KOREAN JOURNAL OF CROP SCIENCE (한국작물학회지)

The Korean Society of Crop Science (한국작물학회)
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Identification of a Locus Associated with Resistance to Phytophthora sojae in the Soybean Elite Line 'CheonAl'

콩 우수 계통 '천알'에서 발견한 역병 저항성 유전자좌

  • Hee Jin You (Department of Crop Science, Chungnam National University) ;
  • Eun Ji Kang (Department of Crop Science, Chungnam National University) ;
  • In Jeong Kang (Division of Crop Cultivation and Environment Research, Department of Central Area Crop Science, National Institute of Crop Science) ;
  • Ji-Min Kim (Department of Crop Science and Biotechnology, Dankook University) ;
  • Sung-Taeg Kang (Department of Crop Science and Biotechnology, Dankook University) ;
  • Sungwoo Lee (Department of Crop Science, Chungnam National University)
  • 유희진 (충남대학교 식물자원학과) ;
  • 강은지 (충남대학교 식물자원학과) ;
  • 강인정 (국립식량과학원 재배환경과) ;
  • 김지민 (단국대학교 식물생명공학과) ;
  • 강성택 (단국대학교 식물생명공학과) ;
  • 이성우 (충남대학교 식물자원학과)
  • Received : 2023.07.26
  • Accepted : 2023.08.04
  • Published : 2023.09.01
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Abstract

Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ2 = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.

콩 역병(Phytophthora root rot, PRR)은 난균(oomycete)인 Phytophthora sojae에 의해 발생하는 콩의 주요 병 중 하나로, 배수가 잘 안 되는 밭이나 습한 토양에서 심하게 발생한다. 역병의 피해를 효과적으로 줄일 수 있는 방법은 주로 역병 저항성 품종을 재배하는 것으로, 이는 저항성 유전자 Rps (resistance to P. sojae)에 대한 연구를 중심으로 이루어진다. 본 연구는 대풍 과 천알(계통명 SS0404-T5-76)을 교배하여 구축한 RIL (recombinant inbred line) 집단을 이용하여 콩 역병 균주40468과 연관된 저항성 유전자좌를 탐색하기 위해 수행되었다. 역병 균주40468에 대한 저항성 평가는 하배축 접종(hypocotyl inoculation) 방법으로 이루어졌다. 저항성 검정 결과, 천알은 저항성,대풍은 감수성을 보였고 집단 내에서는 계통들의 표현형이 분리되는 양상을 보였다. 집단 내에서 표현형 분포는 1:1 (R:S) (χ2 = 0.57, p = 0.75) 분리비와 일치하였으며, 이는 저항성 반응이 단일 유전자에 의해 조절됨을 나타낸다. 대풍, 천알과 각 RIL 계통들은 고밀도 SNP 유전자형 분석을 통해 데이터를 얻었고, 이를 바탕으로 유전자 지도를 작성하였다. 일원분산 분석(Single-marker ANOVA) 및 linkage analysis 결과, 18번 염색체의 55.9~56.4 Mbp에서 높은 통계적 유의성을 보였으며, 이 지역의 표현형 분산은 ~98%로 나타났다. 탐색된 영역은 다수의 선행연구에서 Rps의 위치로 보고된 지역과 겹치며, 콩 표준 유전체 정보를 기반으로 0.5 Mbp 범위 내에서 leucine-rich repeat (LRR) 또는 serine/threonine kinase(STK)을 합성하는 유전자 9개를 포함하고 있다. 천알은 역병 균주40468에 대한 저항성 유전자좌가 밝혀진 첫 국내 콩 품종으로, 본 연구에서 밝힌 천알의 저항성 유전자좌는 향후 역병 저항성 육종 및 연구에서 유용한 재료가 될 것이다.

Keywords

Acknowledgement

본 연구는 농촌진흥청 공동연구사업(수요자맞춤형 육종자원 대량신속 발굴 기술 개발)의 「콩 유전자원 병 저항성, 내재해성, 식품이용적합성 특성평가」(과제번호: PJ01416804)에 의해 수행되었다.

References

  1. Allen, T. W., C. A. Bradley, A. J. Sisson, E. Byamukama, M. I. Chilvers, C. M. Coker, A. A. Collins, J. P. Damicone, A. E. Dorrance, and N. S. Dufault. 2017. Soybean yield loss estimates due to diseases in the United States and Ontario, Canada, from 2010 to 2014. Plant Health Progress 18 : 19-27. https://doi.org/10.1094/PHP-RS-16-0066
  2. Athow, K. L. 1982. Rps6, a major gene for resistance to Phytophthora megasperma f. sp. glycinea in soybean. Phytopathology 72 : 1564-1567. https://doi.org/10.1094/Phyto-72-1564
  3. Athow, K. L., F. A. Laviolette, E. H. Mueller, and J. R. Wilcox. 1980. A new major gene for resistance to Phytophthora megasperma var. sojae in soybean. Phytopathology 70 : 977-980. https://doi.org/10.1094/Phyto-70-977
  4. Bates, D., M. Machler, B. Bolker, and S. Walker. 2015. Fitting linear mixed-effects models using lme4. Journal of Statistical Software 67 : 1-48. https://doi.org/10.18637/jss.v067.i01
  5. Burnham, K., A. Dorrance, D. Francis, R. Fioritto, and S. St Martin. 2003. Rps 8, a new locus in soybean for resistance to Phytophthora sojae. Crop Science 43 : 101-105.
  6. Buzzell, R. I. and T. R. Anderson. 1981. Research notes : another major gene for resistance to Phytophthora megasperma var. sojae in soybeans. Soybean Genetics Newsletter 8 : 30-33.
  7. Cai, G., T. J. Fleury, and N. Zhang. 2019. Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen. Scientific Reports 9 : 7969.
  8. Chen, L., W. Wang, J. Ping, J. C. Fitzgerald, G. Cai, C. B. Clark, R. Aggarwal, and J. Ma. 2021. Identification and molecular mapping of Rps14, a gene conferring broad-spectrum resistance to Phytophthora sojae in soybean. Theoretical and Applied Genetics 134 : 3863-3872.
  9. Cheng, Y., Q. Ma, H. Ren, Q. Xia, E. Song, Z. Tan, S. Li, G. Zhang, and Nian, H. 2017. Fine mapping of a Phytophthora-resistance gene RpsWY in soybean (Glycine max L.) by high-throughput genome-wide sequencing. Theoretical and Applied Genetics 130 : 1041-1051. https://doi.org/10.1007/s00122-017-2869-5
  10. Demirbas, A., B. Rector, D. Lohnes, R. Fioritto, G. Graef, P. Cregan, R. Shoemaker, and J. Specht. 2001. Simple sequence repeat markers linked to the soybean Rps genes for Phytophthora resistance. Crop Science 41 : 1220-1227. https://doi.org/10.2135/cropsci2001.4141220x
  11. Dorrance, A., H. Jia, and T. Abney. 2004. Evaluation of soybean differentials for their interaction with Phytophthora sojae. Plant Health Progress 5 : 9.
  12. Dorrance, A. E. and A. F. Schmitthenner. 2000. New sources of resistance to Phytophthora sojae in the soybean plant introductions. Plant Disease 84 : 1303-1308. https://doi.org/10.1094/PDIS.2000.84.12.1303
  13. Gordon, S., K. Kowitwanich, W. Pipatpongpinyo, S. St. Martin, and A. Dorrance. 2007. Molecular marker analysis of soybean plant introductions with resistance to Phytophthora sojae. Phytopathology 97 : 113-118. https://doi.org/10.1094/PHYTO-97-0113
  14. Guo, N., A. Tahir, X. Cui, J. Xu, J. Sun, N. Zhang, R. Sun, S. Deng, H. Xing, and J. Zhao. 2022. Genome-wide identification of Phytophthora sojae-associated microRNAs and network in a resistant and a susceptible soybean germplasm. Agronomy 12 : 2922.
  15. Jang, I.-H., I. J. Kang, J.-M. Kim, S.-T. Kang, Y. E. Jang, and S. Lee. 2020a. Genetic mapping of a resistance locus to Phytophthora sojae in the Korean soybean cultivar Daewon. The Plant Pathology Journal 36 : 591-599. https://doi.org/10.5423/PPJ.OA.09.2020.0173
  16. Jang, Y. E., I. H. Jang, I. J. Kang, J.-M. Kim, S.-T. Kang, and S. Lee. 2020b. Two isolate-specific resistance loci for Phytophthora sojae in the soybean Socheong2. Korean Journal of Breeding Science 52 : 398-407. https://doi.org/10.9787/KJBS.2020.52.4.398
  17. Jee, H., W. Kim, and W. Cho. 1998. Occurrence of Phytophthora root rot on soybean (Glycine max) and identification of the causal fungus. RDA Journal of Crop Protection 40 : 16-22.
  18. Jiang, B., Y. Cheng, Z. Cai, M. Li, Z. Jiang, R. Ma, Y. Yuan, Q. Xia, and H. Nian. 2020. Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing. BMC Genomics 21.
  19. Kang, I. J., S. Kang, I. H. Jang, Y. W. Jang, H. K. Shim, S., Heu, and S. Lee. 2019. Identification of new isolates of Phytophthora sojae and the reactions of Korean soybean cultivars following hypocotyl inoculation. The Plant Pathology Journal 35 : 698.
  20. Koenning, S. R. and J. A. Wrather. 2010. Suppression of soybean yield potential in the continental United States by plant diseases from 2006 to 2009. Plant Health Progress 11 : 5.
  21. Li, W., M. Liu, Y.-C. Lai, J.-X. Liu, C. Fan, G. Yang, L. Wang, W.-W. Liang, S.-F. Di, D.-Y. Yu, and Y.-D. Bi. 2022. Genome-wide association study of partial resistance to P. sojae in wild soybeans from Heilongjiang province, China. Current Issues in Molecular Biology 44 : 3194-3207. https://doi.org/10.3390/cimb44070221
  22. Li, Y., S. Sun, C. Zhong, X. Wang, X. Wu, and Z. Zhu. 2017. Genetic mapping and development of co-segregating markers of RpsQ, which provides resistance to Phytophthora sojae in soybean. Theoretical and Applied Genetics 130 : 1223-1233. https://doi.org/10.1007/s00122-017-2883-7
  23. Lin, F., M. Zhao, J. Ping, A. Johnson, B. Zhang, T. S. Abney, T. J. Hughes, and J. Ma. 2013. Molecular mapping of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B. Theoretical and Applied Genetics 126 : 2177-2185. https://doi.org/10.1007/s00122-013-2127-4
  24. Meng, L., H. Li, L. Zhang, and J. Wang. 2015. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. The Crop Journal 3 : 269-283. https://doi.org/10.1016/j.cj.2015.01.001
  25. Morris, P. F. and E. Ward. 1992. Chemoattraction of zoospores of the soybean pathogen, Phytophthora sojae, by isoflavones. Physiological and Molecular Plant Pathology 40 : 17-22. https://doi.org/10.1016/0885-5765(92)90067-6
  26. Niu, J., N. Guo, J. Sun, L. Li, Y. Cao, S. Li, J. Huang, J. Zhao, T. Zhao, and H. Xing. 2017. Fine mapping of a resistance gene RpsHN that controls Phytophthora sojae using recombinant inbred lines and secondary populations. Frontiers in Plant Science 8 : 538.
  27. Park, K.-Y., J.-K. Moon, H.-T. Yun, Y.-H. Lee, S.-L. Kim, Y.-H. Ryu, Y.-H. Kim, J.-H. Ku, J.-H. Roh, E.-S. Lee, K.-S. Ha, I.-j. Kim, C.-K. Son, S.-K. Kim, S.-D. Kim, and H.-P. Moon. 2005. A new soybean cultivar for fermented soyfood and tofu with high yield, "Daepung". Korean J Breed Sci. 37 : 111-112.
  28. Rolling, W., R. Lake, A. E. Dorrance, and L. K. McHale. 2020. Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions. PLOS One 15 : e0227710.
  29. Sahoo, D. K., N. S. Abeysekara, S. R. Cianzio, A. E. Robertson, and M. K. Bhattacharyya. 2017. A novel Phytophthora sojae resistance Rps12 gene mapped to a genomic region that contains several Rps genes. PLOS One 12 : e0169950.
  30. Sahoo, D. K., A. Das, X. Huang, S. Cianzio, and M. K. Bhattacharyya. 2021. Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean. Scientific Reports 11.
  31. Sandhu, D., H. Gao, S. Cianzio, and M. K. Bhattacharyya. 2004. Deletion of a disease resistance nucleotide-binding-site leucine-rich-repeat-like sequence is associated with the loss of the Phytophthora resistance gene Rps4 in soybean. Genetics 168 : 2157-2167. https://doi.org/10.1534/genetics.104.032037
  32. Shim, S., M. Y. Kim, J. Ha, Y.-H. Lee, and S.-H. Lee. 2017. Identification of QTLs for branching in soybean (Glycine max (L.) Merrill). Euphytica 213 : 225.
  33. Statistics Korea. 2022. Pulse production. In: Crop production survey. Available at https://kosis.kr/statHtml/statHtml.do?orgId=101&tblId=DT_1ET0025&conn_path=I2&language=en.Last accessed on August 25, 2023.
  34. Sugimoto, T., S. Yoshida, K. Watanabe, M. Aino, T. Kanto, K. Maekawa, and K. Irie. 2007. Identification of SSR markers linked to the Phytophthora resistance gene Rps1-d in soybean. Plant Breeding 127 : 154-159. https://doi.org/10.1111/j.1439-0523.2007.01440.x
  35. Sugimoto, T., S. Yoshida, A. Kaga, M. Hajika, K. Watanabe, M. Aino, K. Tatsuda, R. Yamamoto, T. Matoh, and D. Walker. 2011. Genetic analysis and identification of DNA markers linked to a novel Phytophthora sojae resistance gene in the Japanese soybean cultivar Waseshiroge. Euphytica 182 : 133.
  36. Sun, J., L. Li, J. Zhao, J. Huang, Q. Yan, H. Xing, and N. Guo. 2014. Genetic analysis and fine mapping of RpsJS, a novel resistance gene to Phytophthora sojae in soybean [Glycine max (L.) Merr.]. Theoretical and Applied Genetics 127 : 913-919. https://doi.org/10.1007/s00122-014-2266-2
  37. Sun, S., X. Wu, J. Zhao, Y. Wang, Q. Tang, D. Yu, J. Gai, and H. Xing. 2011. Characterization and mapping of RpsYu25, a novel resistance gene to Phytophthora sojae. Plant Breeding 130 : 139-143. https://doi.org/10.1111/j.1439-0523.2010.01794.x
  38. Tamborski, J. and K. V. Krasileva. 2020. Evolution of plant NLRs: From natural history to precise modifications. Annual Review of Plant Biology 71 : 355-378. https://doi.org/10.1146/annurev-arplant-081519-035901
  39. Team, R. C. 2019. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
  40. Van, K., B.-K. Ha, M. Y. Kim, S.-H. Lee, E. Hwang, and S. Heu. 2003. Molecular characterization of hypernodulation in soybean. The Plant Pathology Journal 19 : 24-29. https://doi.org/10.5423/PPJ.2003.19.1.024
  41. Van, K., W. Rolling, R. M. Biyashev, R. L. Matthiesen, N. S. Abeysekara, A. E. Robertson, D. J. Veney, A. E. Dorrance, L. K. McHale, and M. A. Saghai Maroof. 2021. Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean. The Plant Genome 14 : e20063.
  42. Van Wersch, S. and X. Li. 2019. Stronger When Together: Clustering of plant NLR disease resistance genes. Trends in Plant Science 24 : 688-699. https://doi.org/10.1016/j.tplants.2019.05.005
  43. Weng, C., K. Yu, T. Anderson, and V. Poysa. 2001. Mapping genes conferring resistance to Phytophthora root rot of soybean, Rps1a and Rps7. Journal of Heredity 92 : 442-446. https://doi.org/10.1093/jhered/92.5.442
  44. Wrather, J., W. Stienstra, and S. Koenning. 2001. Soybean disease loss estimates for the United States from 1996 to 1998. Canadian Journal of Plant Pathology 23 : 122-131. https://doi.org/10.1080/07060660109506919
  45. Wrather, J. A. and S. R. Koenning. 2006. Estimates of disease effects on soybean yields in the United States 2003 to 2005. Journal of Nematology 38 : 173.
  46. Wrather, J. A. and S. R. Koenning. 2009. Effects of diseases on soybean yields in the United States 1996 to 2007. Plant Health Progress 10 : 24.
  47. Yu, A., P. Xu, J. Wang, S. Zhang, J. Wu, W. Li, W. Chen, N. Li, S. Fan, and X. Wang. 2010. Genetic analysis and SSR mapping of gene resistance to Phytophthora sojae race 1 in soybean cv Suinong 10. Chinese Journal of Oil Crop Sciences 32 : 462-466.
  48. Zhao, X., D. Bao, W. Wang, C. Zhang, Y. Jing, H. Jiang, L. Qiu, W. Li, and Y. Han. 2020. Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with association and linkage mapping. Molecular Breeding 40 : 100.
  49. Zhong, C., S. Sun, Y. Li, C. Duan, and Z. Zhu. 2017. Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean. Theoretical and Applied Genetics 131 : 525-538. https://doi.org/10.1007/s00122-017-3016-z
  50. Zhong, C., S. Sun, X. Zhang, C. Duan, and Z. Zhu. 2020. Fine mapping, candidate gene identification and co-segregating marker development for the Phytophthora root rot resistance gene RpsYD25. Front Genet 11 : 799.