A BAC- and BIBAC-based physical map of the soybean genome

Abstract

Genome-wide physical maps are crucial to many aspects of advanced genome research. We report a genome-wide, bacterial artificial chromosome (BAC) and plant-transformation-competent binary large-insert plasmid clone (hereafter BIBAC)-based physical map of the soybean genome. The map was constructed from 78001 clones from five soybean BAC and BIBAC libraries representing 9.6 haploid genomes and three cultivars, and consisted of 2905 BAC/BIBAC contigs, estimated to span 1408 Mb in physical length. We evaluated the reliability of the map contigs using different contig assembly strategies, independent contig building methods, DNA marker hybridization, and different fingerprinting methods, and the results showed that the contigs were assembled properly. Furthermore, we tested the feasibility of integrating the physical map with the existing soybean composite genetic map using 388 DNA markers. The results further confirmed the nature of the ancient tetraploid origin of soybean and indicated that it is feasible to integrate the physical map with the linkage map even though greater efforts are needed. This map represents the first genome-wide, BAC/BIBAC-based physical map of the soybean genome and would provide a platform for advanced genome research of soybean and other legume species. The inclusion of BIBACs in the map would streamline the utility of the map for positional cloning of genes and QTLs, and functional analysis of soybean genomic sequences.

Figure 1

Example of the BAC/BIBAC contigs of the soybean physical map. This contig (ctg16) was anchored to the molecular linkage group MLG F of the soybean genetic map by the SSRmarker Satt343f (Cregan et al. 1999a; http://soybase.agron.iastate.edu/). The highlighted clones were the positive clones of the SSRmarker. The contig contains 120 BAC and BIBAC clones and 651 unique bands, estimated to span ∼2643 kb in physical length. The clones prefixed with “IS” or “UM” were from the Williams 82 and Faribault BAC libraries, respectively; and the clones prefixed with “E,” “B,” or “H” were from the Forrest EcoRI BAC, BamHI, and HindIII BIBAC libraries, respectively.

Figure 2

BAC/BIBAC contigs of the soybean physical map containing DNA markers selected from the MLG D1a of the existing soybean composite genetic map (http://soybase.agron.iastate.edu/; Cregan et al. 1999a). The soybean genetic map consists of 20 molecular linkage groups (MLGs). The DNA markers used are listed in the middle column, positions (centimorgans) of the markers in the linkage group in the left column, and the contig(s) containing the marker in the right column of the linkage group. The letter “s” indicates singleton. Note that the contigs shown in rectangles were hybridized with two or more neighboring DNA markers, seven SSRmarkers each were hybridized to only one contig, and two SSRmarkers each were anchored to a singleton. A total of 10 contigs were unambiguously anchored to the genetic map, whereas the exact positions of the remaining contigs remain to be further refined. The names of the DNA markers were after Cregan et al. (1999a) and http://soybase.agron.iastate.edu/, the markers prefixed with “Satt,” “Sat,” or “Sct” representing SSRmarkers and the remaining markers being RFLP markers. The markers suffixed with _1, _2, or _3 indicate that they reside at two or more loci in the soybean genome.