ABSTRACT

Introduction Early studies suggested the existence of signifi cant collinearity between grass genomes, which prompted the expectation that comparative genomics would enable the application of knowledge gained by sequencing the smaller rice genome to help in positional cloning of maize genes underlying important agronomic traits (Goff et al. 2002; Yu et al. 2002). However, substantial differences in gene organization observed between maize inbreds illustrated the surprisingly dynamic nature of the maize genome, underscoring the importance of understanding maize at the genome level (Fu and Dooner 2002). A whole-genome sequence of maize inbred B73 was published in 2009 and genomic techniques centered on DNA sequencing continue to address important questions related to maize gene regulation, epigenetics, genome structure, genome evolution and agronomic improvement (Schnable et al. 2009). This chapter focuses on the technologies, resources and outcomes, both past and present, relevant to sequencing the maize genome, and includes a brief discussion on the use of sequence data from related species for maize comparative genomics. However, our emphasis will be on the major fi ndings of the whole-genome sequence of maize and the subsequent use of second generation, high-throughput sequencing to further sample the maize genome and transcriptome (Schnable et al. 2009). The rapid improvement in DNA sequence technology underpinning the available ‘next-generation’ sequencing (NGS) platforms is facilitating large-scale, high-throughput, sequence-based approaches to better understand the dynamic genome of maize.