Cereal Research Communications

, Volume 42, Issue 2, pp 177–188 | Cite as

Association Mapping Identifies QTLS on Wheat Chromosome 3A for Yield Related Traits

  • M. SajjadEmail author
  • S. H. Khan
  • M. Q. Ahmad
  • A. Rasheed
  • A. Mujeeb-Kazi
  • I. A. Khan


A panel of 94 diverse hexaploid wheat accessions was used to map quantitative trait loci (QTL) underlying the yield related traits on chromosome 3A. Population structure and kinships were estimated using unlinked SSR markers from all 21 chromosomes. Analysis of variance revealed significant difference among accessions; however, genotype × year interaction was non-significant for majority of yield related traits. A mixed linear model (MLM) approach identified six QTLs for four traits that individually accounted for 10.7 to 17.3% phenotypic variability. All QTLs were consistently observed for both study years. New putative QTLs for the maximum fertile florets per spike and spike length were identified. This report on QTLs for yield related traits on chromosome 3A will extend the existing knowledge and may prove useful in marker-assisted selection (MAS) for development of high yielding cultivars.


wheat grain yield population structure linkage disequilibrium association mapping 


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  1. Abdurakhmonov, A.Y., Abdukarimov, A. 2008. Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int. J. Plant. Genom. 2008: 574927.Google Scholar
  2. Ali, M.L., Baenziger, P.S., Ajlouni, Z.A., Campbell, B.T., Gill, K.S., Eskridge, K.M., Mujeeb-Kazi, A., Dweikat, I. 2011. Mapping QTL for agronomic traits on wheat chromosome 3A and a comparision of recombinant inbred chromosome line populations. Crop Sci. 51: 553–566.CrossRefGoogle Scholar
  3. Al-Maskri, A.H., Sajjad, M., Khan, S.H. 2012. Association mapping: A step forward to discovering new alleles for crop improvement. Int. J. Agric. Biol. 14: 153–160.Google Scholar
  4. Anderson, J.R., Zein, I., Wenzel, G., Krützfeldt, B., Eder, J., Ouzunova, M., Lübberstedt, T. 2007. High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theor. Appl. Genet. 114: 307–319.CrossRefGoogle Scholar
  5. Breseghello, F., Sorrells, M.E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165–1177.CrossRefGoogle Scholar
  6. Crossa, J., Burgueno, J., Dreisickacker, S., Vargas, M., Herrera-Foessel, S.A., Lillemo, M., Singh, R.P., Trethowan, R., Warburton, M., Franco, J., Reynolds, M., Crouch, J.H., Ortiz, R. 2007. Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177: 1889–1913.CrossRefGoogle Scholar
  7. DeWan, A., Liu, M., Hartman, S., Zhang, S.S., Liu, D.T.L., Zhao, C., Tam, P.O.S., Chan, W.M., Lam, D.S.C., Snyder, M., Barnstable, C., Pang, C.P., Hoh, J. 2006. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314: 989–992.CrossRefGoogle Scholar
  8. Gupta, P.K., Rustgi, S., Kulwal, P.L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant. Mol. Biol. 57: 461–485.CrossRefGoogle Scholar
  9. Gurung, S., Mamidi, S., Bonman, J.M., Jackson, E.W., del Rýo, L.E., Acevedo, M., Mergoum, M., Adhikari, T.B. 2011. Identification of novel genomic regions associated with resistance to Pyrenophora tritici-repentis races 1 and 5 in spring wheat landraces using association analysis. Theor. Appl. Genet. 123: 1029–1041.CrossRefGoogle Scholar
  10. Huang, X.Q., Borner, A., Roder, M.S., Ganal, M.W. 2002. Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theor. Appl. Genet. 105: 699–707.CrossRefGoogle Scholar
  11. Karlsson, E.K., Baranowska, I., Wade, C.M., Hillbertz, N.H.C.S., Zody, M.C., Anderson, N., Biagi, T.M., Patterson, N., Pielberg, G.R., Kulbokas, E.J.I., Comstock, K.E., Keller, E.T., Mesirov, J.P., Euler, H., Kämpe, O., Hedhammar, A., Lander, E.S., Andersson, G., Andersson, L., Lindblad-Toh, K. 2007. Efficient mapping of Mendelian traits in dogs through genome-wide association. Nat. Genet. 39: 1321–1328.CrossRefGoogle Scholar
  12. Liu, L., Wang, L., Yao, J., Zheng, Y., Zhao, C. 2010. Association mapping of six agronomic traits on chromosome 4A of wheat (Triticum aestivum L.). Mol. Plant Breed. 1: 1–10.Google Scholar
  13. Mengistu, N., Baenziger, P.S., Eskridge, K.M., Dweikat, I., Wegulo, S.N., Gill, K.S., Mujeeb-Kazi, A. 2012. Validation of QTL for grain yield-related traits on wheat chromosome 3A using recombinant inbred chromosome lines. Crop Sci. 52: 1622–1632.CrossRefGoogle Scholar
  14. Palaisa, K.A., Morgante, M., Williams, M., Rafalski, A. 2003. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15: 1795–1806.CrossRefGoogle Scholar
  15. Peng, J.H., Bai, Y., Haley, S.D., Lapitan, N.L.V. 2009. Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid. Genetica 135: 95–122.CrossRefGoogle Scholar
  16. Pritchard, J.K., Stephens, M., Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.PubMedPubMedCentralGoogle Scholar
  17. Ravel, C., Praud, S., Murigneux, A., Linossier, L., Dardevet, M., Balfourier, F., Dufour, P., Brunel, D., Charmet, G. 2006. Identification of Glu-B1-1 as a candidate gene for the quantity of high-molecular-weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study. Theor. Appl. Genet. 112: 738–743.CrossRefGoogle Scholar
  18. Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M.M., Buckler, E.S. IV. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98: 11479–11484.CrossRefGoogle Scholar
  19. Rogowsky, P.M., Guidet, F.L.Y., Langridge, P., Shepherd, K.W., Koebner, R.D.M. 1991. Isolation and characterization of wheat-rye recombinants involving chromosome arm 1DS of wheat. Theor. Appl. Genet. 82: 537–544.CrossRefGoogle Scholar
  20. Roy, J.K., Bandopadhyay, R., Rustgi, S., Balyan, H.S., Gupta, P.K. 2006. Association analysis of agronomically important traits using SSR, SAMPL, and AFLP markers in bread wheat. Curr. Sci. 90: 683–689.Google Scholar
  21. Sajjad, M., Khan, S.H., Mujeeb-Kazi, A. 2012. The lowdown on association mapping in hexaploid wheat (Triticum aestivum L.). J. Crop Sci. Biotech. 15: 147–158.CrossRefGoogle Scholar
  22. Sajjad, M., Khan, S.H., Fatima, N., Rana, R.M., Shah, K.N. 2013. Family and/or friends? Gene mapping at crossroads. Amer. J. Plant. Sci. in pressGoogle Scholar
  23. Sanchez-Pérez, R., Ballester, J., Dicenta, F., Arús, P., Martínez-Gómez, P. 2006. Comparison of SSR polymorphisms using automated capillary sequencers, and polyacrylamide and agarose gel electrophoresis: Implications for the assessment of genetic diversity and relatedness in almond. Sci. Hort. 108: 310–316.CrossRefGoogle Scholar
  24. Somers, D.J., Isaac, P., Edwards, K. 2004. A high density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 109: 1105–1114.CrossRefGoogle Scholar
  25. Stich, B., Melchinger, A.E., Frisch, M., Maurer, H.P., Heckenberger, M., Reif, J.C. 2005. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor. Appl. Genet. 111: 723–730.CrossRefGoogle Scholar
  26. Tenaillon, M.I., Sawkins, M.C., Long, A.D., Gaut, R.L., Oebley, J.F.D., Gaut, B.S. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.). Proc. Natl Acad. Sci. USA 98: 9161–9166.CrossRefGoogle Scholar
  27. Tommasini, L., Schnurbusch, T., Fossati, D., Mascher, F., Keller, B. 2007. Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor. Appl. Genet. 115: 697–708.CrossRefGoogle Scholar
  28. Yao, J., Wang L., Liu, L., Zhao, C., Zheng, Y. 2009. Association mapping of agronomic traits on chromosome 2A of wheat. Genetica 137: 67–75.CrossRefGoogle Scholar
  29. Yu, J., Buckler, E.S. 2006. Genetic association mapping and genome organization of maize. Curr. Opin. Biotech. 17: 155–160.CrossRefGoogle Scholar
  30. 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., Buckler, E.S. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203–208.CrossRefGoogle Scholar
  31. Yu, L.X., Lorenz, A., Rutkoski, J., Singh, R.P., Bhavani, S., Huerta-Espino, J., Sorrells, M.E. 2011. Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor. Appl. Genet. 123: 1257–1268.CrossRefGoogle Scholar

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© Akadémiai Kiadó, Budapest 2013

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Authors and Affiliations

  • M. Sajjad
    • 1
    Email author
  • S. H. Khan
    • 2
  • M. Q. Ahmad
    • 2
  • A. Rasheed
    • 3
  • A. Mujeeb-Kazi
    • 4
  • I. A. Khan
    • 2
  1. 1.Department of Plant Breeding and Genetics, PMASUniversity of Arid AgricultureRawalpindiPakistan
  2. 2.Center of Agricultural Biochemistry and Biotechnology (CABB)University of AgricultureFaisalabadPakistan
  3. 3.Department of Plant SciencesQuaid-i-Azam UniversityIslamabadPakistan
  4. 4.National Institute of Biotechnology and Genetic Engineering (NIBGE)FaisalabadPakistan

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