TY - JOUR
T1 - BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping
AU - Wilkinson, Michael J.
AU - Caligari, Peter D. S.
AU - Dear, P. H.
AU - Vu, Thi-Ha-Giang
N1 - Vu, G.T.H., Dear, P.H., Caligari, P.D.S., Wilkinson, M.J.* (2010). BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping. PLoS One, 5, (2), paper e9089.
IMPF: 03.56
Sponsorship: Biohybrids International and Sumatra Biosciences
PY - 2010/2/8
Y1 - 2010/2/8
N2 - Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical 'contig' maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ~10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual 'BAC-HAPPY-mapping' to convert BAC landing data into BAC linkage contigs is possible.
AB - Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical 'contig' maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ~10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual 'BAC-HAPPY-mapping' to convert BAC landing data into BAC linkage contigs is possible.
U2 - 10.1371/journal.pone.0009089
DO - 10.1371/journal.pone.0009089
M3 - Article
C2 - 20161702
SN - 1932-6203
VL - 5
SP - paper e9089
JO - PLoS ONE
JF - PLoS ONE
IS - 2
ER -