Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean

Abstract

Key message

RpsUN1 and RpsUN2 were fine mapped to two genomic regions harboring disease resistance-like genes. The haplotypes and instability of the regions and candidate genes for the two resistance loci were characterized.

Abstract

Phytophthora root and stem rot caused by Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practical approach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 were identified in a landrace PI 567139B and mapped to a 6.5 cM region on chromosome 3 and a 3.0 cM region on chromosome 16, corresponding to 1387 and 423 kb of the soybean reference genome sequences. By analyzing recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines, RpsUN1 and RpsUN2, were further narrowed to a 151 kb region that harbors five genes including three disease resistance (R)-like genes, and a 36 kb region that contains four genes including five R-like genes, respectively, according to the reference genome. Expressional changes of these nine genes before and after inoculation with the pathogen, as revealed by RNA-seq, suggest that Glyma.03g034600 in the RpsUN1 region and Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between/among R-like genes may have occurred, resulting in the formation of two recombinants with inconsistent genotypic and phenotypic observations. The haplotype variation of genomic regions where RpsUN1 and RpsUN2 reside in the entire soybean germplasm deposited in the US soybean germplasm collection suggests that RpsUN1 and RpsUN2 are most likely novel genes.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. Anderson TR, Buzzell RI (1992) Inheritance and linkage of the Rps7 gene for resistance to Phytophthora rot of soybean. Plant Dis 76:958–959

  2. Cook DE, Lee TG, Guo X et al (2012) Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338:1206–1209

  3. Demirbas A, Rector BG, Lohnes DG, Fioritto RJ, Graef GL, Cregan PB, Shoemaker RC, Specht JE (2001) Simple sequence repeat markers linked to the soybean Rps genes for Phytophthora resistance. Crop Sci 41:1220–1227

  4. Dorrance AE, Berry SA, Anderson TR, Meharg C (2008) Isolation, storage, pathotype characterization, and evaluation of resistance for Phytophthora sojae in soybean. Plant Health Progress. doi:10.1094/PHP-2008-0118-01-DG

  5. Ellis J, Dodds P, Pryor T (2000) Structure, function and evolution of plant disease resistance genes. Curr Opin Plant Biol 3:278–284

  6. Fan A, Wang X, Fang X, Wu X, Zhu Z (2009) Molecular identification of Phytophthora resistance gene in soybean cultivar Yudou 25. Acta Agro Sin 35:1844–1850

  7. Gao H, Bhattacharyya MK (2008) The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences. BMC Plant Biol 8:29

  8. Gao H, Narayanan NN, Ellison L, Bhattacharyya MK (2005) Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean. Mol Plant Microbe Interact 18:1035–1045

  9. Gardner ME, Hymowitz T, Xu SJ, Hartman GL (2001) Physical map location of the Rps1-k allele in soybean. Crop Sci 41:1435–1438

  10. Gordon SG, Martin SKS, Dorrance AE (2006) Rps8 maps to a resistance gene rich region on soybean molecular linkage group F. Crop Sci 46:168–173

  11. Hanson PM, Nickell CD, Gray LE, Sebastian SA (1988) Identification of two dominant genes conditioning brown stem rot resistance in soybean. Crop Sci 28:41–43

  12. Hulbert S (1998) Arming plants against pathogens—recombination in resistance loci. Trends Plant Sci 3:121–122

  13. Kasuga T, Salimath SS, Shi J, Gijzen M, Buzzell RI, Bhattacharyya MK (1997) High resolution genetic and physical mapping of molecular markers linked to the Phytophthora resistance gene Rps1-k in soybean. Mol Plant-Microbe Interact 10:1035–1044

  14. Leister D (2004) Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes. Trends Genet 20:116–122

  15. Lin F et al (2013) Molecular mapping of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B. Theor Appl Genet 126:2177–2185

  16. Lin F et al (2014) Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics. BMC Genom 15:18

  17. Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113–1130

  18. Nagy ED, Bennetzen JL (2008) Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster. Genome Res 18:1918–1923

  19. Ping J, Fitzgerald JC, Zhang C, Lin F, Bai Y, Wang D, Aggarwal R, Rehman M, Crasta O, Ma J (2016) Identification and molecular mapping of Rps11, a novel gene conferring resistance to Phytophthora sojae in soybean. Theor Appl Genet 129:445–451

  20. Polzin KM, Lohnes DG, Nickell CD, Shoemaker RC (1994) Integration of Rps2, Rmd, and Rj2 into Linkage Group J of the soybean molecular map. J Hered 85:300–303

  21. Sandhu D, Gao H, Cianzio S, Bhattacharyya MK (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

  22. Sandhu D, Schallock KG, Rivera-Velez N, Lundeen P, Cianzio S, Bhattacharyya MK (2005) Soybean phytophthora resistance gene Rps8 maps closely to the Rps3 region. J Hered 96:536–541

  23. Schmitthenner AF (1985) Problems and progress in control of phytophthora root-rot of soybean. Plant Dis 69:362–368

  24. Schmutz J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

  25. Song Q, Jia G, Zhu Y, 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

  26. Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One 8:e54985

  27. Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2015) Fingerprinting soybean germplasm and its utility in genomic research. G3 Gene Genomes Genet 5:1999–2006

  28. Sugimoto T, Yashida S, Watanabe K, Aino M, Kanto T, Maekawa K, Irie K (2008) Identification of SSR markers linked to the Phytophthora resistance gene Rps1-d in soybean. Plant Breed 127:154–159

  29. Sugimoto T, Kato M, Yoshida S, Matsumoto I, Kobayashi T, Kaga A, Hajika M, Yamamoto R, Watanabe K, Aino M, Matoh T, Walker DR, Biggs AR, Ishimoto M (2012) Pathogenic diversity of Phytophthora sojae and breeding strategies to develop Phytophthora-resistant soybeans. Breed Sci 61:511–522

  30. Sun S, Wu X, Zhao J, Wang Y, Tang Q, Yu D, Gai J, Xing H (2011) Characterization and mapping of RpsYu25, a novel resistance gene to Phytophthora sojae. Plant Breed 130:139–143

  31. Tian Z et al (2010) Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA 107:8563–8568

  32. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protocol 7:562–578

  33. Weng C, Yu K, Anderson TR, Poysa V (2001) Mapping genes conferring resistance to Phytophthora root rot of soybean, Rps1a and Rps7. J Hered 92:442–446

  34. Wrather JA, Koenning SR (2006) Estimates of disease effects on soybean yields in the United States 2003–2005. J Nematol 38:173–180

  35. Wrather J, Koenning S (2009) Effects of diseases on soybean yields in the United States 1996–2007. Plant Health Progress. doi:10.1094/PHP-2009-0401-01-RS

  36. Wu X, Zhang B, Sun S, Zhao J, Yang F, Guo N, Gai J, Xing H (2011) Identification, genetic analysis and mapping of resistance to Phytophthora sojae of Pm28 in soybean. Agri Sci China 10:1506–1511

  37. Yao H, Wang X, Wu X, Xiao Y, Zhu Z (2010) Molecular mapping of Phytophthora resistance gene in soybean cultivar zaoshu18. J Plant Genet Res 11:213–217

  38. Zhang J, Xia C, Wang X, Duan C, Sun S, Wu X, Zhu Z (2013) Genetic characterization and fine mapping of the novel Phytophthora resistance gene in a Chinese soybean cultivar. Theor Appl Genet 126:1555–1561

Download references

Acknowledgments

This work was supported by North Central Soybean Research Program (No. 205267), National Natural Science Foundation of China (No. 31371647) and Taishan Scholarship.

Author information

Correspondence to Chunmei Cai or Jianxin Ma.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

L. Li and F. Lin contributed equally to the work.

The online version of this article contains supplementary material, which is available to authorized users.

Communicated by D. A Lightfoot.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Li, L., Lin, F., Wang, W. et al. Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean. Theor Appl Genet 129, 2379–2386 (2016). https://doi.org/10.1007/s00122-016-2777-0

Download citation

Keywords

  • Copy Number Variation
  • Phytophthora
  • Cleave Amplify Polymorphic Sequence
  • Cleave Amplify Polymorphic Sequence Marker
  • Unequal Recombination