ArticlePlant methods2006
Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. 'Forrest'): tools for structural and functional genomics.
Article in Plant methods, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.).BMC genomics · 2011Article
- Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- Article
- Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly.BMC genomics · 2008Article
- Separate loci underlie resistance to root infection and leaf scorch during soybean sudden death syndrome.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2008Article
- Soybean genomics: Developments through the use of cultivar "Forrest".International journal of plant genomics · 2008Article
- End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries.BMC genomics · 2007Article
- Development of a pooled probe method for locating small gene families in a physical map of soybean using stress related paralogues and a BAC minimum tile path.Plant methods · 2006Article
- Genomic analysis of the rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode.Molecular genetics and genomics : MGG · 2006Article
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Authors and funding
6 authors.
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Abstract
backgroundThe creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest') showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to create MTP sub-libraries from the soybean cv. Forrest physical map builds 2 to 4.
resultsThe first MTP, named MTP2, was 14,208 clones (of mean insert size 140 kbp) picked from the 5,597 contigs of build 2. MTP2 was constructed from three BAC libraries (BamHI (B), HindIII (H) and EcoRI (E) inserts). MTP2 encompassed the contigs of build 3 that derived from build 2 by a series of contig merges. MTP2 encompassed 2 Gbp compared to the soybean haploid genome of 1 Gbp and does not distinguish regions by ploidy. The second and third MTPs, called MTP4BH and MTP4E, were each based on build 4. Each was semi-automatically selected from 2,854 contigs. MTP4BH was 4,608 B and H insert clones of mean size 173 kbp in the large (27.6 kbp) T-DNA vector pCLD04541. MTP4BH was suitable for plant transformation and functional genomics. MTP4E was 4,608 BAC clones with large inserts (mean 175 kbp) in the small (7.5 kbp) pECBAC1 vector. MTP4E was suitable for DNA sequencing. MTP4BH and MTP4E clones each encompassed about 0.8 Gbp, the 0.7 Gbp diploid regions and 0.05 Gbp each from the tetraploid and octoploid regions. MTP2 and MTP4BH were used for BAC-end sequencing, EST integration, micro-satellite integration into the physical map and high information content fingerprinting. MTP4E will be used for genome sequence by pooled genomic clone index.
conclusionEach MTP and associated BES will be useful to deconvolute and ultimately finish the whole genome shotgun sequence of soybean.
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