BAC-HAPPY Mapping (BAP Mapping): a New and Efficient Protocol for Physical Mapping

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2010 Feb 18

PMID 20161702

Citations 5

Authors

Giang T H Vu

Paul H Dear

Peter D S Caligari

Mike J Wilkinson

Affiliations

Soon will be listed here.

Abstract

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 approximately 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.

Citing Articles

Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding.

Dou J, Dou H, Mu C, Zhang L, Li Y, Wang J Genetics. 2017; 206(3):1237-1250.

PMID: 28468906 PMC: 5500127. DOI: 10.1534/genetics.117.200303.

Major genes determining yield-related traits in wheat and barley.

Nadolska-Orczyk A, Rajchel I, Orczyk W, Gasparis S Theor Appl Genet. 2017; 130(6):1081-1098.

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Whole Genome Mapping with Feature Sets from High-Throughput Sequencing Data.

Pan Y, Wang X, Liu L, Wang H, Luo M PLoS One. 2016; 11(9):e0161583.

PMID: 27611682 PMC: 5017645. DOI: 10.1371/journal.pone.0161583.

An introduction to the medicinal plant genome project.

Chen S, Xiang L, Guo X, Li Q Front Med. 2011; 5(2):178-84.

PMID: 21695623 DOI: 10.1007/s11684-011-0131-0.

Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley.

Vu G, Wicker T, Buchmann J, Chandler P, Matsumoto T, Graner A Funct Integr Genomics. 2010; 10(4):509-21.

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