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Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes

Molecular Biology Reports volume 38, pages 3487–3494 (2011)Cite this article

Abstract

Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer, with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses considerable potential for studying genetic diversity and relationships among peanut accessions.

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References

  1. Kochert G, Stalker HM, Gimenes M, Galgaro L, Lopes CR, Moore K (1996) RFLP and cytogenetic evidence on the origins and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am J Bot 83(10):1282–1291

    Article  CAS  Google Scholar 

  2. Tang RH, Gao GQ, He LQ, Han ZQ, Shan SH, Zhong RC, Zhou CQ, Jiang J, Li YR, Zhuang WJ (2007) Genetic diversity in cultivated groundnut based on SSR markers. J Genet Genom 34(5):449–459

    Article  CAS  Google Scholar 

  3. Tang RH, Zhuang WJ, Gao GQ, He LQ, Han ZQ, Shan SH, Jiang J, Li YR (2008) Phylogenetic relationships in genus Arachis based on SSR and AFLP markers. Agric Sci China 7(4):405–414

    CAS  Google Scholar 

  4. Tahernezhad Z, Zamani MJ, Solouki M, Zahravi M, Imamjomeh AA, Jafaraghaei M, Bihamta MR (2010) Genetic diversity of Iranian Aegilops tauschii Coss. using microsatellite molecular markers and morphological traits. Mol Biol Rep 37(7):3413–3420

    PubMed  Article  CAS  Google Scholar 

  5. Sudheer Pamidimarri DV, Chattopadhyay B, Reddy MP (2009) Genetic divergence and phylogenetic analysis of genus Jatropha based on nuclear ribosomal DNA ITS sequence. Mol Biol Rep 36(7):1929–1935. doi:10.1007/s11033-008-9401-6

    PubMed  Article  CAS  Google Scholar 

  6. Senthil Kumar R, Parthiban KT, Govinda Rao M (2009) Molecular characterization of Jatropha genetic resources through inter-simple sequence repeat (ISSR) markers. Mol Biol Rep 36(7):1951–1956

    PubMed  Article  CAS  Google Scholar 

  7. Sudheer Pamidimarri DV, Singh S, Mastan SG, Patel J, Reddy MP (2009) Molecular characterization and identification of markers for toxic and non-toxic varieties of Jatropha curcas L. using RAPD, AFLP and SSR markers. Mol Biol Rep 36(6):1357–1364

    PubMed  Article  CAS  Google Scholar 

  8. Sudheer Pamidiamarri DV, Pandya N, Reddy MP, Radhakrishnan T (2009) Comparative study of interspecific genetic divergence and phylogenic analysis of genus Jatropha by RAPD and AFLP: genetic divergence and phylogenic analysis of genus Jatropha. Mol Biol Rep 36(5):901–907

    PubMed  Article  CAS  Google Scholar 

  9. Miao L, Shou S, Cai J, Jiang F, Zhu Z, Li H (2009) Identification of two AFLP markers linked to bacterial wilt resistance in tomato and conversion to SCAR markers. Mol Biol Rep 36(3):479–486

    PubMed  Article  CAS  Google Scholar 

  10. Kazachkova N, Fahleson J, Meijer J (2004) Establishment of the amplified fragment length polymorphism (AFLP) technique for genotyping of pollen beetle (Meligethes aeneus)—a noxious insect pest on oilseed rape (Brassica napus). Mol Biol Rep 31(1):37–42

    PubMed  Article  CAS  Google Scholar 

  11. Singh AK, Gurtu S, Jambunathan R (1993) Phylogenetic relationships in the genus Arachis based on seed protein profiles. Euphytica 74(3):219–225

    Article  CAS  Google Scholar 

  12. He GH, Prakash CS (1997) Identification of polymorphic DNA markers in cultivated peanut (Arachis hypogaea L.). Euphytica 97:143–149

    Article  CAS  Google Scholar 

  13. Subramanian V, Gurtu S, Rao RCN, Nigam SN (2000) Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay. Genome 43(4):656–660

    PubMed  Article  CAS  Google Scholar 

  14. Raina SN, Rani V, Kojima T, Ogihara Y, Singh KP, Devarumath RM (2001) RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species. Genome 44(5):763–772

    PubMed  CAS  Google Scholar 

  15. He GH, Prakash CS (2001) Evaluation of genetic relationships among botanical varieties of cultivated peanut (Arachis hypogaea L.) using AFLP markers. Genet Resour Crop Evol 48(4):347–352

    Article  Google Scholar 

  16. Herselman L (2003) Genetic variation among Southern African cultivated peanut (Arachis hypogaea L.) genotypes as revealed by AFLP analysis. Euphytica 133:319–327

    Article  CAS  Google Scholar 

  17. Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 39(4):1243–1247

    Article  CAS  Google Scholar 

  18. Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108(6):1064–1070

    PubMed  Article  CAS  Google Scholar 

  19. Jiang HF, Liao BS, Ren XP, Lei Y, Emma M, Fu TD, Crouch JH (2007) Comparative assessment of genetic diversity of peanut (Arachis hypogaea L.) genotypes with various levels of resistance to bacterial wilt through SSR and AFLP analyses. J Genet Genom 34(6):544–554

    Article  CAS  Google Scholar 

  20. Han ZQ, Gao GQ, Wei PX, Tang RH, Zhong RC (2004) Analysis of DNA polymorphism and genetic relationships in cultivated peanut (Arachis hypogaea L.) using microsatellite markers. Acta Agronomica Sinica 30(11):1097–1101

    CAS  Google Scholar 

  21. Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SCM, Gimenes MA, Martins WS, Valls JFM, Grattapaglia D, Bertioli DJ (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111(6):1060–1071

    PubMed  Article  CAS  Google Scholar 

  22. Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, Nigam SN, Moss BJ, Seetha K, Ravi K, He G, Knapp SJ, Hoisington DA (2009) The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet 118:729–739

    PubMed  Article  CAS  Google Scholar 

  23. Moretzsohn MC, Barbosa AVG, Alves-Freitas DMT, Teixeira C, Leal-Bertioli SCM, Guimaraes PM, Pereira RW, Lopes CR, Cavallari MM, Valls JFM, Bertioli DJ, Gimenes MA (2009) A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9:40. doi:10.1186/1471-2229-9-40

    PubMed  Article  Google Scholar 

  24. Foncéka D, Hodo-Abalo T, Rivallan R, Faye I, Sall MN, Ndoye O, Fávero AP, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF (2009) Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid. BMC Plant Biol 9:103. doi:10.1186/1471-2229-9-103

    PubMed  Article  Google Scholar 

  25. Hong YB, Liang XQ, Chen XP, Liu HY, Zhou GY, Li SX, Wen SJ (2008) Construction of genetic linkage map based on SSR markers in peanut (Arachis hypogaea L.). Agric Sci China 7(8):915–921

    CAS  Google Scholar 

  26. Collard BCY, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27:86–93

    Article  CAS  Google Scholar 

  27. Joshi C, Zhou H, Huang XQ, Chiang VL (1997) Context sequences of translation initiation codon in plants. Plant Mol Biol 35:993–1001

    PubMed  Article  CAS  Google Scholar 

  28. Sawant SV, Singh PK, Gupta SK, Madnala R, Tuli R (1999) Conserved nucleotide sequences in highly expressed genes in plants. J Genet 78:123–131

    Article  CAS  Google Scholar 

  29. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76(10):5269–5273

    PubMed  Article  CAS  Google Scholar 

  30. Singh AK, Smartt J, Simpson CE, Raina SN (1998) Genetic variation vis-a-vis molecular polymorphism in groundnut, Arachis hypogaea L. Genet Resour Crop Evol 45:119–126

    Article  Google Scholar 

  31. Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    PubMed  Article  CAS  Google Scholar 

  32. Halward T, Stalker T, LaRue E, Kochert G (1992) Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plan Mol Biol 18:315–325

    Article  CAS  Google Scholar 

  33. Caetano-Anollés G, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using short arbitrary oligonucleotide primers. Bio/Technology 9:553–557

    PubMed  Article  Google Scholar 

  34. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    PubMed  Article  CAS  Google Scholar 

  35. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    PubMed  Article  CAS  Google Scholar 

  36. Vos P, Hogers R, Bleeper M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    PubMed  Article  CAS  Google Scholar 

  37. Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461

    Article  CAS  Google Scholar 

  38. Hu J, Vick BA (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep 21:289–294

    Article  CAS  Google Scholar 

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Acknowledgments

We are grateful to Dr. J.M. Wu for the technical assistance he has provided for this study. We wish to extend our gratitude to Dr. B.C.Y. Collard (International Rice Research Institute, IRRI), Dr. Y.W. Wei and Dr. W.D. Shi for their valuable discussions in the process of writing the manuscript. This research was supported by the earmarked fund for Modern Agro-Industry Technology Research System and grants from the National Natural Science Foundation of China (No. 30660094) and Guangxi Science Fund (Guikezi 0832088).

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Affiliations

  1. Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China

    Faqian Xiong, Ruichun Zhong, Zhuqiang Han, Jing Jiang, Liangqiong He & Ronghua Tang

  2. Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China

    Faqian Xiong, Zhuqiang Han, Jing Jiang & Ronghua Tang

  3. Fujian Province Key Lab of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    Weijian Zhuang

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  1. Faqian Xiong
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  2. Ruichun Zhong
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Correspondence to Weijian Zhuang or Ronghua Tang.

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Xiong, F., Zhong, R., Han, Z. et al. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep 38, 3487–3494 (2011). https://doi.org/10.1007/s11033-010-0459-6

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  • DOI: https://doi.org/10.1007/s11033-010-0459-6

Keywords

  • Start codon targeted polymorphism (SCoT)
  • Peanut botanical variety
  • Genetic diversity
  • Functional molecular markers