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

Association Mapping: A Useful Tool


Affiliations
1 Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur (C.G.), India
2 Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture and Technology, Pantnagar (Uttarakhand), India
     

   Subscribe/Renew Journal


Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Association mapping, also known as linkage disequilibrium mapping. Association mapping has the promise of higher mapping resolution through exploitation of historical recombination events at the population level that may enable gene level mapping on non-model organisms where linkage-based approaches would not be feasible. Association mapping utilizes ancestral recombinations and natural genetic diversity within a population to dissect quantitative traits and is built on the basis of the linkage disequilibrium concept. One of the working definitions of linkage disequilibrium (which here on will be referred to as LD) is the nonrandom co-segregation of alleles at two loci. In contrast to linkage-based studies, LD-based genetic association studies offer a potentially powerful approach for mapping causal genes with modest effects. The commonly used LD measure, D or D1 (standardized version of D). Besides D, a various different measures of LD (D1, r2, D2, D*, F, X and δ) have been developed to quantify LD. Softwares packages measuring LD, such as "graphical overview of linkage disequilibrium" (GOLD), power marker, and TASSEL (Trait Analysis by association Evolution and Linkage) are available. Applications of AM has been extended from model plant arabidopsis to field crops. The increasing number of AM studies in crop species indicates the potential of this approach in all plant species in near future.

Keywords

Linkage Disequilibrium, Association Mapping, Genetic Diversity, Polymorphism.
Subscription Login to verify subscription
User
Notifications
Font Size


  • Abdurakhmonov, A.Y. and A. Abdukarimov (2008). Application of association mapping to understanding the genetic diversity of plant germplasm resources. Internat. J. Plant Genom., 1-18.

  • Abdurakhomonov, I.Y., Kohel, R.J., Saha, S., Pepper, A.E., Yu, J.Z., Buriev, Z.T., Abdullaev, A., Shermatov, S. Jenkins, J.N. Scheffler, B. and Abdukarimov, A. (2007). Genomewide linkage disequilibrium revealed by microsatellite markers and association study of fibre quality traits in cotton. Proceedings of the 15th Plant and Animal Genome Conference, San Diego, CALIFORNIA, USA.

  • Al-Maskri, A.Y., Sajjad M. and Khan, S.H. (2012). Association mapping: a step forward to discovering new alleles for crop improvement. Internat. J. Agric. Biol., 14 (1) : 153-160.

  • Anonymous (2007). The wellcome trust case control consortium, genomewide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447: 661-678.

  • Aranzana, M., Kim, S., Zhao, K., Bakker, E., Horton, M., Jacob, K., Lister, C., Molitor, J., Shindo, C., Tang, C., Toomajian, C., Traw, B., Zheng, H., Bergelson, J., Dean, C., Marjoram, P. and Nordborg, M. (2005). Genome-wide association mapping in arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genetics, 1(5): 60-65.

  • Barnaud, A., Lacombe, T. and Doligez, A. (2006). Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. Theor. Appl. Genet., 112 (4) : 708-716.

  • Brachi, B., Faure, N., Horton, M., Flahauw, E., Vazquez, A., Nordborg, M., Bergelson, J., Cuguen, J. and Roux, F. (2010). Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet., 6( 5): 940-947.

  • Breseghello, F. and Sorrells, M.E. (2006). Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 172 (2) : 1165-1177.

  • Caldwell, K.S., Russell, J., Langridge, P. and Powell, W. (2006). Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics, 172 (1) : 557-567.

  • Cannon, G.B. (1963). The effects of natural selection on linkage disequilibrium and relative fitness in experimental populations of Drosophila melanogaster. Genetics, 48 (9) : 1201-1216.

  • Ehrenreich, I.M., Stafford, P.A. and Purugganan, M.D. (2007). The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping. Genetics, 176 (2) : 1223-1236.

  • Ersoz, E., Yu, J. and Buckler, E. (2007). Application of linkage disequilibrium and association mapping in crop plants, In: Genomics-assisted crop improvement, pp.97-119. Springer, ISBN 987-1-4020-6294-0, Dordrecht. The NETHERLANDS.

  • Estivill, X. and Armengol, L. (2007). Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PLoS Genetics, 3 (1) : 1787-1799.

  • Flint-Garcia, S.A., Thornsberry, J.M. and Buckler, E.S. (2003). Structure of linkage disequilibrium in plants. Annl. Rev. Plant Biol., 54: 357-374.

  • Gupta, P.K., Rustgi, S. and Kulwal, P.L. (2005). Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molec. Biol., 57 (4) : 461-485.

  • Hamblin, M.T., Mitchell, S.E., White, G.M., Gallego, J., Kukatla, R., Wing, R.A., Paterson, A.H. and Kresovich, S. (2004). Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics, 167 (1) : 471-483.

  • Hirschhorn, J. N. and Daly, M.J. (2005). Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet., 6 : 95-108.

  • Karim S., Lyudmyla, V. Malysheva-Otto, Michelle, G., Wirthensohn, Tarkesh-Esfahani, S. Kraakman, A.T.W., Niks, R.E., Van Den Berg, P.M.M.M., Stam, P. and Van Eeuwijk, F.A. (2004). Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics, 168 (1) : 435-446.

  • Mackay, I. and Powell, W. (2007). Methods for linkage disequilibrium mapping in crops. Trends Plant Sci., 12 (2) : 57-63.

  • Marttinen, P. and Corander, J. (2010). Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. BMC Bioinformatics, 11: 443.

  • Nemri, A., Atwell, S., Tarone, A., Huang, Y., Zhao, K., Studholme, D., Nordborg, M. and Jones, J. (2010). Genome-wide survey of arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proc. National Acad. Sci. United States America, 107 (22): 10302-10307.

  • Oraguzie, N.C., Wilcox, P.L., Rikkerink, E.H.A. and De Silva, H.N. (2007). Linkage disequilibrium. In: (Ed.), Association Mapping in Plants, pp. 11-39. Springer, NEW YORK, U.S.A.

  • Paterson, A.H., DeVerna, J.W., Lanini, B. and Tanksley, S.D. (1990). Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics, 124 (3) : 735-742.

  • Pritchard, K.J. and Wen, W. (2004). Documentation for structure software. The University of Chicago Press, Chicago, Ill, U.S.A.

  • Risch, N. and Menikangas, K. (1996). The future of genetic studies of complex human diseases. Science, 273 (5281) : 1516-1517.

  • Skoet, L., Humphreys, J., Humphreys, M.O., Thorogood, D., Gallagher, J., Sanderson, R., Armstead, I.P. and Thomas, I.D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1) : 535-547.

  • Spielman, R., McGinnis, R. and Ewens, W. (1993). Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). American J. Human Genet., 52(3): 506-516.

  • Stuber, C.W., Lincoln, S.E., Wolff, D.W., Helentjaris, T. and Lander, E.S. (1992). Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics, 132 (3) : 823-839.

  • Thornsberry, J.M., Goodman, M.M., Doebley, J., Kresovich, S., Nielsen, D. and Buckler, E.S. (2001). Dwarf 8 polymorphisms associate with variation in flowering time. Nat. Genet., 28 (3) : 286-289.

  • Wang, W., Thornton, K., Berry, A. and Long, M. (2002). Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science, 295 (5552) : 134-137.

  • Yu, J., Pressoir, G., Briggs, W.H., Bi, I.V., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., Kresovich, S. and Buckler, E.S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet., 38 (2) : 203-208.

  • Zhu, Y.L., Song, Q.J., Hyten, D.L., Van Tassell, C.P., Matukumalli, L.K., Grimm, D.R., Hyatt, S.M., Fickus, E.W., Young, N.D. and Cregan, P.B. (2003). Single-nucleotide polymorphisms in soybean. Genetics, 163 (3) : 1123-1134.


Abstract Views: 532

PDF Views: 2




  • Association Mapping: A Useful Tool

Abstract Views: 532  |  PDF Views: 2

Authors

Hemant Sahu
Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur (C.G.), India
Jairam Amadabade
Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture and Technology, Pantnagar (Uttarakhand), India
Namrata Dhiri
Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur (C.G.), India

Abstract


Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Association mapping, also known as linkage disequilibrium mapping. Association mapping has the promise of higher mapping resolution through exploitation of historical recombination events at the population level that may enable gene level mapping on non-model organisms where linkage-based approaches would not be feasible. Association mapping utilizes ancestral recombinations and natural genetic diversity within a population to dissect quantitative traits and is built on the basis of the linkage disequilibrium concept. One of the working definitions of linkage disequilibrium (which here on will be referred to as LD) is the nonrandom co-segregation of alleles at two loci. In contrast to linkage-based studies, LD-based genetic association studies offer a potentially powerful approach for mapping causal genes with modest effects. The commonly used LD measure, D or D1 (standardized version of D). Besides D, a various different measures of LD (D1, r2, D2, D*, F, X and δ) have been developed to quantify LD. Softwares packages measuring LD, such as "graphical overview of linkage disequilibrium" (GOLD), power marker, and TASSEL (Trait Analysis by association Evolution and Linkage) are available. Applications of AM has been extended from model plant arabidopsis to field crops. The increasing number of AM studies in crop species indicates the potential of this approach in all plant species in near future.

Keywords


Linkage Disequilibrium, Association Mapping, Genetic Diversity, Polymorphism.

References