Theoretical and Applied Genetics

, Volume 113, Issue 4, pp 585–595

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology

  • Shiying Yang
  • Wen Pang
  • Gavin Ash
  • John Harper
  • Jason Carling
  • Peter Wenzl
  • Eric Huttner
  • Xuxiao Zong
  • Andrzej Kilian
Original Paper

Abstract

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies.

Supplementary material

122_2006_317_MOESM1_ESM.doc (872 kb)
Supplementary material 1
122_2006_317_MOESM2_ESM.doc (28 kb)
Supplementary material 2

References

  1. Anderson M (2003) PCO: a FORTRAN computer program for principal coordinate analysis. University of Auckland, New ZealandGoogle Scholar
  2. Anderson JA, Churchill G.A, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186PubMedCrossRefGoogle Scholar
  3. Berger J, Abbo S, Turner NC (2003) Ecogeography of annual wild Cicer species: the poor state of the world collection. Crop Sci 43:1076–1090CrossRefGoogle Scholar
  4. Botstein D, Skolnick M, Davis R (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314–331PubMedGoogle Scholar
  5. Felsenstein J (1989) PHYLIP—phylogeny inference package (Version 3.2). Cladistics 164–166Google Scholar
  6. Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.6. University of Washington, SeattleGoogle Scholar
  7. Frary A, Fulton TM, Zamir D, Tanksley SD (2004) Advanced backcross QTL analysis of a Lycopersicon esculentum × L. pennellii cross and identification of possible orthologs in the Solanaceae. Theor Appl Genet 108:485–96PubMedCrossRefGoogle Scholar
  8. Gonzalez J (1993) Random amplified polymorphic DNA analysis in Hordeum species. Genome 36:1029–1031PubMedCrossRefGoogle Scholar
  9. Huang XQ, Coster H, Ganal MW, Roder MS (2003) Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor Appl Genet 106:1379–89PubMedGoogle Scholar
  10. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29(4):e25PubMedCrossRefGoogle Scholar
  11. Jain A, Bhatia S, Banga S, Lakshmikumaran M (1994) Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis. Theor Appl Genet 88:116–122CrossRefGoogle Scholar
  12. Kumar S, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  13. van der Maesen LJG (1990) Pigeonpea: origin, history, evolution, and taxonomy. In: Nene YL, Hill SH, Sheila VK (eds) The pigeonpea. CABInternational, Wellingford, UK, P15–46 Google Scholar
  14. Mackill D (1995) Classifying Japonica rice cultivars with RAPD markers. Crop Sci 35:889–894CrossRefGoogle Scholar
  15. Miller J (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448Google Scholar
  16. Moretzsohn M de C, Hopkins MS, Mitchell SE, Kresovich S, Valls JF, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 14(4):11CrossRefGoogle Scholar
  17. Ohri D, Singh S (2002) Karyotypic and genome size variation in Cajanus cajan (L.) Millsp (pigeonpea) and some wild relatives. Genet Resour Crop Evol 49:1–10CrossRefGoogle Scholar
  18. Ohri D, Jha S, Kumar S (1994) Variability in nuclear-DNA Content within Pigeonpea, Cajanus cajan (Fabaceae). Plant Syst Evol 189:211–2CrossRefGoogle Scholar
  19. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  20. Ronald D (1999) A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep 17:53–57CrossRefGoogle Scholar
  21. Saxena K, Yang S (2000) ICRISAT Pigeonpea Jumps over Himalayas. Int Chickpea and Pigeonpea Newslett 2–3Google Scholar
  22. Saxena K, Zong X, Yang S, Li Z, Zhou C (2000) Potential of Pigeonpea in China and its Genetic Improvement at ICRISAT, ICETS 2000, BeijingGoogle Scholar
  23. Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1433–1441PubMedCrossRefGoogle Scholar
  24. Sivaramakrishnan, Reddy L (2002) Diversity in selected wild and cultivated species of pigeonpea using RFLP of mtDNA. Euphytica 125:121–128 CrossRefGoogle Scholar
  25. Stein N (2001) A new DNA extraction method for high-throughput marker analysis in a large-genome species such as Triticum aestivum. Plant Breed 120:354–356CrossRefGoogle Scholar
  26. Vos P, Hoger R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  27. Wang D, Fan J, Siao C, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J et al (1998) Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science 280(5366):1077–1082PubMedCrossRefGoogle Scholar
  28. Weber J, May P (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44(3):388–396PubMedGoogle Scholar
  29. Wenzl P, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101(26):9915–9920PubMedCrossRefGoogle Scholar
  30. Williams J, Kubelik A, Livak K, Rafalski J, Tingey S (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18(22):6531–6535PubMedCrossRefGoogle Scholar
  31. Wittenberg AH, Van der Lee T, Cayla C, Kilian A, Visser RG, Schouten HJ (2005) Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol Gen Genomics, 274:30–39CrossRefGoogle Scholar
  32. Xia L, Peng K, Yang S, Wenzl P, Carmen de Vicente M, Fregene M, Kilian A (2005) DArT for high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098 DOI:101007/s100122-101005-101937-101004Google Scholar
  33. Yang S, Pang W, Zong X, Li Z, Zhou C, Saxena K, Liang H (2001) A potential fodder crop for Guangxi province of China. Int Chickpea Pigeonpea Newslett 54Google Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Shiying Yang
    • 1
    • 2
    • 3
    • 4
  • Wen Pang
    • 2
  • Gavin Ash
    • 3
  • John Harper
    • 3
  • Jason Carling
    • 1
  • Peter Wenzl
    • 1
  • Eric Huttner
    • 1
  • Xuxiao Zong
    • 5
  • Andrzej Kilian
    • 1
  1. 1.DArT P/LYarralumlaAustralia
  2. 2.Guangxi Academy of Agricultural SciencesNanningPeople’s Republic of China
  3. 3.EH Graham Centre for Agricultural Innovation, School of Agricultural and Veterinary SciencesCharles Sturt UniversityWagga WaggaAustralia
  4. 4.Center for the Application of Molecular Biology to International Agriculture (CAMBIA)CanberraAustralia
  5. 5.Chinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

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