Sequencing, Assembly, and Annotation of the Soybean Genome

Abstract

Genome sequencing yields an exceptional resource of genetic information. Knowledge of whole genome sequence information helps characterize individual genomes, transcriptional states and genetic variation in populations and provide genetic architecture associated with each trait. After the release of the first human genome assembly, other model organism assemblies became available; including the model plant Arabidopsis thaliana. The soybean community published the first reference genome of the variety Williams 82 in 2010. Soybean has important syntenic relationships with the other legume species and is a model plant for the legumes. In this chapter, we discuss about the soybean genome assemblies and annotations, and its fine-tuning in view of the next-generation sequencing technologies and bioinformatics tools. In addition, comparison of the structural variations between the cultivated reference genome with the available wild soybean genome information will be discussed. This is followed by the discussion on the opportunities of next-generation sequencing technologies and challenges that we anticipate on the development of more pangenomes and reference genomes for soybean. This will significantly affect the discovery of rare alleles associated with key agronomic and quality traits and shape up the next-generation breeding technologies and crop improvement.