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 78,001 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.

Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.)

“…Further studies of homeologous regions in soybean are warranted to better understand the evolutionary history of this paleopolyploid genome. On the basis of the G. max cultivar Forrest physical map, the portions of linkage groups C1 (adjacent to marker A_059_1) and C2 to which the homeologous BACs mapped are excellent candidates to study duplicated regions due to the higher-than-average number of BACs identified by A_059_1 on linkage group C1 (Wu et al 2004;Schultz et al 2006). Additionally, neither of the BACs mapped to the pBng_181 locus on A2 (http:// www.soybase.org) although pBng181 showed a high similarity to the HCBT EST contig sequences.…”

Achievement, Challenge and Future Perspective of BAC Library Technology with a Focus on its Application to Soybean Genomics Researches

“…In 2004, Wu et al, constructed (BIBAC)-based physical map of the soybean genome based on plant-transformation-competent binary large-insert plasmid clone, which will benefit research in positional cloning of genes and QTLs. The BIBAC library contained 78,001 clones representing 9.6 haploid genomes [36,37]. Together with previous build BIBAC library for soybean cv.…”

An Overview of Genetic Transformation of Soybean

“…To improve plant genetic traits, many soybean research labs have developed tools for soybean functional genomics, such as several libraries containing large inserts of bacterial artificial chromosome (BAC) and plant transformation competent binary plasmids clone (BIBAC) (81). In functional genomic research, bacterial artificial chromosome (BAC) is a single copy artificial chromosome vector and is based on the E. coli fertility (F-factor) plasmid.…”