International Journal of Plant Sciences

Open Access Open Access  Restricted Access Subscription Access
Open Access Open Access Open Access  Restricted Access Restricted Access Subscription Access

Identification and Tagging of QTLs for Arjunolic Acid in Terminalia arjuna among Indian Sub Populations by Association Mapping and Linkage Disequilibrium


Affiliations
1 Department of Life Science, National Institute of Technology, Rourkela (Odisha), India
     

   Subscribe/Renew Journal


The content of cardiotonic arjunolic acid in Terminalia arjuna vary among the population. We studied the population structure and the association between the molecular markers and its active ingredient among 140 plants collected from various agroclimatic zones in India. Large variation was detected for the arjunolic acid in this study showing suitableness of the genotypes. The maximum arjunolic acid content was approximately 238 per cent higher than the lowest value for the genotypes and was found to be considerably correlated to bark thickness, bark fresh weight and bark dry weight. The population structure studies described the existence of nine subpopulations. As the distance increased between the associated markers, Linkage disequilibrium (LD) reduction and a considerable reduction in LD decay was ascertained. Eleven QTL regions associated with arjunolic acid were identified from a genome-wide marker-trait association study. Fine-scale resolution detected significant LD among 3.4 per cent RAPD paired loci and 8.7 per cent ISSR paired loci and 6.7 per cent RAPD paired loci and 13.3 per cent ISSR paired loci. Importantly LD decay found to start at a distance of >20bp from the loci on the genome of T. arjuna accessions. Finally, association mapping (AM) in arjun tightly linked to OPT09 which can be a possible substitute to QTL mapping methodology.

Keywords

Arjunolic Acid, Association Mapping, Linkage Disequilibrium, QTL, Marker-Trait Association.
Subscription Login to verify subscription
User
Notifications
Font Size


  • Abdurakhmonov, I.Y., Kohel, J. R., Yu, J.Z., Pepper, A.E., Abdullaev, A. A., Kushanov, F.N., Salakhutdinov, I.B., Buriev, Z.T., Saha, Sz., Scheffler, B.E. and Jenkins, J.N. (2008). Molecular diversity and association mapping of fibre quality traits in exotic G. hirsutum L. germplasm. Genomics, 92 : 478–487.

  • Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S. (2007). TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23: 2633–2635.

  • Campoy, J.A., Lerigoleur-Balsemin, E., Christmann, H., Beauvieux, R., Girollet, N. and Quero-García, J. (2016). Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars. BMC Plant Bio., 16 (49): 1-15.

  • Cardon, R.L. and Bell, J.I. (2001). Association study designs for complex disease. Nat. Rev. Genet., 2 : 91- 99.

  • Cervera, M.T., Sewell, M.M., Faivre-Rampant, P., Storme, V., Van Montagu, M. and Boerjan, W. (2004). Genome mapping in populus. In: Kumar S, Fladung M (eds) Molecular genetics and breeding of forest trees. Haworth’s Food Products Press, New York, pp. 387-410.

  • Dangi, B., Varsha, K.K., Kothari, S.L. and Kachhwaha, S. (2014). Micropropagation of Terminalia bellerica from nodal explants of mature tree and assessment of genetic fidelity using ISSR and RAPD markers. Physiol. Mol. Bio. Plants., 20 : (4): 509–516.

  • Evanno, G., Regnaut, S. and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol., 14: 2611-2620.

  • Freeman, J.S., Potts, B.M., Downes, G.M., Pilbeam, D., Thavamanikumar, S. and Vaillancourt, R. (2013). Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments in Eucalyptus globulus. New Phytol., 198 : 1121-1134.

  • Holland, J.B. (2007). Genetic architecture of complex traits in plants. Curr. Opin. Plant. Biol., 10: 156–161.

  • Lespinasse, D., Rodier-Goud, M., Grivet, L., Leconte, A., Legnate, H. and Seguin, M. (2000). A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite, and isozyme markers. Theor. Appl. Genet., 100 : 127–138.

  • Li, J. and Jin, Z. (2007). Genetic variation and differentiation in Torreya jackii Chun, an endangered plant endemic to China. Plant Sci., 172: 1048-1053.

  • Maccaferri, M., Sanguineti, M.C., Noli, E. and Tuberosa, R. (2005). Population structure and long-range linkage disequilibrium in a drum wheat elite collection. Mol. Breed., 15: 271–289.

  • Mather, K. A., Caicedo, A.L., Polato, N.R., Olsen, K.M., Mc Couch, S. and Purugganan, M. D. (2007). The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics, 177 (4): 2223-2232.

  • Neumann, K., Kobiljski, B., Dencic, S., Varshney, R.K. and Borner, A. (2011). Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol. Breed., 27: 37–58.

  • Pritchard, J. K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multi-locus genotype data. Genetics., 155: 945–959.

  • Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M. M. and Buckler, E.S. (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS, 98 : 11479-11484.

  • Roldán-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A. and De Loose, M. (2000). AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol. Breed., 6 : 125–134.

  • Scalfi, M., Troggio, M., Piovani, P., Leonardi, S., Magnaschi, G., Vendramin, G. G. and Menozzi, P. (2003). A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.). Theo. Appl. Genet., 108 (3): 433–441.

  • Sewell, M.M., Sherman, B.K. and Neale, D.B. (1999). A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics, 151: 321-330.

  • Stich, B., Mohring, J., Piepho, H. P., Heckenberger, M., Buckler, E. S. and Melchinger, A.E. (2008). Comparison of mixed-model approaches for association mapping. Genetics, 178: 1745–1754.

  • Tenaillon, M.I., Sawkins, M.C., Long, A. D., Gaut, R. L., Doebley, J. F. and Gaut, B. S. (2001). Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays L.). Proc. Natl. Acad. Sci. USA., 98: 9161–9166.

  • Wright (1978). Evolution and the genetics of populations: variabilitywithin and among natural populations. Univ Chicago Press, Chicago.IL.

  • Zhu, C., Gore, M.A., Buckler, E.S. and Yu, J. (2008). Status and prospects of association mapping in plants. Plant Genome, 1: 5-20.


Abstract Views: 495

PDF Views: 0




  • Identification and Tagging of QTLs for Arjunolic Acid in Terminalia arjuna among Indian Sub Populations by Association Mapping and Linkage Disequilibrium

Abstract Views: 495  |  PDF Views: 0

Authors

Sonu Bharti
Department of Life Science, National Institute of Technology, Rourkela (Odisha), India

Abstract


The content of cardiotonic arjunolic acid in Terminalia arjuna vary among the population. We studied the population structure and the association between the molecular markers and its active ingredient among 140 plants collected from various agroclimatic zones in India. Large variation was detected for the arjunolic acid in this study showing suitableness of the genotypes. The maximum arjunolic acid content was approximately 238 per cent higher than the lowest value for the genotypes and was found to be considerably correlated to bark thickness, bark fresh weight and bark dry weight. The population structure studies described the existence of nine subpopulations. As the distance increased between the associated markers, Linkage disequilibrium (LD) reduction and a considerable reduction in LD decay was ascertained. Eleven QTL regions associated with arjunolic acid were identified from a genome-wide marker-trait association study. Fine-scale resolution detected significant LD among 3.4 per cent RAPD paired loci and 8.7 per cent ISSR paired loci and 6.7 per cent RAPD paired loci and 13.3 per cent ISSR paired loci. Importantly LD decay found to start at a distance of >20bp from the loci on the genome of T. arjuna accessions. Finally, association mapping (AM) in arjun tightly linked to OPT09 which can be a possible substitute to QTL mapping methodology.

Keywords


Arjunolic Acid, Association Mapping, Linkage Disequilibrium, QTL, Marker-Trait Association.

References