Mapping Some Seed Quality Traits in Bread Wheat (Triticum aestivum L.) by Association Mapping Using SSR Markers

Document Type: Original Article


1 Department of Agronomy and Plant Breeding, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran

2 Cereal Chemistry and Technology Unit, Seed and Plant Improvement Institute, Karaj, Iran

3 Department of Agronomy and Plant Breeding, University of Tehran, Iran

4 Department of Plant Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran


Introduction: Quality characteristics including grain protein content, gluten, falling number, and SDS sedimentation volume are important contributors to the grain yield and quality of the wheat. To identify the markers associated with such traits, this study run in two separated experiments: under-field and in laboratory.
Materials and Methods: One hundred wheat genotypes were evaluated in an alpha lattice design with two replications. Association mapping using Structure and Tassel software was carried out using 102 SSR markers: 66 unlinked and 36 quantitative trait loci (QTL)-linked SSR markers. Correction for population structure was performed using genome-wide SSR markers so that genotypes were divided into six subpopulations.
Results: Thoroughly, 34 SSR markers linked with the above-mentioned traits were identified, twelve of them being QTL-linked markers. These markers were already mapped on the wheat chromosomes in previous studies containing known QTLs controlling kernel traits of the wheat. Our results confirmed 5, 3, 2, and 2 QTLs respectively for the grain protein, gluten, falling number, and SDS sedimentation volume which were previously tagged on the wheat chromosomes. Additionally, 3 QTLs were identified for the grain protein on the chromosomes 2A, 5A, 5D, and 7B. Whereas, 6 QTLs for gluten were detected on chromosomes 1A, 2D, 5A, 5B, 6B, and 7B; four QTLs were located on the chromosomes 2D, 5A, 5B, 5D, and 7D for falling number; and finally nine QTLs were found for SDS sedimentation volume on the chromosomes 1A, 1B, 2B, 3A, 3B, 4B, 6A, 6B, 7A, and 7B.
Conclusions: The results of this study indicated that association mapping is a useful method for detecting and complementing QTL information; thus, this information can be used for further wheat improvement based on a molecular marker.


  1. Sorrells ME, Yu J. Linkage Disequilibrium and Association Mapping in the Triticeae. In: Muehlbauer GJ, Feuillet C, eds. Genetics and Genomics of the Triticeae. New York, NY: Springer US; 2009:655- 683.
  2. Oraguzie NC, Wilcox PL. An overview of association mapping. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN, eds. Association Mapping in Plants. New York: Springer-Verlag; 2007:1-10.
  3. Benjamin S, Melchinger AE. An introduction to association mapping in plants. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 2010;5 (039):1-9. doi:10.1079/PAVSNNR20105039.
  4. Cardon LR, Bell JI. Association study designs for complex diseases. Nat Rev Genet. 2001;2(2):91-99. doi:10.1038/35052543.
  5. Jannink J, Bink MC, Jansen RC. Using complex plant pedigrees to map valuable genes. Trends Plant Sci. 2001;6(8):337-342. doi:10.1016/S1360-1385(01)02017-9.
  6. Zhang Y, Tang J, Zhang Y, et al. QTL mapping for quantities of protein fractions in bread wheat (Triticum aestivum L.). Theor Appl Genet. 2011;122(5):971-987. doi:10.1007/s00122-010-1503-6.
  7. Campbell KG, Bergman CJ, Gualberto DG, et al. Quantitative trait loci associated with kernel traits in a soft × hard wheat cross. Crop Sci. 1999;39(4):1184-1195. doi:10.2135/cropsci1999.0011183X 003900040039x.
  1. Galande AA, Tiwari R, Ammiraju JSS, et al. Genetic analysis of kernel hardness in bread wheat using PCR-based markers. Theor Appl Genet. 2001;103(4):601-606. doi:10.1007/pl00002915.
  2. Huang XQ, Cloutier S, Lycar L, et al. Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.). Theor Appl Genet. 2006;113(4):753-766. doi:10.1007/s00122-006- 0346-7.
  3. Kunert A, Naz AA, Dedeck O, Pillen K, Leon J. AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (T. turgidum ssp. dicoccoides x T. tauschii) as a source of favourable alleles for milling and baking quality traits. Theor Appl Genet. 2007;115(5):683-695. doi:10.1007/s00122-007-0600-7.
  4. Sun X, Marza F, Ma H, Carver BF, Bai G. Mapping quantitative trait loci for quality factors in an inter-class cross of US and Chinese wheat. Theor Appl Genet. 2010;120(5):1041-1051. doi:10.1007/ s00122-009-1232-x.
  5. Emebiri LC, Oliver JR, Mrva K, Mares D. Association mapping of late maturity α-amylase (LMA) activity in a collection of synthetic hexaploid wheat. Mol Breed. 2010;26(1):39-49. doi:10.1007/ s11032-009-9375-7.
  6. Prasad M, Kumar N, Kulwal PL, et al. QTL analysis for grain protein content using SSR markers and validation studies using NILs in bread wheat. Theor Appl Genet. 2003;106(4):659-667. doi:10.1007/s00122-002-1114-y.
  7. Groos C, Robert N, Bervas E, Charmet G. Genetic analysis of grain protein-content, grain yield and thousand-kernel weight in bread wheat. Theor Appl Genet. 2003;106(6):1032-1040. doi:10.1007/ s00122-002-1111-1.
  8. Breseghello F, Finney PL, Gaines C, et al. Genetic loci related to kernel quality differences between a soft and a hard wheat cultivar. Crop Sci. 2005;45(5):1685-1695. doi:10.2135/cropsci2004.0310.
  9. Kuchel H, Langridge P, Mosionek L, Williams K, Jefferies SP. The genetic control of milling yield, dough rheology and baking quality of wheat. Theor Appl Genet. 2006;112(8):1487-1495. doi:10.1007/s00122-006-0252-z.
  10. Tsilo TJ, Hareland GA, Simsek S, Chao S, Anderson JA. Genome mapping of kernel characteristics in hard red spring wheat breeding lines. Theor Appl Genet. 2010;121(4):717-730. doi:10.1007/ s00122-010-1343-4.
  11. Blanco A, Mangini G, Giancaspro A, et al. Relationships between grain protein content and grain yield components through quantitative trait locus analyses in a recombinant inbred line population derived from two elite durum wheat cultivars. Mol Breed. 2012;30(1):79-92. doi:10.1007/s11032-011-9600-z.
  12. Tadesse W, Ogbonnaya FC, Jighly A, et al. Genome-wide association mapping of yield and grain quality traits in winter wheat genotypes. PLoS One. 2015;10(10):e0141339. doi:10.1371/ journal.pone.0141339.
  13. Blanco A, Bellomo MP, Lotti C, et al. Genetic mapping of sedimentation volume across environments using recombinant inbred lines of durum wheat. Plant Breed. 1998;117(5):413-417. doi:10.1111/j.1439-0523.1998.tb01965.x.
  14. Rousset M, Brabant P, Kota RS, Dubcovsky J, Dvorak J. Use of recombinant substitution lines for gene mapping and QTL analysis of bread making quality in wheat. Euphytica. 2001;119(1):81-87. doi:10.1023/a:1017530002612.
  15. Li Y, Song Y, Zhou R, Branlard G, Jia J. Detection of QTLs for bread-making quality in wheat using a recombinant inbred line population. Plant Breed. 2009;128(3):235-243. doi:10.1111/ j.1439-0523.2008.01578.x.
  16. Zanke CD, Ling J, Plieske J, et al. Analysis of main effect QTL for thousand grain weight in European winter wheat (Triticum aestivum L.) by genome-wide association mapping. Front Plant Sci. 2015;6:644. doi:10.3389/fpls.2015.00644.
  17. Zondervan KT, Cardon LR. The complex interplay among factors that influence allelic association. Nat Rev Genet. 2004;5(2):89- 100. doi:10.1038/nrg1270.
  18. Yu J, Zhang Z, Zhu C, et al. Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. Plant Genome. 2009;2(1):63-77. doi:10.3835/plantgenome2008.09.0009.
  19. Breseghello F, Sorrells ME. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics. 2006;172(2):1165-1177. doi:10.1534/genetics.105.044586.
  20. Neumann K, Kobiljski B, Dencic S, Varshney RK, Börner A. Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed. 2011;27(1):37-58. doi:10.1007/ s11032-010-9411-7.
  21. Reif JC, Gowda M, Maurer HP, et al. Association mapping for quality traits in soft winter wheat. Theor Appl Genet. 2011;122(5):961- 970. doi:10.1007/s00122-010-1502-7.
  22. Abdollahi Mandoulakani B, Nasri S, Dashchi S, Arzhang S, Bernousi I, Abbasi Holasou H. Preliminary evidence for associations between molecular markers and quantitative traits in a set of bread wheat (Triticum aestivum L.) cultivars and breeding lines. C R Biol. 2017;340(6-7):307-313. doi:10.1016/j.crvi.2017.05.001.
  23. Shahzad M, Khan SH, Khan AS, Sajjad M, Rehman A, Khan AI. Identification of QTLs on chromosome 1B for grain quality traits in bread wheat (Triticum aestivum L.). Cytol Genet. 2016;50(2):89- 95. doi:10.3103/s0095452716020110.
  24. Kumari S, Jaiswal V, Mishra VK, Paliwal R, Balyan HS, Gupta PK. QTL mapping for some grain traits in bread wheat (Triticum aestivum L.). Physiol Mol Biol Plants. 2018;24(5):909-920. doi:10.1007/s12298-018-0552-1.
  25. Krystkowiak K, Langner M, Adamski T, et al. Interactions between Glu-1 and Glu-3 loci and associations of selected molecular markers with quality traits in winter wheat (Triticum aestivum L.) DH lines. J Appl Genet. 2017;58(1):37-48. doi:10.1007/s13353- 016-0362-5.
  26. Kaur P, Vyas P, Sharma P, Sheikh I, Kumar R, Dhaliwal HS. Marker-Assisted Breeding of Recombinant 1RS.1BL Chromosome for Improvement of Bread Making Quality and Yield of Wheat (Triticum aestivum L.). In: Mukhopadhyay K, Sachan A, Kumar M, eds. Applications of Biotechnology for Sustainable Development. Singapore: Springer; 2017:181-190. doi:10.1007/978-981-10- 5538-6_21.
  27. American Association of Cereal Chemists (AACC). Approved Method of the AACC. 10th ed. St. Paul: AACC; 2000.
  28. Doyle JJ. Isolation of plant DNA from fresh tissue. Focus. 1990;12:13-15.
  29. Somers DJ, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet. 2004;109(6):1105-1114. doi:10.1007/s00122-004-1740- 7.
  30. ALPHANAL. A program for analysis of alpha lattice incomplete block experiments version 1.1. Edinburg: AFRC unit of statistics; 1986.
  31. Pritchard JK, Wen X, Falush D. Documentation for structure Software, version 2.3. Chicago: Department of Human Genetics University of Chicago; 2010.
  32. Pritchard JK, Wen X. Documentation for structure Software, version 2.3. Chicago: Department of Human Genetics University of Chicago; 2007.
  33. Zhu C, Gore M, Buckler ES, Yu J. Status and Prospects of Association Mapping in Plants. Plant Genome. 2008;1(1):5-20. doi:10.3835/ plantgenome2008.02.0089.
  34. Zhao L, Zhang KP, Liu B, Deng ZY, Qu HL, Tian JC. A comparison of grain protein content QTLs and flour protein content QTLs across environments in cultivated wheat. Euphytica. 2010;174(3):325- 335. doi:10.1007/s10681-009-0109-z.
  35. Kerfal S, Giraldo P, Rodriguez-Quijano M, et al. Mapping quantitative trait loci (QTLs) associated with dough quality in a soft×hard bread wheat progeny. J Cereal Sci. 2010;52(1):46-52. doi:10.1016/j.jcs.2010.03.001.
  36. Rezaeizad A, Wittkop B, Snowdon R, et al. Identification of QTLs for phenolic compounds in oilseed rape (Brassica napus L.) by association mapping using SSR markers. Euphytica. 2011;177(3):335-342. doi:10.1007/s10681-010-0231-y.
  37. Blanco A, Pasqualone A, Troccoli A, Di Fonzo N, Simeone R. Detection of grain protein content QTLs across environments in tetraploid wheats. Plant Mol Biol. 2002;48(5-6):615-623. doi:10.1023/a:1014864230933.
  38. Blanco A, Simeone R, Gadaleta A. Detection of QTLs for grain protein content in durum wheat. Theor Appl Genet. 2006;112(7):1195-1204. doi:10.1007/s00122-006-0221-6.
  39. Joppa LR, Du C, Hart GE, Hareland GA. Mapping gene (s) for grain protein in tetraploid wheat (Triticum turgidum L.) using a population of recombinant inbred chromosome lines. Crop Sci. 1997;37(5):1586-1589. doi:10.2135/cropsci1997.0011183X0037 00050030x.
  40. Chee PW. Introgression of a high protein gene from LDN (DIC- 6B) substitution line. In A. E. Slinkard AE, ed. International Wheat Genetics Symposium. 9th ed. Vol 2. Saskatoon: University of Saskatchewan; 1998:179-181.
  41. Pshenichnikova TA, Ermakova MF, Chistyakova AK, et al. Mapping of the quantitative trait loci (QTL) associated with grain quality characteristics of the bread wheat grown under different environmental conditions. Russ J Genet. 2008;44(1):74-84. doi:10.1134/s1022795408010109.
  42. Varshney RK, Tuberosa R. Genomics-Assisted Crop Improvement -- Volume 2: Genomics Applications in Crops. Springer; 2007:25- 50. doi:10.1007/978-1-4020-6297-1.
  43. Derera NF. The effects of preharvest rain. In: Derera NF, ed. Preharvest Field Sprouting in Cereals. Boca Raton, USA: CRS Press Inc; 1989:1-14.
  44. Edwards RA, Ross AS, Mares DJ, Ellison FW, Tomlinson JD. Enzymes from rain-damaged and laboratory-germinated wheat I. Effects on product quality. J Cereal Sci. 1989;10(2):157-167. doi:10.1016/S0733-5210(89)80044-X.
  45. Ersoz ES, Yu J, Buckler ES. Applications of linkage disequilibrium and association mapping in maize. In: Kriz AL, Larkins BA, eds. Molecular genetic approaches to maize improvement, biotechnology in agriculture and forestry. Berlin: Springer; 2009:173-195.