From Hype to Hope: Genome-Wide Association Studies in Soybean

Abstract

Association mapping studies in plants including soybean contribute to not only detecting the genetic basis of variation in yield, physiological, developmental, and morphological traits but also bringing together researchers to assemble core collections and develop genetic platforms for genotyping, phenotyping, analysis, and interpretation. The establishment of the unified mixed model greatly facilitated association mapping studies in plants and further methodology work in general. Association mapping is well positioned to exploit the advances in next-generation genomic technologies and high-through-put phenotyping. Genome-wide association studies are expected to increase dramatically once genome sequences are obtained. Moving forward, researchers in soybean and all other major plant genetics need to develop improved genetic designs and computational tools to address several challenges such as missing heritability, new gene identification, genotyping-by-sequencing, rare variants, imputation, high-throughput phenotyping, and integration of collective biological information and analytical tools into GWAS. In this chapter, we describe major progress in understanding population structure, advancements in design, and implementation of association mapping and summarize examples of association mapping in soybean. Finally, major opportunities with potential implications in soybean genetics are discussed as well.