Linkage Disequilibrium Mapping: An Alternative to QTL Mapping
Author: Prasanta Kumar Majhi
M. Sc. (Agri.), Junior Research Scholar, Department of Genetics and Plant Breeding, College of Agriculture, UAS, Dharwad, Karnataka, India


  • DNA based molecular markers have been extensively used for the variety of studies in plant and animal system. The molecular markers mainly used for genome wide molecular mapping and linkage analysis of simple and complex traits.
  • So for this, we have to first develop a mapping population than used in the study. That creates a limitation in the use of molecular markers because in many cases development of mapping population is not easy. The crops like perennial fruit crop, forest trees, crossing is very difficult so sufficient mapping population can’t developed.
  • Keeping these limitations in view, alternative approaches have been developed and linkage disequilibrium mapping is one of such which don’t need any mapping population and it utilizes the natural population.
  • This LD mapping approach has the potential to identify and map QTLs but also to identify causal polymorphism within a gene that is responsible for the difference in two alternative phenotypes.

  • If the haplotype frequencies observed in the population is similar to multiplied allelic frequencies, then the two alleles are said to be linkage equilibrium.
  • In other words, when linkage disequilibrium value is zero then it is said to be linkage equilibrium.
  • Linkage equilibrium can be thought of as the two locus version of the Hardy-Weinberg ratio, but it is a haplotype not genotype.

  • The linkage disequilibrium (LD) signifies that a specific allele at a locus occurs with a specific allele at the second locus more often than the expected on the basis of random assortment of the two loci.
  • In simple words, LD is the non-random association between alleles of the two or more loci.
  • These two loci may be two gene/QTLs or two markers or may be one gene and one marker.
  • LD is also called gametic phase disequilibrium (GPD) or gametic linkage disequilibrium (GLD). It is ideally applied to random mating populations that exhibit Hardy-Weinberg equilibrium.

  • The tendency of two or more genes or loci being inherited together is known as linkage. They have a tendency to pass to the same gametes during segregation, and don’t show independent segregation.
  • But, LD is the occurrence of non-random associations between alleles of the two or more loci in a population irrespective of their physical location in the genome.

  • Linkage disequilibrium mapping and Association mapping have been mostly used interchangeably in the literature. But some basic difference is there.
  • Association mapping considers high association of a molecular marker with a trait.
  • Whereas, Linkage disequilibrium refers to non-random association between two markers or two gene or one QTLs and one marker.
  • Therefore, association mapping is one of the applications of linkage disequilibrium.
  • Statistically, association is covariance of a marker polymorphism and a trait of interest, whereas linkage disequilibrium refers to covariance of polymorphisms represented by two molecular markers/genes.

Consider two loci and each having two alleles. Suppose, locus ‘A’ has alleles ‘A’ and ‘a’, and locus ‘B’ has alleles ‘B’ and ‘b’ with their allelic frequencies 0.7 (A), 0.3 (a), 0.4 (B) and 0.6 (b) respectively. The allelic frequency of When independent segregation takes place between the two loci than the following four haplotype combinations found with their respective frequencies.

Alleles A (0.7) a (0.3) Total
B (0.4) AB (0.28) aB (0.12) 0.4
b (0.6) Ab (0.42) ab (0.18) 0.6
Total 0.7 0.3

Independent segregation of genes A and B

Here, pAB.pab = pAb.paB

(0.28 × 0.18) = (0.12 × 0.42)

0.0504 = 0.0504

D = (pAB.pab) − (pAb.paB) = 0.0504 − 0.0504 = 0

Where, D = Linkage disequilibrium coefficient

The difference between the products of two diagonal haplotypes is zero; it means the linkage disequilibrium coefficient is zero. So the two loci are in linkage equilibrium condition. If ‘D’ value except zero, any other numerical value than we can say that the population is at linkage disequilibrium condition.


  • Marker-trait association followed by marker assisted selection.
  • Population genetics and evolutionary studies.
  • Demographic history study.
  • Haplotype block identification and SNP tagging.

Advantage of linkage disequilibrium mapping over conventional linkage mapping population:

  • Much higher resolution mapping can be constructing.
  • Much larger and more representative gene pool can be utilized.
  • Greater number of allelic diversity can be analyzed.
  • No need of bi-parental mapping population.
  • Ultimately searching time is less.
  • It has ability of mapping many traits in one set of genotypes.
  • It has potentiality not only to identify and map QTLs but also to identify the causal polymorphism within a gene.

There are several software packages are available for association based linkage disequilibrium study, out of them some are free and some are chargeable. Some of them are as follows: TASSEL, STRUCTURE, SAS, EMMA, PLINK, JMP, GGT, MIDAS, SVS7, Genstat, FaST-LMM etc.


1. Flint-Garcia, S. A., Thornsberry, J. M. and Buckler, E. S., 2003, Structure of linkage disequilibrium in plants. Annu. Rev. Plant Bio., 54: 357-374.
2. Gupta, P. K., Rustagi, S. and Pawan, L.K., 2005, Linkaghe diserquilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Bio., 57: 461-485.
3. Karim, S., Lyudmyla, V., Michelle, G. and Wirthensohn, S. T., 2008, Linkage Disequilibrium, genetic association mapping and gene localization in crop plants. Gen. and Mol. Bio., 31: 805-814.
4. Singh, B. D. and Singh, A. K., 2015, Marker Assisted Plant breeding: Principles ands Practices. Springer (India) Pvt. Ltd., 8: 226-235.

About Author / Additional Info:
I am currently continuing my M. Sc. (Agri.) on Genetics and Plant Breeding, College of Agriculture, UAS, Dharwad, Karnataka.