Hostname: page-component-586b7cd67f-r5fsc Total loading time: 0 Render date: 2024-11-21T11:42:01.407Z Has data issue: false hasContentIssue false
  • English
  • Français

Efficiency of three DNA markers in revealing genetic variation among wild Cajanus species

Published online by Cambridge University Press:  09 September 2008

Rupakula Aruna ,
D. Manohar Rao ,
S. Sivaramakrishnan ,
L. Janardhan Reddy ,
Paula Bramel  and
Hari Upadhyaya
Rupakula Aruna*
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India
D. Manohar Rao
Affiliation:
Department of Genetics, Osmania University, Hyderabad 500 007, Andhra Pradesh, India
S. Sivaramakrishnan
Affiliation:
Department of Biotechnology, Acharya NG Ranga Agricultural University, Hyderabad 500 030, Andhra Pradesh, India
L. Janardhan Reddy
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India
Paula Bramel
Affiliation:
International Institute of Tropical Agriculture, PMB 5320 Ibadan, Nigeria
Hari Upadhyaya
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India
*
*Corresponding author. E-mail: a.rupakula@cgiar.org
Get access Rights & Permissions [Opens in a new window]

Abstract

Wild relatives of pigeonpea (Cajanus cajan L.) possess many useful genes that can be utilized for crop improvement, most importantly genes for resistance to Helicoverpa armigera, the legume pod borer. The present study aimed at quantifying diversity in a collection of Cajanus scarabaeoides, Cajanus sericeus, Cajanus reticulatus and C. cajan species selected from a wide geographic range using two PCR-based marker systems, amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs), and the hybridization-based restriction fragment length polymorphism (RFLP). Polymorphism was higher among the wild accessions than among the cultivated genotypes. Wild and cultivated Cajanus accessions belonging to different species clustered into four distinct major groups largely based on the interspecific differences. C. scarabaeoides accessions derived from same geographical origins formed one group reflecting similar genetic makeup of these accessions. Dendrograms generated using AFLP, RFLP and SSR marker data were comparable with minor clustering differences, which suggests that either method, or a combination of both can be applied to expanded genetic studies in Cajanus. Mantel testing confirmed the congruence between the genetic distances of three markers, indicating that the markers segregated independently, giving similar grouping patterns of all accessions having similar genetic origin.

Keywords

AFLPmantel testMDS plotsprincipal coordinate analysisRFLPSSRs
Type
Research Article
Information
Plant Genetic Resources , Volume 7 , Issue 2 , August 2009 , pp. 113 - 121
Copyright
Copyright © NIAB 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Akkaya, MS, Bhagwat, AA and Cregan, PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132: 1131–1139.CrossRefGoogle ScholarPubMed
Anderson, JA, Churchill, GA, Autrique, JE, Sollers, ME and Tanskley, SD (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181–186.CrossRefGoogle ScholarPubMed
Aruna, R, Reddy, LJ and Chandra, S (2004) Assessment of phenotypic and genotypic diversity in C. scarabaeoides, a wild relative of pigeonpea, Pages 101–104 In: Assessment of Risk of Loss of Biodiversity in Traditional Cropping Systems: A Case Study of Pigeonpeas (Cajanus cajan L. Millspaugh) in Andhra Pradesh. (Bramel, P [ed]). International Crops Research Institute for the Semi-Arid Tropics, ICRISAT: Andhra Pradesh, Patancheru, India. ICRISAT, India.Google Scholar
Aruna, R, Manohar Rao, D, Reddy, LJ, Upadhyaya, HD and Sharma, HC (2005) Inheritance of trichomes and resistance to pod borer (Helicoverpa armigera) and their association in Interspecific crosses between cultivated Pigeonpea (Cajanus cajan) and its wild relatives C. scarabaeoides. Euphytica 145: 247–257.Google Scholar
Beckmann, J and Soller, M (1983) Restriction fragment length polymorphisms in genetic improvement of agricultural species. Euphytica 35: 111–124.CrossRefGoogle Scholar
Botstein, B, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Annual Journal of Human Genetics 32: 314–331.Google ScholarPubMed
Bowcock, C (1994) Association between molecular markers and quantitative traits in oat germplasm pool: can we infer linkage? Journal of Agriculture and Genetics 3: 11–18.Google Scholar
Breyne, P, Rombaut, D, VanGysel, A, and Gerats, T (1999) AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes. Molecular Genetics 261: 627–634.Google Scholar
Burns, MJ, Edwards, KJ, Newbury, HJ, Ford-Lloyd, BV and Baggot, CD (2001) Development of simple sequence repeats (SSR) markers for the assessment of gene flow and genetic diversity in Pigeonpea (Cajanus cajan L.). Molecular Ecology Notes 1(4): 283–285.CrossRefGoogle Scholar
Cervera, MT, Canbezas, JA, Sancha, JC, Martinez de Toda, F and Martinez Zapater, JM (1998) Application of AFLPs to the characterisation os grapevine (Vitis vinifera L.) genetic resources. A case study with accessions from Rioja (Spain). Theoretical and Applied Genetics 97(1–2): 51–58.Google Scholar
Clegg, M, Brown, V and Whitefield, PR (1984) Chloroplast DNA diversity in wild and cultivated barley: implications for genetic conservation. Genetics Research 43: 339–343.Google Scholar
Condit, R and Hubell, SP (1991) Abundance and DNA sequences of two bases repeat regions in tropical tree genomes. Genome 34: 66–71.Google Scholar
Dewey, RE, Levings, III CS and Timothy, DH (1985) Nucleotide sequence of ATPase subunit 6 gene of Maize mitochondria. Plant Physiology 79: 914–919.Google Scholar
Ennos, RA, Sinclair, WT, Hu, XS and Langdon, A (1999) Using organelle markers to elucidate the history, ecology and evolution of plant populations. In: Hollingsworth, PM, Bateman, RM and Gornall, RJ (eds) Molecular systematics and plant evolution. London: Taylor and Francis, pp. 1–19.Google Scholar
FAO Statistics, 2006. Available at http://WWW.FAO.ORG.Google Scholar
Feinburg, AP and Vogelstein, B (1983) A technique for radiolabelling DNA restriction fragments to high specific activity. Annals of Biochemistry 132: 6–13.Google Scholar
Gepts, P (1995) Genetic markers and core collection. In: Hodgkin, T, Brown, AHD, Van Hintum, ThJC and Morales, EAV (eds), Core Collections of Plant Genetic Resources. John Wiley and Sons, pp. 127–146.Google Scholar
Goldstein, DB and Schlotterer, C (1999) Microsatellites: Evolution and Applications. New York: Oxford University Press.Google Scholar
Green, PWC, Stevenson, PC, Simmonds, MSJ and Sharma, HC (2002) Can larvae of the pod borer, Helicoverpa armigera (Lepidoptera: Noctuidae), select between wild and cultivated pigeonpea [Cajanus sp. (Fabaceae)]? Bulletin of Entomological Research 92: 45–51.CrossRefGoogle Scholar
Isaac, PG, Jones, VP and Leaver, CJ (1985) The maize cytochrome C Oxidase subunit I gene sequence, expression and rearrangement in cytoplasmic male sterile plants. The EMBO J 4: 1617–1623.Google Scholar
Jarne, P and Lagoda, PJL (1996) Microsatellites, from molecules to populations and back. Trends in Ecological Evolution 11: 424–429.Google Scholar
Kamala, V (2003) Diversity analysis and identification of sources resistant to downy mildew, shoot fly and stem borer in wild sorghums PhD Thesis Osmania University, Hyderabad..Google Scholar
Kollipara, KP, Singh, L and Hymowitz, T (1994) Genetic variation of trypsin and chymotrypsin inhibitors in Pigeonpea [(Cajanus cajan L.) Millsp.] and its wild relatives. Theoretical Applied Genetics 8: 986–993.Google Scholar
Krishna, TG and Reddy, LJ (1982) Specific affinities between Cajanus cajan L. and some Atylosia species based on esterase isozymes. Euphytica 31: 709–713.CrossRefGoogle Scholar
Law, JR, Domini, P, Koebner, RMD and Reeves, JC (1998) DNA profiling and plant variety registration. The statistical assessment of distinctness in wheat using amplified fragment length polymorphisms. Euphytica 102: 335–342.CrossRefGoogle Scholar
Mantel, N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27: 209–220.Google Scholar
Moretzsohn, MC, Hopkins, SE, Mitchell, S, Kresovich, JF, Valls, M and 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 Biology 4: 11.Google Scholar
Morgante, M and Oliveri, AM (1993) PCR amplified microsattelites as markers in plant genetics. Plant Journal 3: 175–182.Google Scholar
Murray, MG and Thompson, ES (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 19: 4321–4325.CrossRefGoogle Scholar
Nadimpalli, BG, Jarret, RL, Phatak, SC and Kochert, G (1993) Phylogenetic relationships of pigeon pea based on nuclear restriction fragment length polymorphisms. Genome 36: 216–223.Google Scholar
Nei, M and Li, WH (1973) Genetic distance between populations. The American Naturalist 106: 283–292.CrossRefGoogle Scholar
Nei, M and Li, WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of National Academy of Sciences, USA 76: 5269–5273.CrossRefGoogle ScholarPubMed
Odeny, DA, Jayashree, B, Ferguson, M, Hoisington, D, Crouch, J and Gebhardt, C (2007) Development, characterization and utilization of microsatellite markers in Pigeonpea. Plant Breeding 126(2): 130–136.CrossRefGoogle Scholar
Pangaluri, SK, Janaiah, K, Govil, JN, Kumar, PA and Sharma, PC (2006) AFLP Finger printing in Pigeonpea (Cajanus cajan L.) and its wild relatives. Genetic Resources and Crop Evolution 53: 523–531.Google Scholar
Parani, M, Lakshmi, M, Senthilkumar, P and Parid, A (2000) Ribosomal DNA variation and phylogenetic relationships among Cajanus cajan (L.) Millsp. and its wild relatives. Current Science 78(10): 1235–1238.Google Scholar
Pejic, I, Ajmone-Marsan, P, Morgante, M, Kozumplick, V, Castiglioni, P, Taramino, G and Motto, M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theoretical and Applied Genetics 97: 1248–1255.CrossRefGoogle Scholar
Powell, W, Morgante, M, Andre, C, Hanafey, M, Vogel, T, Tingey, S and Rafalski, JA (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 3: 225–238.Google Scholar
Pundir, RPS and Singh, RB (1985a) Biosystematic relationships among Cajanus. Atylosia and Rhyncosia species and evolution of pigeonpea (Cajanus cajan(L.) Millsp.). Theoretical and Applied Genetics 69: 531–534.Google Scholar
Pundir, RPS and Singh, RB (1985b) Crossability relationships among Cajanus Atylosia, and Rhyncosia species and detection of crossing barriers. Euphytica 34: 303–308.CrossRefGoogle Scholar
Rafalski, JA and Vogel, T (1996) RAPD markers a new technology for genetic molecular mapping and Plant breeding. Agribiotech News Info 3: 645–648.Google Scholar
Ratnaparkhe, MB, Gupta, VS, VenMurthy, MR and Ranjekar, PK (1995) Genetic fingerprinting of pigeonpea [Cajanus cajan (L.) Millsp.] and its wild relatives using RAPD markers. Theoretical and Applied Genetics 91: 893–898.Google Scholar
Remanandan, P (1988) Pigeonpea: Genetic Resources. In: Nene, YL, Hall, SD and Sheila, VK (eds) Wallingord, Oxen: CAB International, pp. 89–116.Google Scholar
Rohlf, FJ (1997) NTSYS – Pc. Numerical Taxonomy and Multivariate Analysis System version 2.1. Setauket, NY: Exeter Software, p. 7..Google Scholar
Russell, J, Fuller, J, Young, G, Thomas, B, Taramino, G, Macaulay, M, Waugh, R and Powell, G (1997) Discriminating between barley genotypes using microsattelites. Genome 442: 450.Google Scholar
Saxena, KB, Singh, L, Reddy, MV, Singh, U, Lateef, SS, Sharma, SB and Remanandam, P (1990) Intra species variation in Atylosia scarabaeoides (L.) Benth. a wild relative of pigeonpea (Cajanus cajanL.) Millsp.). Euphytica 49: 185–191.CrossRefGoogle Scholar
Sivaramakrishnan, S (1999) RFLP analysis of cytoplasmic male sterile lines in Pigeonpea (Cajanus cajan L. Millsp.). Euphytica 126: 293–299.Google Scholar
Sivaramakrishnan, S, Seetha, K, Kamala, V, Reddy, LJ, Rai, KN, Reddy, BVS, Saxena, KB and Paula, BJC (2001) RFLP analysis of mitochondrial DNA for the identification of cytoplasmic male sterile systems and detection of genetic variability in Pearl millet, Sorghum and Pigeonpea. Plant and Animal Genome VIII Conference, San Deigo, CA, January 9–12, 2001..Google Scholar
Sivaramakrishnan, S, Kannan, S and Reddy, LJ (2002) Diversity in selected wild and cultivated species of pigeonpea using RFLP of mt DNA. Euphytica 125: 21–28.Google Scholar
Sokal, RR and Micherner, CD (1958) A statistical method for evaluating systematic relationships. Science Bulletin 38: 1409.Google Scholar
Taramino, G and Tingey, S (1996) Simple sequence repeats for germplasm analysis and mapping in maize. Genome 39: 277–287.CrossRefGoogle ScholarPubMed
Tautz, D (1989) Hypervariability of simple sequences as a general source of polymorphism DNA markers. Nucleic Acids Research 17: 6463–6471.Google Scholar
Tautz, D and Renz, M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research 12: 4127–4138.Google Scholar
Van der Maesen, LJG (1986) Cajanus D C and Alylosia W & A (Leguminosae). Wageningen: Agricultural University, pp. 84–85.Google Scholar
Van der Maesen, LJG (1990) Pigeonpea: origin, history, evolution, and taxonomy. The Pigeonpea. In: Nene, YL, Hall, SD and Sheila, VK (eds) India: CAB Int. ICRISAT, pp. 15–46.Google Scholar
Wang, ZY and Tanksley, SD (1992) Restriction fragment length polymorphism in Oryza sativaL. Genome 32: 1113–1118.Google Scholar
Zabeau, M and Vos, P (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting European Patent Application number: 92402629.7, Publication Number EP 0534858..Google Scholar