Application of association mapping and linkage disequilibrium in plant genomic studies with emphasis on cereal genome

Knowledge of genetic diversity and understanding of the genetic architecture of complex traits in crop species can play a key role in exploiting genetic diversity and lead to the adaptation, development and expansion of crop cultivation in different geographical environments. In this regard, identifying and utilizing informative markers related to quantitative traits is a prerequisite for application in breeding programs and marker-assisted selection (MAS). One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis. In genome-wide association study (GWAS) and genomic selection (GS), determining of extent and level of linkage disequilibrium (LD) is critical in sample size and marker density. Moreover, selection for increasing of frequency in new mutations that are advantageous only in a subset of populations leaves some signatures in the genome. Locations of selection signatures are often correlated with genes and QTLs affecting economically important traits. Access to next generation sequencing technologies, high phenotypic data and a variety of sophisticated statistical tools have enabled LD-based association mapping studies in plants to be successful in identifying gene loci controlling quantitative traits. Alternatively, the LD-based association mapping (AM) approach can enhance the genetic map resolution to a greater extent due to the representation of a wider gene pool and more recombination events in history. Association mapping, has emerged as a tool to resolve complex trait variation down to the sequence level by exploiting evolutionary recombination events at the population level. Genetic diversity, LD extent in genome and intra-population relationship, determine quality of mapping, marker diversity, statistical methods and power of mapping. LD in population is the foundation of GWAS, whereas it always affected by genetic draft, population stratification and natural selection. Of the above threats, population stratification is recognized as a major one to the validity of GWAS results. Therefore, knowledge concerning the pattern of LD is important for performing GWAS and GS. As one of the most important measures in population genetics, LD is the basis of effective population size estimation, genomic selection, GWAS study and QTL mapping. Due to the importance of LD method in mapping studies of the quantitative traits, in this review we will present LD, its application in population, current status, limitations, and its use in plant breeding especially in cereals. Finally, this study provides some information about commonly used statistical software and packages in calculation of LD, and the challenges and perspectives of this approach have been discussed in this study as well.