yano. 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nature genetics. 40(8) : 1023-1028. https://doi.org/10.1038/ng.169
  25. Song, X.-J., W. Huang, M. Shi, M.-Z. Zhu, and H.-X. Lin. 2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature genetics. 39(5) : 623-630. https://doi.org/10.1038/ng2014
  26. Tang, Y., M. Horikoshi, and W. Li. 2016. ggfortify: unified interface to visualize statistical results of popular R packages. The R Journal. 8(2) : 478-489.
  27. Wang, S., S. Li, Q. Liu, K. Wu, J. Zhang, S. Wang, Y. Wang, X. Chen, Y. Zhang et al. 2015. The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature genetics. 47(8) : 949-954. https://doi.org/10.1038/ng.3352
  28. Wang, S., K. Wu, Q. Yuan, X. Liu, Z. Liu, X. Lin, R. Zeng, H. Zhu, G. Dong et al. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nature genetics. 44(8) : 950. https://doi.org/10.1038/ng.2327
  29. Weng, J., S. Gu, X. Wan, H. Gao, T. Guo, N. Su, C. Lei, X. Zhang, Z. Cheng et al. 2008. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell research. 18(12) : 1199. https://doi.org/10.1038/cr.2008.307
  30. Wu, K., X. Xu, N. Zhong, H. Huang, J. Yu, Y. Ye, Y. Wu, and X. Fu. 2018. The rational design of multiple molecular modulebased assemblies for simultaneously improving rice yield and grain quality. J Genomics Genet. 45 : 337-341. https://doi.org/10.1016/j.jgg.2018.03.007
  31. Yan, S., G. Zou, S. Li, H. Wang, H. Liu, G. Zhai, P. Guo, H. Song, C. Yan et al. 2011. Seed size is determined by the combinations of the genes controlling different seed characteristics in rice. Theor Appl Genet. 123(7) : 1173-1181. https://doi.org/10.1007/s00122-011-1657-x
  32. Zhang, X., J. Wang, J. Huang, H. Lan, C. Wang, C. Yin, Y. Wu, H. Tang, Q. Qian et al. 2012. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences. 109(52) : 21534-21539. https://doi.org/10.1073/pnas.1219776110
  33. Zhong, H., C. Liu, W. Kong, Y. Zhang, G. Zhao, T. Sun, and Y. Li. 2019. Effect of multi-allele combination on rice grain size based on prediction of regression equation model. Mol Genet Genomic. 295 : 465-474. https://doi.org/10.1007/s00438-019-01627-y