Whole-Genome Validation of High-Information-Content Fingerprinting

• Published in: Plant physiology (Bethesda) Vol. 139; no. 1; pp. 27 - 38
• Main Authors: Nelson, William M, Bharti, Arvind K, Butler, Ed, Wei, Fusheng, Fuks, Galina, Kim, HyeRan, Wing, Rod A, Messing, Joachim, Soderlund, Carol
• Format: Journal Article
• Language: English
• Published: Rockville, MD American Society of Plant Biologists 01.09.2005; American Society of Plant Physiologists
• Subjects: bacterial artificial chromosomes; Bioinformatics; Biological and medical sciences; computer software; Corn; DNA fingerprinting; DNA Fingerprinting - methods; DNA Fingerprinting - standards; Dyes; Enzymes; fingerprinted contigs; Fundamental and applied biological sciences. Psychology; Genes. Genome; genome; Genome, Plant; Genomes; Genomics; high information content fingerprinting; inbred lines; Libraries; Map libraries; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; physical chromosome mapping; plant genetics; Reproducibility of Results; Rice; Sequencing; Software; Zea mays; Zea mays - genetics; Zea mays subsp. mays; Monocotyledones; Spermatophyta; Zea mays; Gramineae; Angiospermae
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.105.061978

Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.