Association Mapping: A New Paradigm for Dissection of Complex Traits in Crops

Abstract

This book chapter provides basic information about association mapping (AM), also called as linkage disequilibrium (LD) mapping. Association mapping has emerged as one of the successful, faster and high-resolution method for investigating the genetic architecture of complex traits in plants. Apart from unlocking the genetic information underlying the traits, association mapping also helps in exploiting the existing genetic diversity for crop improvement. The potential of the genetic diversity is not yet fully explored in plant breeding, and association mapping can aid in detecting and including more useful alleles into breeding germ plasm. The recent advent of cheap genotyping and sequencing technologies has eased the marker availability in the majority of the crops contributing to the increased interest in association mapping. Population structure resulting in false associations is one of the major constrains in reliable interpretation and usage of association mapping results. However, the advancement in the appropriate statistical methods for whole-genome association mapping has resulted in mitigating the population structure problems to an extent. Here we discuss basic concepts of AM and LD decay measurements and in depth the principles and steps involved in association mapping. The chapter discusses the advantages of LD mapping over linkage mapping, constrains involved in LD mapping, statistical approaches used for LD mapping and determination and interpretation of LD mapping results.