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 ( approximately 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).

Figure 1. Sequencing pipeline for MTP clone selection and gap analysis.

(A) An example of STC-based clone walking. Candidate walking clone list for seed BAC c0245B14. The list showed clones in which BES shared >95% sequence identity with the seed BAC; (B) Gbrowse view of sequence and trace alignment of candidate clone b0566J07 to seed BAC c0245B14. (C) Gap analysis pipeline to check gaps between adjoining clones.

Figure 2. Use of the maize optical map for FPC contig anchoring.

In each panel, the top blue fragments represent a maize optical SwaI restriction map, and the bottom orange fragments represent the in silico optical SwaI restriction map from contig-based pseudomolecules. Red fragments in (B) and (C) indicate a mis-sassmbly in the pseudomolecule that required manual editing. (A) Well-anchored Ctg36 helped to orient Ctg33, which was previously only ordered, but not oriented. (B) Anchored Ctg407 aided order and orientation of Ctg470, which was neither ordered nor oriented. (C). The newly anchored Ctg470 facilitated ordering and orienting of Ctg459.

Figure 3. Direct comparison of sequence overlap between adjacent clones before (A) and after (B) the semi automated AGP pipeline.