Application of association mapping to understanding the genetic diversity of plant germplasm resources

Abstract

Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a "powerful gene tagging" tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.

Figure 1

The scheme of association mapping for tagging a gene of interest using germplasm accessions. Note that the outlined scheme may vary based on population characteristics and methodology chosen for association study.

Figure 2

The TASSEL generated triangle plot for pairwise LD between marker sites in a hypothetical genome fragment, where pairwise LD values of polymorphic sites are plotted on both the X- and Y-axis; above the diagonal displays r ² values and below the diagonal displays the corresponding p-values from rapid 1000 shuffle permutation test. Each cell represents the comparison of two pairs of marker sites with the color codes for the presence of significant LD. Colored bar code for the significance threshold levels in both diagonals is shown. The genetic distance scale for a hypothetical genome fragment was manually drawn. Note: this is for demonstration purposes only and does not have any real impact or correspond to any genomic fragment of an organism.

Figure 3

Linkage disequilibrium (LD) decay plot depicted from the LD values of a hypothetical marker data to demonstrate a measure of an average genome-wide LD block sizes. A pairwise LD values (r ²) are plotted against a genetic distance. Inner fitted trend line is a nonlinear logarithmic regression curve of r ² on genetic distance. LD decay is considered below r ² = 0.1 threshold and based on trend line it is around 38–40 cM in above plot. A pairwise LD between unlinked marker loci is assigned to 100 cM distance point. Note: this is for demonstration purposes only and does not have any real impact or correspond to any genomic fragment of an organism.