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.
Highlights
The level of the genetic diversity is pivotal for world food security and survival of human civilization on earth
We provide a brief description for the concept of genetic mapping; as a flourish of the crop genomics era, we thoroughly review one of the powerful genetic mapping tools for crops, linkage disequilibrium (LD)-based association study, as a high-resolution, broader allele coverage, and cost effective gene tagging approach in plant germplasm resources
LD rapidly declines in crop variety groups compared to populations derived from biparental crosses, which provides an advantage of discovery more polymorphisms in the variety germplasms than biparental populations of self-pollinated crops [56]; (2) the extent of LD varies across the genomic regions, among population samples and between species with the examples of “localized LD”; (3) LD measures differ per marker systems used as a reflection of capturing of different historic information in a genome due to different mutation rate (e.g., SNP versus SSR or AFLP versus SSR); (4) an estimate of genome-wide averages for the extent of LD in plant germplasm may not adequately reflect LD patterns of specific regions or specific population groups
Summary
The level of the genetic diversity is pivotal for world food security and survival of human civilization on earth. Plant germplasm resources worldwide, comprising of wild plant species, modern cultivars, and their crop wild relatives, are the important reservoirs of natural genetic variations, originated from a number of historical genetic events as a respond to environmental stresses and selection through crop domestication [1, 5] The efficient exploiting these ex situ conserved genetic diversities is vital to overcome future problems associated with narrowness of genetic base of modern cultivars. We provide a brief description for the concept of genetic mapping; as a flourish of the crop genomics era, we thoroughly review one of the powerful genetic mapping tools for crops, linkage disequilibrium (LD)-based association study, as a high-resolution, broader allele coverage, and cost effective gene tagging approach in plant germplasm resources This provides an opportunity to widely dissect and exploit existing natural variations for crop improvement
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