Molecular Breeding

, Volume 24, Issue 1, pp 63–76 | Cite as

Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean

  • Ying-Hui Li
  • Chen Zhang
  • Zhong-Shan Gao
  • Marinus Johannes Maria Smulders
  • Zulu Ma
  • Zhang-Xiong Liu
  • Hai-Yang Nan
  • Ru-Zhen Chang
  • Li-Juan Qiu
Article

Abstract

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26–27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima’s D and Fu and Li’s F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T > C. Two SNPs (689C > A and 757C > T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCN-resistant cultivars.

Keywords

Haplotype SCN SNP marker Soybean 

Abbreviations

ACAS

Agarose gel-based co-dominant allele-specific

ADAS

Agarose gel-based dominant allele-specific

LD

Linkage disequilibrium

LRR

Leucine-rich repeats

MAS

Marker-assisted breeding

QTNs

Quantitative trait nucleotide

RLK

Receptor-like kinase

STSs

Sequence-tagged sites

STYKc

Serine threonine kinase domain

TM

Trans-membrane domain

UTR

Untranslated region

Notes

Acknowledgments

This research was supported by the State High-tech (863) (nos. 2006AA10A110, 2006AA10Z164, 2006AA10A111), the National Natural Science Foundation of China (nos. 30490251 and 30471096), the National Key Technologies R&D Program in the 11th Five-Year Plan (no. 2006BAD13B05), the State Key Basic Research and Development Plan of China (973) (no. 2004CB117203), and the Academy and Institute Foundation for Basic Scientific Research in Institute of Crop Science, Chinese Academy of Agricultural Sciences. We thank Dr Robert McIntosh for revision and suggestions on the manuscript. We greatly appreciate the revision and good suggestion from reviewers and editors.

References

  1. Afzal AJ, Lightfoot DA (2007) Soybean disease resistance protein RHG1-LRR domain expressed, purified and refolded from Escherichia coli inclusion bodies: preparation for a functional analysis. Protein Expr Purif 53:346–355. doi:10.1016/j.pep.2006.12.017 PubMedCrossRefGoogle Scholar
  2. Afzal AJ, Kazi SH, Yaegashi S, Gillum J, Lightfoot DA (2004) Polymorphic nucleotides within alleles of the soybean cyst nematode resistance gene rhg1 from 116 SCN resistant plant introductions from China. Genbank AY597055–AY597126Google Scholar
  3. Afzal AJ, Wood AJ, Lightfoot DA (2008) Plant receptor-like serine threonine kinases: roles in signaling and plant defense. Mol Plant Microbe Interact 21:507–517. doi:10.1094/MPMI-21-5-0507 PubMedCrossRefGoogle Scholar
  4. Arai M, Hayashi M, Takahashi M, Shimada S, Harada K (2005) Expression and sequence analysis of systemic regulation gene for symbiosis, NTS1/GmNARK in supernodulating soybean cultivar, Sakukei 4. Breed Sci 55:147–152. doi:10.1270/jsbbs.55.147 CrossRefGoogle Scholar
  5. Arelli AP, Anand SC, Wrather JA (1992) Soybean resistance to soybean cyst nematode race 3 is conditioned by an additional dominant gene. Crop Sci 32:862–864Google Scholar
  6. Brucker E, Carlson S, Wright E, Niblack T, Diers B (2005) Rhg1 alleles from soybean PI437654 and PI88788 respond differentially to isolates of Heterodera glycines in the greenhouse. Theor Appl Genet 111:44–49. doi:10.1007/s00122-005-1970-3 PubMedCrossRefGoogle Scholar
  7. Cahill DJ, Schmidt DH (2004) Use of marker assisted selection in a product development breeding program. Proc 4th Int Crop Sci Cong. Available in web site www.cropscience.org.au
  8. Caldwell BE, Brim CA, Ross JP (1960) Inheritance of resistance of soybeans to the cyst nematode, Heterodera glycines. Agron J 52:635–636Google Scholar
  9. Caviness CE (1992) Breeding for resistance to soybean cyst nematode. In: Riggs RD, Wrather JA (eds) Biology and management of the soybean cyst nematode. APS Press, St Paul, pp 143–156Google Scholar
  10. Chang SJC, Doubler TW, Kilo V, Suttner RJ, Klein J, Schmidt ME, Gibson PT, Lightfoot DA (1997) Association of loci underlying field resistance to soybean sudden death syndrome (SDS) and cyst nematode (SCN) race 3. Crop Sci 372:965–971Google Scholar
  11. Collins FS, Guyer MS, Chakravarti A (1997) Variations on a theme: cataloging human DNA sequence variation. Science 279:1580–1581. doi:10.1126/science.278.5343.1580 CrossRefGoogle Scholar
  12. Concibido VC, Denny RL, Boutin SR, Hautea R, Orf JH, Young ND (1994) DNA marker analysis of loci underlying resistance to soybean cyst nematode (Heterodera glycines Ichinohe). Crop Sci 34:240–246CrossRefGoogle Scholar
  13. Concibido VC, Boutin S, Denny RL, Hautea R, Orf J, Young ND (1996) Targeted comparative genome analysis and qualitative mapping of a major partial resistance gene to the soybean cyst nematode. Theor Appl Genet 93:234–241. doi:10.1007/BF00225751 CrossRefGoogle Scholar
  14. Concibido VC, Lange DA, Denny RL, Hautea R, Orf J, Young ND (1997) Genome mapping soybean cyst nematode resistance genes in Peking, PI90763 and PI88788 using DNA markers. Crop Sci 37:258–264Google Scholar
  15. Concibido VC, Diers BW, Arelli PR (2004) A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci 44:1121–1131Google Scholar
  16. Coordinative Group of Evaluation of SCN (1993) Evaluation of soybean germplasm for resistance to races 1, 3 and 4 of the soybean cyst nematode. Soybean Sci 12(2):91–99Google Scholar
  17. Cregan PB, Mudge J, Fickus EW, Denny R, Danesh R, Young ND (1999) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811–818. doi:10.1007/s001220051300 CrossRefGoogle Scholar
  18. Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oegner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124:1483–1492. doi:10.1104/pp.124.4.1483 PubMedCrossRefGoogle Scholar
  19. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709PubMedGoogle Scholar
  20. Gao ZS, Weg WE, Schaart JG, Meer IM, Kodde L, Laimer M, Breiteneder H, Hoffmann-Sommergruber K, Gilissen LJWJ (2005) Linkage map positions and allelic diversity of two Mal d 3 (non-specific lipid transfer protein) genes in the cultivated apple (Malus domestica). Theor Appl Genet 110:479–491. doi:10.1007/s00122-004-1856-9 PubMedCrossRefGoogle Scholar
  21. Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463–473PubMedGoogle Scholar
  22. Guo B, Sleper DA, Nguyen HT, Arelli PR, Shannon JG (2006a) Quantitative trait loci underlying resistance to three soybean cyst nematode populations in soybean PI404198A. Crop Sci 46:224–233. doi:10.2135/cropsci2004.0757 CrossRefGoogle Scholar
  23. Guo B, Sleper DA, Lu P, Shannon JG, Nguyen HT, Arelli PR (2006b) QTLs associated with resistance to soybean cyst nematode in soybean: meta-analysis of QTL locations. Crop Sci 46:595–602. doi:10.2135/cropsci2005.04-0036-2 CrossRefGoogle Scholar
  24. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80:524–535Google Scholar
  25. Hauge BM, Wang ML, Parsons JD, Parnell LD (2001) Nucleic acid molecules and other molecules associated with soybean cyst nematode resistance. WO 01/51627 PCT/US01/00552 Patent # 20030005491Google Scholar
  26. Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220. doi:10.1007/s00122-003-1553-0 PubMedCrossRefGoogle Scholar
  27. Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 113:251–260. doi:10.1007/s00122-006-0290-6 PubMedCrossRefGoogle Scholar
  28. Hedrick PW (1987) Gametic disequilibrium measures: proceed with caution. Genetics 117:331–341PubMedGoogle Scholar
  29. Heer JA, Knap HT, Mahalingam R, Shipe ER, Arelli PR, Matthews BF (1998) Molecular markers for resistance to Heterodera glycines in advanced soybean germplasm. Mol Breed 4:359–367. doi:10.1023/A:1009673422067 CrossRefGoogle Scholar
  30. Hofmann NE, Arelli PR, Mattews BF, Gley CVQ, Cregan PB (2002) Molecular beacons to select for SCN resistance at rhg1 and Rhg4. Proc 9th Biennial Conf of Cellular and Molecular Biology of Soybean. 211 (http://www.ars.usda.gov/research/publications/publications.htm?SEQ_NO_115 = 139677)
  31. Huang N, Parco A, Mew T, Magpantay G, McCouch S, Guiderdoni E, Xu J, Subudhi P, Angeles ER, Kush GS (1997) RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthop-per resistance in a double haploid rice population. Mol Breed 3:105–113. doi:10.1023/A:1009683603862 CrossRefGoogle Scholar
  32. Jeong SC, Maroof MAS (2004) Detection and genotyping of SNPs tightly linked to two disease resistance loci, Rsv1 and Rsv3, of soybean. Plant Breed 123:305–310. doi:10.1111/j.1439-0523.2004.00981.x CrossRefGoogle Scholar
  33. Jia YL, Sean AM, Gregory TB, Howard PH, Barbara V (2000) Direct interaction of resistance gene and a virulence gene products confers rice blast resistance. EMBO J 19:4004–4014. doi:10.1093/emboj/19.15.4004 PubMedCrossRefGoogle Scholar
  34. Kanazin D, Talbert VH, Blake T (2000) Electrophoretic detection of single-nucleotide polymorphisms. Biotechniques 28:710–716PubMedGoogle Scholar
  35. Kim MY, Ha BK, Jun TH, Hwang EY, Van K, Kuk YI, Lee SK (2004) Single nucleotide polymorphism discovery and linkage mapping of lipoxygenase-2 gene (Lx2) in soybean. Euphytica 135:169–177. doi:10.1023/B:EUPH.0000014909.40136.20 CrossRefGoogle Scholar
  36. Kim MY, Van K, Lestari P, Moon JK, Lee SH (2005) SNP identification and SNAP marker development for a GmNARK gene controlling supernodulation in soybean. Theor Appl Genet 110:1003–1010. doi:10.1007/s00122-004-1887-2 PubMedCrossRefGoogle Scholar
  37. Li WD, He CL, Tian BM (1991) Identification and distribution of soybean cyst nematode in Henan province. Acta Agric Boreali-Sin 6(suppl):111–114Google Scholar
  38. Lightfoot DA, Meksem K (2000) Novel polynucleotides and polypeptides relating to loci underlying resistance to soybean cyst nematode and methods of use thereof. Patent pending # 09/772,134) Filing date 01-29-2000Google Scholar
  39. Liu PY (2005) Advances in study of screening and utilization for antigen to soybean cyst nematode. Heilongjiang Agric Sci 6:44–47Google Scholar
  40. Liu WZ, Liu Y, Chen PS (1984) The primary identification of soybean cyst nematode in part of county of NorthEast region in China. J Shenyang Agric Coll 2:75–78Google Scholar
  41. Liu HQ, Shang SG, Huo H, Wu HL (1989) Resistance of soybean varieties to races 1, 3 and 4 of soybean cyst nematode. Soybean Sci 3:113–114Google Scholar
  42. Lu WG, Gai JY, Li WD (2006) Sampling survey and identification of races of soybean cyst nematode (Heterodera glycines Ichinohe) in Huang-Huai valleys. Sci Agric Sin 39:306–312Google Scholar
  43. Meksem K, Pantazopoulos P, Njiti VN, Hyten LD, Arelli PR, Lightfoot DA (2001a) ‘Forrest’ resistance to soybean cyst nematode is bigenic: saturation mapping of the Rhg1 and Rhg4 loci. Theor Appl Genet 103:710–714. doi:10.1007/s001220100597 CrossRefGoogle Scholar
  44. Meksem K, Ruben E, Hyten DL, Schmidt ME, Lightfoot DA (2001b) High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using TaqmanTM probes. Mol Breed 7:63–71. doi:10.1023/A:1009610009663 CrossRefGoogle Scholar
  45. Moreno-Vázquez S, Ochoa OE, Faber N, Chao S, Jacobs JME, Maisonneuve B, Kesseli RV, Michelmore RW (2003) SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa). Genome 46:1059–1069. doi:10.1139/g03-073 PubMedCrossRefGoogle Scholar
  46. Prabhu RR, Njiti V, Bell-Johnson B, Johnson JE, Schmidt ME, Klein J, Lightfoot DA (1999) Selecting soybean cultivars for dual resistance to soybean cyst nematode and sudden death syndrome using two DNA markers. Crop Sci 39:982–987Google Scholar
  47. Qiu LJ, Chang RZ, Wang WH, Cregan P, Wang DC, Chen YW, Ma FM (2003) Single nucleotide polymorphism (SNPs) at both loci of rhg1 and Rhg4 in soybean resistant germplasm. J Plant Genet Res 4(2):89–93Google Scholar
  48. Riggs RD, Schmidt DP (1988) Complete characterization of the race scheme for Heterodera glycines. J Nematol 20:392–395PubMedGoogle Scholar
  49. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175. doi:10.1093/bioinformatics/15.2.174 PubMedCrossRefGoogle Scholar
  50. Ruben E, Aziz J, Afzal J, Njiti VN, Triwitayakorn K, Iqbal MJ, Yaegashi S, Arelli P, Town C, Meksem K, Lightfoot DA (2006) Genomic analysis of the rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode. Mol Genet Genomics 276:503–516. doi:10.1007/s00438-006-0150-8 PubMedCrossRefGoogle Scholar
  51. Shang SG, Liu HQ (1989) The distribution of soybean cyst nematode races in the Northeast region in China. Soybean Sci 4:382Google Scholar
  52. Shin JH, Kwon SJ, Lee JK, Min HK, Kim NS (2006) Genetic diversity of maize kernel starch-synthesis genes with SNAPs. Genome 49:1287–1296. doi:10.1139/G06-116 PubMedCrossRefGoogle Scholar
  53. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  54. Wang WH, Qiu LJ, Chang RZ, Ma FM, Xie H, Lin FY (2003) Characteristics of alleles at Satt309 locus associated with rhg1 gene resistant to SCN of Chinese soybean germplasm. Soybean Sci 22:246–250Google Scholar
  55. Webb DM, Baltazar BM, Arelli AP, Schupp J, Keim P, Clayton K, Ferreira AR, Owens T, Beavis WD (1995) QTL affecting soybean cyst nematode resistance. Theor Appl Genet 91:574–581. doi:10.1007/BF00223282 CrossRefGoogle Scholar
  56. Weir BS (1996) Genetic data analysis II. Sinauer, SunderlandGoogle Scholar
  57. Wu HL, Yao ZC, Li XL, Liu HQ, Shang SG (1982) Studies on the screening of resistant sources to cyst nematode of soybean. Sci Agric Sin 6:19–24Google Scholar
  58. Xie M, Arelli PR, Sleper DA (1998) Genetic relationships among soybean plant introductions with resistance to Heterodera glycines using RFLP’s. Soybean Genet Newslett 25:157–159Google Scholar
  59. Xie H, Chang RZ, Cao RS, Zhang MH, Fen ZF, Qiu LJ (2003) Selection of core SSR loci by using Chinese autumn soybean. Sci Agric Sin 36:360–366Google Scholar
  60. Yuan CP, Li YH, Liu ZX, Guan RX, Chang RZ, Qiu LJ (2007) A method of SNP genotyping in soybean. Soybean Sci 26:447–459Google Scholar
  61. Yue P, Sleper DA, Arelli PR (2001) Mapping resistance of multiple races of Heterodera glycines in soybean PI89772. Crop Sci 41:1589–1595Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Ying-Hui Li
    • 1
  • Chen Zhang
    • 1
  • Zhong-Shan Gao
    • 2
  • Marinus Johannes Maria Smulders
    • 3
  • Zulu Ma
    • 1
    • 4
  • Zhang-Xiong Liu
    • 1
  • Hai-Yang Nan
    • 1
  • Ru-Zhen Chang
    • 1
  • Li-Juan Qiu
    • 1
  1. 1.The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm & Biotechnology (MOA), Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
  2. 2.Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality ImprovementZhejiang UniversityHangzhouChina
  3. 3.Plant Research International, Wageningen URWageningenThe Netherlands
  4. 4.BengBu Medical CollegeBengbuPeople’s Republic of China

Personalised recommendations