The Physical and Genetic Framework of the Maize B73 Genome

Abstract

Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map (∼1,993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1). Maize has been a cultural icon and staple food crop of Americans since the discovery of the new world in 1492. Contemporary society is now faced with growing demands for food and fuel in the face of global climate change and the potential for increased disease pressure. To provide a comprehensive foundation to systematically understand maize biology with the goal of breeding higher yielding, disease-resistant, and drought-tolerant cultivars, our consortium sequenced the B73 genome of maize. In this study, we used a comprehensive physical and genetic framework map to develop a minimum tiling path (MTP) of over 16,000 BAC clones across the genome. The MTP was generated dynamically and integrated numerous data types, such as in-coming genome sequence, over 8,000 sequence-based genetic markers, and the maize optical map. This allowed us to genetically anchor, order, and orient the majority of the maize physical map and genome sequence to the genetic map. Post-genome sequencing, we constructed a golden path (AGP) of sequence-based pseudomolecules representing the ten chromosomes of the maize B73 genome (B73 RefGen_v1). This unprecedented integration of genetic, physical, and genomic sequence into one framework will greatly facilitate all aspects of plant biological research.