Functional Markers in Hexaploid Wheat: An overview

In recent years, many alternative molecular marker techniques have been developed for allelic variation in plants by using different approaches like association studies and to identify sequence motifs leads to affect phenotypic variation towards targeted functional markers. Functional markers are DNA markers derived from functionally characterized sequence motifs or polymorphic site within genes casually affecting phenotypic variations and are superior to random DNA markers such as RAPDs, RFLPs, SSRs and AFLPS. It differs from random DNA markers (RDMs) that derived at random from polymorphic sites in the genome; whereas gene targeted markers (GTMs) are derived from polymorphisms within genes. Wheat is one of the most strategic food crops, currently it is grown worldwide over diverse climatic condition and it is highly sensitive to severity of biotic and abiotic constraints. Biotic and abiotic stresses factors such as salinity, heat, cold, moisture stress and new races of pathogen and pest negatively impact the agricultural production systems that leads to decrease in public sector investment in agriculture world over, being complex in nature these stresses are serious challenges to be met urgently in order to sustain and enhance productivity of wheat crop. Under the influence of global climate changes, the situation is getting worse by way of destabilization of our ecosystem. One of the effective approaches to meet this formidable challenge follows the genetic route in which new and effective genes can be deployed in the target agricultural species. The available germplasm serves, as the source of such genes amply supporting the much needed genetic enhancement. By increasing human population breeders and biotechnologists need to develop crop plants that are able to grow under unfavourable condition. In total of 16 loci with 62 alleles for quality or end-use quality traits have been cloned and 56 functional markers have been developed. The end-use quality traits of wheat based product are highly associated with high and low molecular weight glutenin protein subunits (HMW-GS and LMW-GS), polyphenol oxidase (PPO) activity, lipoxynase (LOX) activity, kernel hardness, and starch properties.

HMW-GS and LMW-GS are the most storage proteins and encoded by the Glu-1 and Glu-3 loci, respectively and play important roles in determining dough quality. Polyphenol oxidase activity is encoded by POP gene (on 2A and 2D chromosome) and causing undesirable brown discoloration particularly in Asian noodles. LOX gene encodes a protein lipoxynase having effect on color and processing quality of wheat based product. Genes Pina-D1 and Pinb-D1 encoding puroindoline-a and puroindoline-b protein, respectively for kernel hardness, which has major effect on milling and end-use quality.

Six genes for disease resistance were cloned during the past decade in wheat. Among them, functional markers are available for alleles at the Pm3 locus for reaction to powdery mildew and for the Lr34/Yr18/Pm38 locus for resistance to leaf rust, stripe rust and powdery mildew.

Seven allele specific molecular markers were reported and successfully discriminate allelic variants at Pm3 locus, due to nucleotide polymorphism of coding sequences and adjacent untranslated regions of Pm3 resistance alleles.


1 Geng, H. W, Z. H. He, L. P. Zhang, Y. Y. Qu, and X. C. Xia. 2012. Cloning the lipoxygenase gene on chromosome 4BS and development of functional markers in common wheat. Crop Science 52.

2 He, X. Y., Z. H. He, L. P. Zhang, D. J. Sun, C. F. Morris, E. P. Fuerst, and X. C. Xia. 2007. Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat. Theoretical Applied Genetics 115: 47-58.

3 Su, Z. Q., C. Y. Hao, L. F. Wang, Y. C. Dong, and X. Y. Zhang. 2011. Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theoretical Applied Genetics 122: 211-223

About Author / Additional Info:
I am currently pursuing Doctoral degree in Agricultural Biotechnology from Maharana Pratap University of Agriculture and Technology, Udaipur. I have also worked with molecular markers in M.Sc. and published several research papers and article in repute journals.